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List of works by Harold A. Scheraga

1.21 Computation of Structure, Dynamics, and Thermodynamics of Proteins

A Hierarchical Multiscale Approach to Protein Structure Prediction: Production of Low‐Resolution Packing Arrangements of Helices and Refinement of the Best Models with a United‐Residue Force Field

A Proposal of Standard Conventions and Nomenclature for the Description of Polypeptide Conformation ⬇️

scientific article published in February 1966

A Raman spectroscopic investigation of the disulfide conformation in oxytocin and lysine vasopressin

scientific article published on October 4, 1977

A Statistical Model to Decipher Protein Folding/unfolding at a Local Scale.

scientific article published on 15 February 2018

A comparison of the CHARMM, AMBER and ECEPP potentials for peptides. II. Phi-psi maps for N-acetyl alanine N'-methyl amide: comparisons, contrasts and simple experimental tests

scientific article published in December 1989

A comparison of the predicted and X-ray structures of angiogenin. Implications for further studies of model building of homologous proteins

scientific article published in October 1994

A comprehensive analysis of the computed tautomer fractions of the imidazole ring of histidines in Loligo vulgaris

scientific article published on 8 September 2017

A convenient incorporation of conformationally constrained 5,5-dimethylproline into the ribonuclease A 89-124 sequence by condensation of synthetic peptide fragments

scientific article

A generalized G-SFED continuum solvation free energy calculation model ⬇️

scientific article published on February 19, 2013

A hypothesis for the pathway of the thermally-induced unfolding of bovine pancreatic ribonuclease ⬇️

scientific article published on September 1, 1975

A localized specific interaction alters the unfolding pathways of structural homologues.

scientific article

A method for optimizing potential-energy functions by a hierarchical design of the potential-energy landscape: application to the UNRES force field

scientific article

A method for the cloning of unpurified single-stranded oligonucleotides

scientific article

A model for hydration of peptides and its application to the conformational analysis of terminally blocked amino acids and dipeptides ⬇️

scientific article published on December 1, 1978

A new approach to empirical intermolecular and conformational potential energy functions. I. Description of model and derivation of parameters

scientific article

A new approach to empirical intermolecular and conformational potential energy functions. II. Applications to crystal packing, rotational barriers, and conformational analysis ⬇️

scientific article published on March 1, 1975

A new force field (ECEPP-05) for peptides, proteins, and organic molecules

scientific article

A new method for rapid characterization of the folding pathways of multidisulfide-containing proteins

scientific article published in March 2004

A possible folding pathway of bovine pancreatic RNase ⬇️

scientific article published on December 1, 1979

A preliminary three-dimensional structure of angiogenin

scientific article published on April 1986

A proposal of standard conventions and nomenclature for the description of polypeptide conformations ⬇️

scientific article published in January 1966

A role for intermolecular disulfide bonds in prion diseases?

scholarly article

A set of Macintosh computer programs for the design and analysis of synthetic genes.

scientific article published in July 1989

A statistical analysis of side-chain conformations in proteins: comparison with ECEPP predictions

scientific article

A study of the α-helical intermediate preceding the aggregation of the amino-terminal fragment of the β amyloid peptide (Aβ(1-28))

scientific article published on 18 October 2011

A unified coarse-grained model of biological macromolecules based on mean-field multipole-multipole interactions

scientific article

A united residue force-field for calcium-protein interactions.

scientific article

Ab initio folding of multiple-chain proteins.

scientific article

Ab initio self-consistent field and potential-dependent partial equalization of orbital electronegativity calculations of hydration properties of N-acetyl-N'-methyl-alanineamide

scientific article

Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains

scientific article

Ab initio structure prediction of two alpha-helical oligomers with a multiple-chain united-residue force field and global search

scientific article published in March 2003

Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides

scientific article

Accounting for a mirror-image conformation as a subtle effect in protein folding

scientific article

Acidic-basic properties of three alanine-based peptides containing acidic and basic side chains: comparison between theory and experiment

scientific article

Addition of side chains to a known backbone with defined side-chain centroids

scientific article published in January 2003

Agreement with the disulfide stretching frequency-conformation correlation of Sugeta, Go, and Miyazawa

scientific article published on May 1986

Alternative approach to protein structure prediction based on sequential similarity of physical properties

scientific article

Amino Acid Residues at Protein−Protein Interfaces: Why Is Propensity so Different from Relative Abundance?

Amino acid sequences of portions of the α and β chains of bovine fibrinogen ⬇️

scientific article published on January 1, 1979

An approach to the multiple-minima problem by relaxing dimensionality

scientific article published on May 1986

An approach to the multiple-minima problem in protein folding by relaxing dimensionality. Tests on enkephalin

scientific article published in August 1987

An atomically detailed study of the folding pathways of protein A with the stochastic difference equation

scientific article

An efficient method for calculating atomic charges of peptides and proteins from electronic populations

scientific article published on 10 April 2008

An improved functional form for the temperature scaling factors of the components of the mesoscopic UNRES force field for simulations of protein structure and dynamics.

scientific article

Analysis for disulfide bonds in peptides and proteins

scientific article published on January 1987

Analysis of Conformations of Amino Acid Residues and Prediction of Backbone Topography in Proteins

article

Analysis of the structure of ribonuclease A in native and partially denatured states by time-resolved noradiative dynamic excitation energy transfer between site-specific extrinsic probes

scientific article published in December 1995

Anomalous diffusion and dynamical correlation between the side chains and the main chain of proteins in their native state ⬇️

scientific article published on June 11, 2012

Application of Multiplexed Replica Exchange Molecular Dynamics to the UNRES Force Field: Tests with alpha and alpha+beta Proteins

scientific article published on March 2009

Are accurate computations of the 13C' shielding feasible at the DFT level of theory?

scientific article published on 03 December 2013

Assessing the One-Bond Cα-H Spin-Spin Coupling Constants in Proteins: Pros and Cons of Different Approaches

scientific article published on 23 January 2020

Assessing the accuracy of protein structures by quantum mechanical computations of 13C(alpha) chemical shifts

scientific article

Assessing the fractions of tautomeric forms of the imidazole ring of histidine in proteins as a function of pH ⬇️

scientific article published on March 21, 2011

Assessment of some problems associated with prediction of the three-dimensional structure of a protein from its amino-acid sequence ⬇️

scientific article published on April 1, 1975

Assignment of the histidine peaks in the nuclear magnetic resonance spectrum of ribonuclease ⬇️

scientific article

Atomically detailed folding simulation of the B domain of staphylococcal protein A from random structures

scientific article

Beta-bend conformation of CH3CO-Pro-Pro-Gly-Pro-NHCH3: implications for posttranslational proline hydroxylation in collagen

scientific article published on July 1984

Block copolymers of amino acids. I. Synthesis and structure of copolymers of L-alanine or L-phenylalanine with D,L-Lysine-d7 or D,L-lysine

scientific article

Block copolymers of amino acids. II. Physicochemical data on copolymers containing L-alanine or L-phenylalanine

scientific article published on September 1, 1977

Bovine pancreatic ribonuclease A: oxidative and conformational folding studies

scientific article (publication date: 2001)

Calculation of conformational properties of oligomers of L-proline

scientific article published in September 1974

Calculation of polypeptide conformation.

scientific article

Calculation of protein backbone geometry from alpha-carbon coordinates based on peptide-group dipole alignment

scientific article

Calculation of protein conformation as an assembly of stable overlapping segments: application to bovine pancreatic trypsin inhibitor

scientific article published on May 1991

Calculation of protein conformation by global optimization of a potential energy function.

scientific article

Calculation of protein conformation by the build-up procedure. Application to bovine pancreatic trypsin inhibitor using limited simulated nuclear magnetic resonance data

scientific article

Calculation of the three-dimensional structure of the membrane-bound portion of melittin from its amino acid sequence

scientific article

Calorimetric measurement of enthalpy change in the isothermal helix-coil transition of poly(L-ornithine) in aqueous solution ⬇️

scientific article published on September 1, 1976

Catalysis of the oxidative folding of bovine pancreatic ribonuclease A by protein disulfide isomerase

scientific article

Cayley-Menger coordinates

scientific article published on April 1986

Chain reversals in proteins

scientific article (publication date: 20 April 1973)

Challenges in structure prediction of oligomeric proteins at the united-residue level: searching the multiple-chain energy landscape with CSA and CFMC.

scientific article published in March 2003

Characterization of the fast-forming intermediate, des [30-75], in the reductive unfolding of onconase

scientific article published in March 2004

Characterizing the unstructured intermediates in oxidative folding

scientific article

CheShift-2 resolves a local inconsistency between two X-ray crystal structures

scientific article

CheShift-2: graphic validation of protein structures

scientific article

Coarse-Grained Models of Proteins: Theory and Applications

Coarse-grained force field: general folding theory

scientific article

Coarse-grained model of nucleic acid bases

scientific article published in June 2010

Coexistence of phases in a protein heterodimer

scientific article

Combined solid-phase/solution synthesis of large ribonuclease A C-terminal peptides containing a non-natural proline analog

scientific article

Combined-information protein structure refinement: Potential energy-constrained real-space method for refinement with limited diffraction data.

scientific article

Common functionally important motions of the nucleotide-binding domain of Hsp70

scientific article

Communications to the editor: Stable conformations of dipeptides.

scientific article

Comparison of structures of various human fibrinogens and a derivative thereof by a study of the kinetics of release of fibrinopeptides ⬇️

scientific article published on September 25, 1984

Comparison of three-dimensional structures of macromolecules ⬇️

scientific article published on November 1, 1972

Computation of structures of homologous proteins. .alpha.-Lactalbumin from lysozyme ⬇️

scientific article published on February 12, 1974

Computation of the free energy of liquid water by the Monte Carlo recursion method

Computation of the sterically allowed conformations of peptides ⬇️

scientific article published in April 1966

Computational study of packing a collagen-like molecule: quasi-hexagonal vs "Smith" collagen microfibril model

scientific article published in January 1996

Computational techniques for efficient conformational sampling of proteins

scientific article published on 22 January 2008

Computer-aided discrimination between active and inactive mutants of the N-terminal domain of the bacteriophage lambda repressor

scientific article published in March 1996

Conformation of the 18-23 loop region of bovine prothrombin in the absence and presence of a model Ca2+ ion. An energy minimization study

scientific article published in May 1986

Conformation-family Monte Carlo: a new method for crystal structure prediction

scientific article

Conformational analysis of cyclized dipeptide models for specific types of beta-bends by two-dimensional nuclear Overhauser spectroscopy

scientific article

Conformational analysis of the 20 naturally occurring amino acid residues using ECEPP

scientific article published on January 1, 1977

Conformational analysis of the 20-residue membrane-bound portion of melittin by conformational space annealing ⬇️

scientific article published on August 1, 1998

Conformational analysis of thyrotropin releasing factor.

scientific article

Conformational characteristics of the N-acetyl-N'-methylamides of the four (Lys, Tyr) dipeptides ⬇️

scientific article published on May 1, 1981

Conformational characterization of a single-site mutant of murine epidermal growth factor (EGF) by 1H NMR provides evidence that leucine-47 is involved in the interactions with the EGF receptor

scientific article

Conformational effects of substituting amino acids for glutamine-61 on the central transforming region of the P21 proteins

scientific article

Conformational energy analysis of melanostatin ⬇️

scientific article published on February 1, 1982

Conformational energy calculations of enzyme-substrate complexes of lysozyme. I. Energy minimization of monosaccharide and oligosaccharide inhibitors and substrates of lysozyme

scientific article published on December 1, 1976

Conformational energy calculations of enzyme-substrate interactions. I. Computation of preferred conformations of some substrates of -chymotrypsin

scientific article published in January 1972

Conformational energy calculations of enzyme-substrate interactions. II. Computation of the binding energy for substrates in the active site of -chymotrypsin

scientific article published in January 1972

Conformational energy calculations on polypeptides and proteins: use of a statistical mechanical procedure for evaluating structure and properties

scientific article

Conformational energy refinement of horse-heart ferricytochrome c ⬇️

scientific article published on August 12, 1975

Conformational energy studies of oxytocin and its cyclic moiety

scientific article published on December 1972

Conformational energy studies of β-sheets of model silk fibroin peptides. I. Sheets of poly(Ala-Gly) chains ⬇️

scientific article published on November 1, 1991

Conformational propensities of protein folding intermediates: distribution of species in the 1S, 2S, and 3S ensembles of the [C40A,C95A] mutant of bovine pancreatic ribonuclease A.

scientific article published in February 2002

Conformational properties of trans Ac-Asn-Pro-Tyr-NHMe and trans Ac-Tyr-Pro-Asn-NHMe in dimethylsulfoxide and in water determined by multinuclear n.m.r. spectroscopy.

scientific article

Conformational studies of a peptide corresponding to a region of the C-terminus of ribonuclease A: implications as a potential chain-folding initiation site

scientific article published in August 1991

Conformational studies of poly-L-alanine in water.

scientific article

Conformational studies of somatostatin and selected analogues by Raman spectroscopy ⬇️

scientific article published on April 1, 1980

Conformational studies of the C-terminal 16-amino-acid-residue fragment of the B3 domain of the immunoglobulin binding protein G from Streptococcus

scientific article

Conformational study of [Leu5]-enkephalin by laser Raman spectroscopy.

scientific article published on September 1980

Conformational unfolding in the N-terminal region of ribonuclease A detected by nonradiative energy transfer

scientific article published on April 1986

Conformations of cyclo(L-alanyl-L-alanyl-epsilon-aminocaproyl) and of cyclo(L-alanyl-D-alanyl-epsilon-aminocaproyl); cyclized dipeptide models for specific types of beta-bends.

scientific article published on February 1982

Conformations of poly-L-valine in solution

scientific article published in January 1968

Contractility and Conformation ⬇️

scientific article

Contribution of physical chemistry to an understanding of protein structure and function ⬇️

scientific article published on May 1, 1992

Conversion from a virtual-bond chain to a complete polypeptide backbone chain

scientific article published in July 1984

Correction to Maximum Likelihood Calibration of the UNRES Force Field for Simulation of Protein Structure and Dynamics

scientific article published on 28 December 2017

Correlation between the conformation of cytochrome c peptides and their stimulatory activity in a T-lymphocyte proliferation assay

scientific article published on June 1983

Correlation of beta-bend conformations of tetrapeptides with their activities in CD4-receptor binding assays

scientific article

Coupling between conformation and proton binding in proteins

scientific article published in October 2005

Coupling of conformational folding and disulfide-bond reactions in oxidative folding of proteins

scientific article

Crystal structure prediction of small organic molecules: a second blind test

article

Crystal structures of two mutants that have implications for the folding of bovine pancreatic ribonuclease A ⬇️

scientific article published on May 1, 1998

Current status of the water-structure problem; application to proteins ⬇️

scientific article published on March 30, 1973

Cyclized dipeptide model for a beta-bend ⬇️

scientific article published on June 1, 1979

DNA Duplex Formation with a Coarse-Grained Model

scientific article

Deamidation of the asparaginyl-glycyl sequence

scientific article published on July 1986

Definition of amide protection factors for early kinetic intermediates in protein folding ⬇️

scientific article published on April 14, 1998

Dependence of the Formation of Tau and Aβ Peptide Mixed Aggregates on the Secondary Structure of the N-Terminal Region of Aβ

scientific article published on 10 July 2018

Designing potential energy functions for protein folding

scientific article

Detecting native folds in mixtures of proteins that contain disulfide bonds

scientific article published on 17 February 2008

Determination of effective potentials for the stretching of C(α) ⋯ C(α) virtual bonds in polypeptide chains for coarse-grained simulations of proteins from ab initio energy surfaces of N-methylacetamide and N-acetylpyrrolidine

scientific article

Determination of molecular weights by differential cryoscopy on small volumes of dilute solutions of oligopeptides

scientific article

Determination of side-chain-rotamer and side-chain and backbone virtual-bond-stretching potentials of mean force from AM1 energy surfaces of terminally-blocked amino-acid residues, for coarse-grained simulations of protein structure and folding. II

scientific article

Determination of the Cysteine and Cystine Content of Proteins by Amino Acid Analysis: Application to the Characterization of Disulfide-Coupled Folding Intermediates ⬇️

scientific article published on January 1, 1998

Determination of the Potentials of Mean Force for Rotation about Cα−CαVirtual Bonds in Polypeptides from the ab Initio Energy Surfaces of Terminally Blocked Glycine, Alanine, and Proline†

Development of Physics-Based Energy Functions that Predict Medium-Resolution Structures for Proteins of the α, β, and α/β Structural Classes

article

Development of a novel method to populate native disulfide-bonded intermediates for structural characterization of proteins: implications for the mechanism of oxidative folding of RNase A.

scientific article published in May 2002

Development of a novel method to study the rate-determining step during protein regeneration: application to the oxidative folding of RNase A at low temperature reveals BPTI-like kinetic traps

scientific article published in March 2001

Dissimilarity in the oxidative folding of onconase and ribonuclease A, two structural homologues

scientific article published on 31 January 2008

Dissimilarity in the reductive unfolding pathways of two ribonuclease homologues

scientific article published in May 2004

Distributions of intramolecular distances in the reduced and denatured states of bovine pancreatic ribonuclease A. Folding initiation structures in the C-terminal portions of the reduced protein

scientific article

Disulfide bond dihedral angles from Raman spectroscopy

scientific article

Disulfide bonding arrangements in active forms of the somatomedin B domain of human vitronectin

scientific article

Disulfide bonds and protein folding

scientific article (publication date: 13 June 2000)

Disulfide bonds and protein folding.

scientific article

Dynamics of Disulfide-Bond Disruption and Formation in the Thermal Unfolding of Ribonuclease A.

scientific article

Effect of mutation of proline 93 on redox unfolding/folding of bovine pancreatic ribonuclease A.

scientific article published in July 2001

Effect of protein disulfide isomerase on the rate-determining steps of the folding of bovine pancreatic ribonuclease A.

scientific article

Effect of protein-solvent interactions on protein conformation

scientific article published on January 1981

Effect of sequence-specific interactions on the stability of helical conformations in polypeptides

scientific article published in January 1988

Effect of side chain-backbone electrostatic interactions on the stability of alpha-helices

scientific article published on September 1985

Effects of compact volume and chain stiffness on the conformations of native proteins ⬇️

scientific article published on July 15, 1992

Effects of mutation, truncation, and temperature on the folding kinetics of a WW domain

scientific article published on 2 May 2012

Effects of tyrosine mutations on the conformational and oxidative folding of ribonuclease a: a comparative study

scientific article published on May 2009

Effects on protein structure and function of replacing tryptophan with 5-hydroxytryptophan: single-tryptophan mutants of the N-terminal domain of the bacteriophage lambda repressor

scientific article

Electron paramagnetic resonance spectroscopy as a monitor of the pathway of the thermal unfolding of ribonuclease A ⬇️

scientific article published on February 7, 1977

Eliminating a Protein Folding Intermediate by Tuning a Local Hydrophobic Contact

scientific article

Elucidating Important Sites and the Mechanism for Amyloid Fibril Formation by Coarse-Grained Molecular Dynamics

scientific article published on 18 November 2016

Empirical solvation models can be used to differentiate native from near-native conformations of bovine pancreatic trypsin inhibitor

scientific article

Empirical solvation models in the context of conformational energy searches: application to bovine pancreatic trypsin inhibitor

scientific article

Energetics of multihelix interactions in protein folding: application to myoglobin

scientific article published in July 1985

Energetics of the structure and chain tilting of antiparallel beta-barrels in proteins

scientific article

Energetics of the structure of the four-alpha-helix bundle in proteins

scientific article

Energy of stabilization of the right-handed beta alpha beta crossover in proteins

scientific article published in January 1989

Energy parameters in polypeptides. V. Empirical hydrogen bond potential function based on molecular orbital calculations ⬇️

scientific article published on February 3, 1972

Energy-based de novo protein folding by conformational space annealing and an off-lattice united-residue force field: application to the 10-55 fragment of staphylococcal protein A and to apo calbindin D9K.

scientific article published on March 1999

Enkephalin: conformational analysis by means of empirical energy calculations ⬇️

scientific article published on February 1, 1977

Equilibria in the fibrinogen-fibrin conversion. IX. Effects of calcium ions on the reversible polymerization of fibrin monomer

scientific article

Equilibrium and kinetic constants for the thiol-disulfide interchange reaction between glutathione and dithiothreitol ⬇️

scientific article published on September 1, 1992

Evidence, from simulations, of a single state with residual native structure at the thermal denaturation midpoint of a small globular protein

scientific article

Exact calculation of the volume and surface area of fused hard-sphere molecules with unequal atomic radii

article by K.D. Gibson & Harold A. Scheraga published 10 December 1987 in Molecular Physics

Exercises in prognostication: crystal structures and protein folding

scholarly article

Experimental and Theoretical Aspects of Protein Folding

scientific article published on January 1, 1975

Experimental identification of a theoretically predicted "left-sided" binding mode for (GlcNAc)6 in the active site of lysozyme

scientific article

Exploring the parameter space of the coarse-grained UNRES force field by random search: selecting a transferable medium-resolution force field

scientific article published on October 2009

Expression and folding of recombinant bovine prethrombin-2 and its activation to thrombin

scientific article published on January 1995

Expression of wild-type and mutant bovine pancreatic ribonuclease A in Escherichia coli

scientific article

Extension of UNRES force field to treat polypeptide chains with D-amino-acid residues

scientific article

FAMBE-pH: a fast and accurate method to compute the total solvation free energies of proteins

scientific article published on 07 August 2008

Factors affecting the use of 13C(alpha) chemical shifts to determine, refine, and validate protein structures

scientific article

Fast and accurate computation of the 13C chemical shifts for an alanine-rich peptide

scientific article

Folding of Polypeptide Chains in Proteins: A Proposed Mechanism for Folding ⬇️

scientific article published on September 1, 1971

Folding of a Disulfide-Bonded Protein Species with Free Thiol(s): Competition between Conformational Folding and Disulfide Reshuffling in an Intermediate of Bovine Pancreatic Ribonuclease A ⬇️

scientific article published on December 11, 2001

Folding of ribonuclease A from a partially disordered conformation. Kinetic study under folding conditions

scientific article published in October 1982

Folding of the villin headpiece subdomain from random structures. Analysis of the charge distribution as a function of pH.

scientific article

Formation of the hydrophobic core of ribonuclease A through sequential coordinated conformational transitions

scientific article

From a highly-disordered to a metastable state: Uncovering insights of α-synuclein

scientific article published on 16 February 2018

From helix-coil transitions to protein folding.

scientific article

Geometrical criteria for formation of coiled-coil structures of polypeptide chains

scientific article published on May 1, 1976

George Hess: A scientific appreciation

scientific article

Global informatics and physical property selection in protein sequences

scientific article published on February 2016

Global optimization of clusters, crystals, and biomolecules.

scientific article

Gouy Diffusion Studies of Bovine Serum Albumin

H and 13C nuclear magnetic resonance spectra of some peptides with fibrinogen-like reactivity ⬇️

scientific article published on March 1, 1979

Hairpin bend and interhelical interactions in α-helical poly(l-alanine) in water ⬇️

scientific article published on December 1, 1972

Helical stability of de novo designed alpha-aminoisobutyric acid-rich peptides at high temperatures

scientific article published on February 1995

Helix probability profiles of denatured proteins and their correlation with native structures

scientific article

Helix-Coil Stability Constants for the Naturally Occurring Amino Acids in Water. 11. Lysine Parameters from Random Poly(hydroxybutylglutamine-co-L-lysine) ⬇️

scientific article published on September 1, 1976

Helix-Coil Stability Constants for the Naturally Occurring Amino Acids in Water. IX. Glutamic Acid Parameters from Random Poly(hydroxybutylglutamine-co-L-glutamic acid) ⬇️

scientific article published on July 1, 1975

Helix-Coil Stability Constants for the Naturally Occurring Amino in Water. VII Phenylalanine Parameters from Random Poly(hydroxypropylglutamine-co-L-L-phenylalanine) ⬇️

scientific article published on March 1, 1973

Helix-coil stability constants for the naturally occurring amino acids in water. 16. Aspartic acid parameters from random poly(hydroxybutylglutamine-co-L-aspartic acid)

scientific article published on November 1, 1977

Helix-coil transition theory including long-range electrostatic interactions: application to globular proteins

scientific article

Helix-coil transitions re-visited

scientific article

Hidden protein folding pathways in free-energy landscapes uncovered by network analysis

scientific article

High level production of bovine angiogenin in E. coli by an efficient refolding procedure

scientific article published in October 2004

High-resolution NMR studies of fibrinogen-like peptides in solution: interaction of thrombin with residues 1-23 of the A alpha chain of human fibrinogen

scientific journal article

Homolog detection using global sequence properties suggests an alternate view of structural encoding in protein sequences

scientific article published on 24 March 2014

How main-chains of proteins explore the free-energy landscape in native states

scholarly article

How optimization of potential functions affects protein folding

scientific article published on May 1996

Hydrodynamic and Thermodynamic Properties of Bovine Serum Albumin at Low pH

Hydrophobicity, hydrophilicity, and the radial and orientational distributions of residues in native proteins ⬇️

scientific article published on December 1, 1977

Hypothesis about the Mechanism of Protein Folding ⬇️

scientific article published on March 1, 1977

Identification of Formation of Initial Native Structure in Onconase from an Unfolded State ⬇️

scientific article published on December 14, 2011

Identification of GATC- and CCGG-recognizing Type II REases and their putative specificity-determining positions using Scan2S--a novel motif scan algorithm with optional secondary structure constraints

scientific article published on May 2008

Identification of a new site of conformational heterogeneity in unfolded ribonuclease A.

scientific article published in October 1990

Identification of two anti-parallel beta-sheet conformations in the solution structure of murine epidermal growth factor by proton magnetic resonance

scientific article

Identifying native-like protein structures with scoring functions based on all-atom ECEPP force fields, implicit solvent models and structure relaxation

scientific article

Immunochemical determination of conformational equilibria for fragments of the B beta chain of fibrinogen

scientific article published on February 1985

Impact of an easily reducible disulfide bond on the oxidative folding rate of multi-disulfide-containing proteins

scientific article

Implementation of a Serial Replica Exchange Method in a Physics-Based United-Residue (UNRES) Force Field

scientific article published on August 2008

Implementation of a k/k0 Method to Identify Long-Range Structure in Transition States during Conformational Folding/Unfolding of Proteins

scientific article

Implementation of a symplectic multiple-time-step molecular dynamics algorithm, based on the united-residue mesoscopic potential energy function

scientific article published in November 2006

Implementation of molecular dynamics and its extensions with the coarse-grained UNRES force field on massively parallel systems; towards millisecond-scale simulations of protein structure, dynamics, and thermodynamics.

scientific article

Implementations of Nosé-Hoover and Nosé-Poincaré thermostats in mesoscopic dynamic simulations with the united-residue model of a polypeptide chain

scientific article published on June 2008

Improved conformational space annealing method to treat β-structure with the UNRES force-field and to enhance scalability of parallel implementation

article published in 2004

Improved genetic algorithm for the protein folding problem by use of a Cartesian combination operator

scientific article

Improvements in the prediction of protein backbone topography by reduction of statistical errors ⬇️

scientific article published on February 20, 1979

Influence of Water on Protein Structure. An Analysis of the Preferences of Amino Acid Residues for the Inside or Outside and for Specific Conformations in a Protein Molecule ⬇️

scientific article published on January 1, 1978

Influence of an extrinsic cross-link on the folding pathway of ribonuclease A. Kinetics of folding-unfolding

scientific article published in May 1985

Influence of charge and size of terminal amino-acid residues on local conformational states and shape of alanine-based peptides

scientific article

Influence of local interactions on protein structure. I. Conformational energy studies of N-acetyl-N'-methylamides of Pro-X and X-Pro dipeptides

scientific article published on April 1, 1977

Influence of lysine content and pH on the stability of alanine-based copolypeptides

scientific article

Influence of temperature, friction, and random forces on folding of the B-domain of staphylococcal protein A: all-atom molecular dynamics in implicit solvent

scientific article published in April 2007

Influence of the Length of the Alanine Spacer on the Acidic-Basic Properties of the Ac-Lys-(Ala)(n)-Lys-NH(2) Peptides (n = 0, 1, 2, …, 5).

scientific article

Inhibitor design by wrapping packing defects in HIV-1 proteins

scholarly article

Insufficiently dehydrated hydrogen bonds as determinants of protein interactions

scholarly article

Interactions between an alpha-helix and a beta-sheet. Energetics of alpha/beta packing in proteins

scientific article published in December 1985

Interactions between two beta-sheets. Energetics of beta/beta packing in proteins

scientific article published in April 1986

Interactions that favor the native over the non-native disulfide bond among residues 58-72 in the oxidative folding of bovine pancreatic ribonuclease A.

scientific article published in December 2002

Intermolecular anti-parallel beta sheet: Comparison of predicted and observed conformations of gramicidin S.

scientific article

Intermolecular potentials from crystal data. V. Crystal packing of poly(beta-(p-chlorobenzyl)-L-aspartate).

scientific article published on July 1974

Interplay of charge distribution and conformation in peptides: comparison of theory and experiment

scientific article published in January 2005

Intramolecular steric effects and hydrogen bonding in regular conformations of polyamino acids

scientific article published in September 1966

Intramolecular versus intermolecular disulfide bonds in prion proteins

scientific article published on 24 June 2002

Introduction of short-range restrictions in a protein-folding algorithm involving a long-range geometrical restriction and short-, medium-, and long-range interactions

scientific article

Investigation of Phosphorylation-Induced Folding of an Intrinsically Disordered Protein by Coarse-Grained Molecular Dynamics

scientific article published on 29 April 2021

Investigation of protein folding by coarse-grained molecular dynamics with the UNRES force field

scientific article

Kinetic Folding Pathway of a Three-Disulfide Mutant of Bovine Pancreatic Ribonuclease A Missing the [40−95] Disulfide Bond ⬇️

scientific article published on May 19, 1998

Kinetics and mechanism of the refolding of denatured ribonuclease A.

scientific article published in July 1985

Kinetics of competitive binding with application to thrombin complexes

scientific article published in May 1997

Kinks, loops, and protein folding, with protein A as an example

scientific article

Lattice neural network minimization. Application of neural network optimization for locating the global-minimum conformations of proteins

scientific article published in August 1993

Lessons from application of the UNRES force field to predictions of structures of CASP10 targets

scientific article

Like-charged residues at the ends of oligoalanine sequences might induce a chain reversal

scientific article

Limiting Values of the one-bond C-H Spin-Spin Coupling Constants of the Imidazole Ring of Histidine at High-pH.

scientific article published on 8 January 2017

Local and long-range interactions in the thermal unfolding transition of bovine pancreatic ribonuclease A.

scientific article

Local interactions in bends of proteins ⬇️

scientific article published on October 1, 1977

Local structure in a tryptic fragment of performic acid oxidized ribonuclease A corresponding to a proposed polypeptide chain-folding initiation site detected by tyrosine fluorescence lifetime and proton magnetic resonance measurements

scientific article published in March 1987

Local structure involving histidine-12 in reduced S-sulfonated ribonuclease A detected by proton NMR spectroscopy under folding conditions

scientific article

Local vs global motions in protein folding

scientific article published on July 2013

Localization of a fibrin gamma-chain polymerization site within segment Thr-374 to Glu-396 of human fibrinogen

scientific article published on October 1984

Location of peptide fragments in the fibrinogen molecule by immunoelectron microscopy

scientific article

Location of the antigenic determinants of bovine pancreatic ribonuclease ⬇️

scientific article published on October 2, 1979

Low-energy structures of two dipeptides and their relationship to bend conformations

scientific article published in November 1974

Lysosomal enzyme tripeptidyl peptidase 1 destabilizes fibrillar Aβ by multiple endoproteolytic cleavages within the β-sheet domain

scientific article published on 29 January 2018

MPSA short communications

article by Eugene M. Barnes et al published July 1994 in The Protein Journal

Matrix formulation of the transition from a statistical coil to an intramolecular antiparallel beta sheet

scientific article published in September 1984

Maximum Likelihood Calibration of the UNRES Force Field for Simulation of Protein Structure and Dynamics

scientific article published on 15 August 2017

Mean-field interactions between nucleic-acid-base dipoles can drive the formation of a double helix

scientific article published in Physical Review Letters

Mechanism of action of thrombin on fibrinogen. 3. Partial mapping of the active sites of thrombin and trypsin

scientific article published in September 1973

Mechanism of action of thrombin on fibrinogen. I. Synthesis of fibrinogen-like peptides, and their proteolysis by thrombin and trypsin

scientific article published on February 1971

Mechanism of action of thrombin on fibrinogen. II. Kinetics of hydrolysis of fibrinogen-like peptides by thrombin and trypsin ⬇️

scientific article published on November 1, 1971

Mechanism of action of thrombin on fibrinogen. IV. Further mapping of the active sites of thrombin and trypsin.

scientific article published in January 1974

Mechanism of action of thrombin on fibrinogen. Reaction of the N-terminal CNBr fragment from the Aalpha chain of human fibrinogen with bovine thrombin

scientific article published in October 1974

Mechanism of action of thrombin on fibrinogen. Size of the A alpha fibrinogen-like peptide that contacts the active site of thrombin

scientific article

Mechanism of action of thrombin on fibrinogen: NMR evidence for a beta-bend at or near fibrinogen A alpha Gly(P5)-Gly(P4).

scientific article

Mechanism of fiber assembly: treatment of Aβ peptide aggregation with a coarse-grained united-residue force field

scientific article

Mechanism of formation of the C-terminal beta-hairpin of the B3 domain of the immunoglobulin binding protein G from Streptococcus. I. Importance of hydrophobic interactions in stabilization of beta-hairpin structure

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Mechanism of formation of the C-terminal beta-hairpin of the B3 domain of the immunoglobulin binding protein G from Streptococcus. II. Interplay of local backbone conformational dynamics and long-range hydrophobic interactions in hairpin formation

scientific article published on August 2009

Mechanism of formation of the C-terminal beta-hairpin of the B3 domain of the immunoglobulin binding protein G from Streptococcus. III. Dynamics of long-range hydrophobic interactions

scientific article published on February 2010

Mechanism of formation of the C-terminal beta-hairpin of the B3 domain of the immunoglobulin-binding protein G from Streptococcus. IV. Implication for the mechanism of folding of the parent protein

scientific article

Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins

scientific article

Minimization of polypeptide energy, iii. Application of a rapid energy minimization technique to the calculation of preliminary structures of gramicidin-s

scientific article

Minimization of polypeptide energy, vi. Systematic searches for low-energy conformations of deca-L-alanine and the octapeptide loop of ribonuclease

scientific article published on May 1969

Minimization of polypeptide energy. 8. Application of the deflation technique to a dipeptide

scientific article

Minimization of polypeptide energy. I. Preliminary structures of bovine pancreatic ribonuclease S-peptide ⬇️

scientific article

Minimization of polypeptide energy. II. Preliminary structures of oxytocin, vasopressin, and an octapeptide from ribonuclease ⬇️

scientific article

Minimization of polypeptide energy. IX. A procedure for seeking the global minimum of functions with many minima ⬇️

scientific article published on August 1, 1970

Minimization of polypeptide energy. VII. Second derivatives and statistical weights of energy minima for deca-L-alanine

scientific article

Minimization of polypeptide energy. XI. The method of gentlest ascent

scientific article

Model for the crystal packing and conformational changes of biphenyl in incommensurate phase transitions

scientific article published on 18 March 2004

Model of protein folding: inclusion of short-, medium-, and long-range interactions ⬇️

scientific article published on October 1, 1975

Model of protein folding: incorporation of a one-dimensional short-range (Ising) model into a three-dimensional model ⬇️

scientific article published on April 1, 1977

Modification and optimization of the united-residue (UNRES) potential energy function for canonical simulations. I. Temperature dependence of the effective energy function and tests of the optimization method with single training proteins.

scientific article

Molecular dynamics of protein A and a WW domain with a united-residue model including hydrodynamic interaction

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Molecular dynamics with the United-residue force field: ab initio folding simulations of multichain proteins

scientific article published on January 2007

Molecular dynamics with the united-residue model of polypeptide chains. I. Lagrange equations of motion and tests of numerical stability in the microcanonical mode

scientific article published on July 2005

Molecular dynamics with the united-residue model of polypeptide chains. II. Langevin and Berendsen-bath dynamics and tests on model alpha-helical systems

scientific article published on July 2005

Molecular modeling of the binding modes of the iron-sulfur protein to the Jac1 co-chaperone from Saccharomyces cerevisiae by all-atom and coarse-grained approaches

scientific article published on 6 June 2015

Molecular theory of the helix-coil transition in polyamino acids, I. Formulation ⬇️

scientific article

Molecular weight of bovine fibrinogen by sedimentation equilibrium ⬇️

scientific article published on June 1, 1971

Monte Carlo recursion evaluation of free energy

Monte Carlo-minimization approach to the multiple-minima problem in protein folding ⬇️

scientific article

Multiple pathways for regenerating ribonuclease A.

scientific article published on January 1984

My 65 years in protein chemistry

scientific article

NMR structural analysis of an analog of an intermediate formed in the rate-determining step of one pathway in the oxidative folding of bovine pancreatic ribonuclease A: automated analysis of 1H, 13C, and 15N resonance assignments for wild-type and [

scientific article

Native conformational tendencies in unfolded polypeptides: development of a novel method to assess native conformational tendencies in the reduced forms of multiple disulfide-bonded proteins

scientific article published in February 2003

New Insights into Protein (Un)Folding Dynamics

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New Method for Calculating the Conformational Entropy of a Regular Helix ⬇️

scientific article published on January 1, 1974

New developments of the electrostatically driven monte carlo method: Test on the membrane-bound portion of melittin ⬇️

scientific article published on August 1, 1998

Nonexponential decay of internal rotational correlation functions of native proteins and self-similar structural fluctuations

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Nonnative isomers of proline-93 and -114 predominate in heat-unfolded ribonuclease A.

scientific article published in September 1990

Nuclear Magnetic Resonance Spectrum of Lysine-Vasopressin in Aqueous Solution and Its Structural Implications ⬇️

scientific article published on August 1, 1972

Nuclear Magnetic Resonance Studies of Lysine-Vasopressin: Structural Constraints ⬇️

scientific article published on December 1, 1971

Nuclear magnetic resonance spectrum of deamino-lysine-vasopression in aqueous solution and its structural implications

scientific article published on November 1972

Nuclear magnetic resonance spectrum of lysine-vasopressin and its structural implications

scientific article published on May 1971

Nuclear magnetic resonance studies of intramolecular motions and side-chain interactions in water-soluble polyamino acids ⬇️

scientific article published on May 12, 1970

Nuclear magnetic resonance study of fibrinogen-like peptides and their structure in dimethyl sulfoxide and water ⬇️

scientific article published on March 21, 1978

Nuclear overhauser effects and the conformation of gramicidin S ⬇️

scientific article published on July 11, 1977

Nuclearmagnetic resonance study of the N-terminal fragment of bovine pancreatic ribonuclease

scientific article published in June 1972

On the biologically active structures of cholecystokinin, little gastrin, and enkephalin in the gastrointestinal system

scientific article

On the multiple-minima problem in the conformational analysis of polypeptides. I. Backbone degrees of freedom for a perturbed alpha-helix

scientific article published in January 1987

On the multiple-minima problem in the conformational analysis of polypeptides. II. An electrostatically driven Monte Carlo method--tests on poly(L-alanine).

scientific article published in August 1988

On the multiple-minima problem in the conformational analysis of polypeptides. V. Application of the self-consistent electrostatic field and the electrostatically driven monte carlo methods to bovine pancreatic trypsin inhibitor ⬇️

scientific article published on January 1, 1991

On the orientation of the backbone dipoles in native folds

scientific article

On the pH-conformational dependence of the unblocked SYPYD peptide

scientific article published in September 1999

Optical rotatory dispersion and RNA base pairing in ribosomes and in tobacco mosaic virus

scientific article published in October 1967

Optimization of a Nucleic Acids united-RESidue 2-Point model (NARES-2P) with a maximum-likelihood approach

scientific article

Optimization of the UNRES Force Field by Hierarchical Design of the Potential-Energy Landscape. 1. Tests of the Approach Using Simple Lattice Protein Models

Optimization of the UNRES Force Field by Hierarchical Design of the Potential-Energy Landscape. 2. Off-Lattice Tests of the Method with Single Proteins

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Optimization of the UNRES Force Field by Hierarchical Design of the Potential-Energy Landscape. 3. Use of Many Proteins in Optimization

article by Stanislaw Oldziej et al published October 2004 in Journal of Physical Chemistry

Origin of the right-handed twist of beta-sheets of poly(LVal) chains

scientific article

Oxidative folding and N-terminal cyclization of onconase

scientific article published on 18 April 2007

Oxidative folding pathway of onconase, a ribonuclease homologue: insight into oxidative folding mechanisms from a study of two homologues

scientific article published on March 2009

PDZ binding to the BAR domain of PICK1 is elucidated by coarse-grained molecular dynamics

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PMFF: Development of a Physics-Based Molecular Force Field for Protein Simulation and Ligand Docking

scientific article published on 29 January 2020

Packing helices in proteins by global optimization of a potential energy function

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Parametrization of Backbone−Electrostatic and Multibody Contributions to the UNRES Force Field for Protein-Structure Prediction from Ab Initio Energy Surfaces of Model Systems†

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Pathways of folding of reduced bovine pancreatic ribonuclease ⬇️

scientific article published on August 13, 1974

Physical reasons for the unusual alpha-helix stabilization afforded by charged or neutral polar residues in alanine-rich peptides

scientific article

Physics-Based Potentials for Coarse-Grained Modeling of Protein-DNA Interactions

scientific article published on January 2015

Physics-based method to validate and repair flaws in protein structures

2013 scientific article

Physics-based potentials for the coupling between backbone- and side-chain-local conformational states in the UNited RESidue (UNRES) force field for protein simulations

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Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: assessment in two blind tests.

scientific article

Plasmid purification using reverse-phase high performance liquid chromatography resin PRP-∞ ⬇️

scientific article published on August 25, 1988

Polyproline II helix conformation in a proline-rich environment: a theoretical study

scientific article

Predicted conformations for the immunodominant region of the circumsporozoite protein of the human malaria parasite Plasmodium falciparum

scientific article published on August 1986

Predicting 13Calpha chemical shifts for validation of protein structures

scientific article published on 9 June 2007

Prediction of conformation of rat galanin in the presence and absence of water with the use of Monte Carlo methods and the ECEPP/3 force field

scientific article published on May 1994

Prediction of probable pathways of folding in globular proteins

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Prediction of protein conformation on the basis of a search for compact structures: test on avian pancreatic polypeptide

scientific article

Prediction of structural homology between bovine α-lactalbumin and hen egg white lysozyme ⬇️

scientific article published on June 1, 1971

Prediction of the location of structural domains in globular proteins

scientific article

Prediction of the native conformation of a polypeptide by a statistical-mechanical procedure. I. Backbone structure of enkephalin

scientific article published in August 1985

Prediction of the native conformation of a polypeptide by a statistical-mechanical procedure. III. Probable and average conformations of enkephalin

scientific article published in July 1987

Prediction of the structures of proteins with the UNRES force field, including dynamic formation and breaking of disulfide bonds.

scientific article

Prediction of the three-dimensional structures of complexes of lysozyme with cell wall substrates ⬇️

scientific article published on July 7, 1981

Prediction of three-dimensional structures of enzyme-substrate and enzyme-inhibitor complexes of lysozyme ⬇️

scientific article published on December 1, 1976

Preferred conformation of the tert-butoxycarbonyl-amino group in peptides

scientific article published on August 1980

Preliminary crystallographic data for cross-linked (lysine7-lysine41)-ribonuclease A.

scientific article

Principal component analysis for protein folding dynamics

scientific article published on 15 October 2008

Proline Isomerization in Bovine Pancreatic Ribonuclease A. 2. Folding Conditions ⬇️

scientific article published on May 20, 2003

Proline cis-trans isomerization and protein folding

scientific article published in December 2002

Proline-induced constraints in alpha-helices

scientific article

Protein structure prediction by global optimization of a potential energy function.

scientific article

Protein-Folding Dynamics: Overview of Molecular Simulation Techniques

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Proton NMR assignments and regular backbone structure of bovine pancreatic ribonuclease A in aqueous solution

scientific article

Quantum chemical 13C(alpha) chemical shift calculations for protein NMR structure determination, refinement, and validation

scholarly article

Quantum-mechanics-derived 13Calpha chemical shift server (CheShift) for protein structure validation

scientific article

Raman and resonance raman spectroscopy

scientific article published on January 1, 1978

Reaching the global minimum in docking simulations: A Monte Carlo energy minimization approach using Bezier splines ⬇️

scientific article published on July 7, 1998

Recent developments in the theory of protein folding: searching for the global energy minimum

scientific article published on April 1996

Recent improvements in prediction of protein structure by global optimization of a potential energy function.

scientific article

Refinement of the X-ray Structure of Rubredoxin by Conformational Energy Calculations

scientific article

Refinement of the molecular structure of actinomycin D by energy minimization

scientific article published in January 1973

Refinement of the x-ray structure of lysozyme by complete energy minimization

scientific article published in February 1974

Regeneration of RNase A from the reduced protein: models of regeneration pathways

scientific article

Regeneration of bovine pancreatic ribonuclease A. 1. Steady-state distribution

scientific article published in March 1993

Regeneration of bovine pancreatic ribonuclease A. 2. Kinetics of regeneration

scientific article published in March 1993

Regeneration of bovine pancreatic ribonuclease A. 3. Dependence on the nature of the redox reagent

scientific article published in March 1993

Regeneration of bovine pancreatic ribonuclease A. 4. Temperature dependence of the regeneration rate

scientific article published in March 1993

Regeneration of ribonuclease A from the reduced protein. Energetic analysis

scientific article published in September 1982

Regeneration of ribonuclease A from the reduced protein. Isolation and identification of intermediates, and equilibrium treatment

scientific article published in July 1981

Regeneration of ribonuclease A from the reduced protein. Rate-limiting steps

scientific article published in September 1982

Relation between free energy landscapes of proteins and dynamics

scientific article published on February 2010

Replica Exchange and Multicanonical Algorithms with the coarse-grained UNRES force field

scientific article published on January 2006

Resistance to receptor-mediated degradation of a murine epidermal growth factor analogue (EGF-Val-47) potentiates its mitogenic activity

scientific article published in November 1990

Resonance Raman spectroscopy of arsanilazocarboxypeptidase A: Determination of the nature of the azotyrosyl-248·zinc complex ⬇️

scientific article published on August 1, 1977

Respice, Adspice, and Prospice ⬇️

scientific article published on January 1, 2011

Retention of the Cis Proline Conformation in Tripeptide Fragments of Bovine Pancreatic Ribonuclease A Containing a Non-natural Proline Analogue, 5,5-Dimethylproline

scientific article published in 1999

Revised Backbone-Virtual-Bond-Angle Potentials to Treat the l- and d-Amino Acid Residues in the Coarse-Grained United Residue (UNRES) Force Field

scientific article

Revisiting the carboxylic acid dimers in aqueous solution: interplay of hydrogen bonding, hydrophobic interactions, and entropy

scientific article published on 19 September 2007

Role of Medium-Range Interactions in Proteins ⬇️

scientific article published on March 1, 1973

Role of hydrophobicity and solvent-mediated charge-charge interactions in stabilizing alpha-helices

scientific article

Role of interchain interactions in the stabilization of the right-handed twist of beta-sheets

scientific article published in August 1983

Role of loop-helix interactions in stabilizing four-helix bundle proteins ⬇️

scientific article published on August 15, 1992

Role of non-native aromatic and hydrophobic interactions in the folding of hen egg white lysozyme

scientific article published in October 1996

Search for low-energy conformations of a neurotoxic protein by means of predictive rules, tests for hard-sphere overlaps, and energy minimization

scientific article published in January 1976

Sensitive quantitative analysis of disulfide bonds in polypeptides and proteins

scientific article

Separation of time scale and coupling in the motion governed by the coarse-grained and fine degrees of freedom in a polypeptide backbone

scientific article published in October 2007

Sequence-, structure-, and dynamics-based comparisons of structurally homologous CheY-like proteins

scientific article published on 31 January 2017

Sequential nearest-neighbor effects on computed 13Calpha chemical shifts

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Shielding effects of the D-Phe aromatic ring in the 1H NMR spectrum of gramicidine S.

scientific article

Shifting the competition between the intramolecular Reshuffling reaction and the direct oxidation reaction during the oxidative folding of kinetically trapped disulfide-insecure intermediates

scientific article published in September 2003

Significant progress in predicting the crystal structures of small organic molecules--a report on the fourth blind test

scientific article

Simple Physics-Based Analytical Formulas for the Potentials of Mean Force of the Interaction of Amino Acid Side Chains in Water. VII. Charged-Hydrophobic/Polar and Polar-Hydrophobic/Polar Side Chains

scientific article published on 21 December 2016

Simple physics-based analytical formulas for the potentials of mean force of the interaction of amino-acid side chains in water. V. Like-charged side chains

scientific article

Simple physics-based analytical formulas for the potentials of mean force of the interaction of amino-acid side chains in water. VI. Oppositely charged side chains

scientific article

Simulation of the opening and closing of Hsp70 chaperones by coarse-grained molecular dynamics

scientific article

Simultaneous characterization of the reductive unfolding pathways of RNase B isoforms by top-down mass spectrometry

scientific article

Solution NMR evidence for a cis Tyr-Ala peptide group in the structure of [Pro93Ala] bovine pancreatic ribonuclease A.

scientific article

Solution conformation of enkephalin. A nuclear magnetic resonance study of 13C-enriched carbonyl carbons in [Leu5]-enkephalin ⬇️

scientific article published on May 1, 1979

Solution of the embedding problem and decomposition of symmetric matrices

scientific article published on April 1985

Solution structure of human type-alpha transforming growth factor determined by heteronuclear NMR spectroscopy and refined by energy minimization with restraints

scientific article

Solution structure of murine epidermal growth factor determined by NMR spectroscopy and refined by energy minimization with restraints

scientific article

Solution structure of murine epidermal growth factor: determination of the polypeptide backbone chain-fold by nuclear magnetic resonance and distance geometry

scientific article

Stabilization of collagen fibrils by hydroxyproline

scientific article published in June 1986

Stable conformations of aliphatic disulfides: influence of 1,4 interactions involving sulfur atoms ⬇️

scientific article published on January 1, 1977

Statistical Mechanical Treatment of Protein Conformation. 5. Multistate Model for Specific-Sequence Copolymers of Amino Acids ⬇️

scientific article published on January 1, 1977

Statistical Mechanical Treatment of Protein Conformation. I. Conformational Properties of Amino Acids in Proteins ⬇️

scientific article published on January 1, 1976

Statistical Mechanical Treatment of Protein Conformation. II. A Three-State Model for Specific-Sequence Copolymers of Amino Acids ⬇️

scientific article published on January 1, 1976

Statistical Mechanical Treatment of Protein Conformation. III. Prediction of Protein Conformation Based on a Three-State Model ⬇️

scientific article published on January 1, 1976

Statistical and energetic analysis of side-chain conformations in oligopeptides

scientific article published in July 1983

Statistical mechanical treatment of protein conformation. 4. A four-state model for specific-sequence copolymers of amino acids

scientific article published on September 1, 1976

Statistical mechanical treatment of protein conformation. 6. Elimination of empirical rules for prediction by use of a high-order probability. Correlation between the amino acid sequences and conformations for homologous neurotoxin proteins

scientific article published on March 1, 1977

Status of empirical methods for the prediction of protein backbone topography

scientific article

Steady-state kinetic study of the bovine thrombin-fibrinogen interaction

scientific article published in May 1980

Steps in the pathway of the thermal unfolding of ribonuclease A. A nonspecific photochemical surface-labeling study ⬇️

scientific article published on June 12, 1979

Stepwise deamidation of ribonuclease A at five sites determined by top down mass spectrometry

scientific article published on January 2006

Strong interaction between disulfide derivatives and aromatic groups in peptides and proteins ⬇️

scientific article published on January 30, 1981

Structural Studies of Paramyosin. I. Hydrogen Ion Equilibria* ⬇️

scientific article published on 01 January 1962

Structural Studies of Paramyosin. II. Conformational Changes* ⬇️

scientific article published on 01 January 1962

Structural determinants of oxidative folding in proteins ⬇️

scholarly article

Structure and free energy of complex thermodynamic systems

Structure of liquid water. II. Improved statistical thermodynamic treatment and implications of a cluster model

Structure of liquid water. III. Thermodynamic properties of liquid deuterium oxide

Structure of the interferon-receptor complex determined by distance constraints from double-mutant cycles and flexible docking ⬇️

scientific article published on November 6, 2001

Structures of enzyme-substrate complexes of lysozyme ⬇️

scientific article published on July 1, 1977

Study of protein topography with flash photolytically generated nonspecific surface-labeling reagents: surface labeling of ribonuclease A ⬇️

scientific article published on February 8, 1977

Study of the state of ionization of [Leu5]-enkephalin in the crystal and in solution.

scientific article published on September 1980

The Effect of Neighboring Charges on the Helix Forming Ability of Charged Amino Acids in Proteins ⬇️

scientific article published on July 1, 1975

The determination of intermolecular potentials from crystal data, I. General theory and application to crystalline benzene at several temperatures

scientific article

The effect of the L-azetidine-2-carboxylic acid residue on protein conformation. II. Homopolymers and copolymers

scientific article

The effect of the L-azetidine-2-carboxylic acid residue on protein conformation. III. Collagen-like poly(tripeptide)s

scientific article published in January 1990

The influence of long-range interactions on the structure of myoglobin ⬇️

scientific article

The influence of short-range interactions on protein conformation. 3. Dipeptide distributions in proteins of known sequence and structure

scientific article

The influence of short-range interactions on protein conformation. I. Side chain-backbone interactions within a single peptide unit ⬇️

scientific article

The influence of short-range interactions on protein onformation. II. A model for predicting the alpha-helical regions of proteins

scientific article

The intrinsic helix-forming tendency of L-alanine

scientific article published on August 1992

The multiple-minima problem in the conformational analysis of polypeptides. III. An electrostatically driven Monte Carlo method: tests on enkephalin

scientific article published in April 1989

The oxidative folding rate of bovine pancreatic ribonuclease is enhanced by a covalently attached oligosaccharide

scientific article published in July 2005

The role of hydrophobic interactions in initiation and propagation of protein folding

scholarly article

The thrombin-fibrinogen interaction

scientific article

Theoretical Studies of Interactions between O-Phosphorylated and Standard Amino-Acid Side-Chain Models in Water

scientific article

Theoretical and experimental studies of conformations of polypeptides ⬇️

scientific article published on April 1, 1971

Theoretical prediction of a crystal structure

scientific article published on March 1996

Theoretical studies of protein conformation by means of energy computations

scientific article

Theory of hydrophobic interactions

scientific article

Theory of the Cooperative Transition between Two Ordered Conformations of Poly(L-proline). I. Phenomenological Theory ⬇️

scientific article published on July 1, 1975

Theory of the Cooperative Transition between Two Ordered Conformations of Poly(L-proline). II. Molecular Theory in the Absence of Solvent ⬇️

scientific article published on July 1, 1975

Theory of the Cooperative Transition between Two Ordered Conformations of Poly(L-proline). III. Molecular Theory in the Presence of Solvent ⬇️

scientific article published on July 1, 1975

Thermodynamics of the quenching of tyrosyl fluorescence by dithiothreitol

scientific article published on September 1987

Toward an understanding of the folding of ribonuclease A.

scientific article

Towards Temperature Dependent Coarse-grained Potential of Side-chain Interactions for Protein Folding Simulations

Towards crystal structure prediction of complex organic compounds--a report on the fifth blind test

scientific article published on 17 November 2011

Tracking the Mechanism of Fibril Assembly by Simulated Two-Dimensional Ultraviolet Spectroscopy ⬇️

scientific article published on 07 January 2013

U-3'-BCIP: a chromogenic substrate for the detection of RNase A in recombinant DNA expression systems

scientific article published in January 1991

Ultrarapid mixing experiments shed new light on the characteristics of the initial conformational ensemble during the folding of ribonuclease A

scientific article

Unblocked statistical-coil tetrapeptides in aqueous solution: quantum-chemical computation of the carbon-13 NMR chemical shifts

scientific article published in June 2003

Unfolding and refolding of the native structure of bovine pancreatic trypsin inhibitor studied by computer simulations ⬇️

scientific article published on September 21, 1993

Use of 13C(alpha) chemical shifts for accurate determination of beta-sheet structures in solution

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Use of 13Calpha chemical shifts in protein structure determination

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Use of a Symmetry Condition to Compute the Conformation of Gramicidin S ⬇️

scientific article published on November 1, 1975

Use of buildup and energy-minimization procedures to compute low-energy structures of the backbone of enkephalin

scientific article published in August 1985

Use of decoys to optimize an all-atom force field including hydration

scientific article published on 23 May 2008

Use of the Transferred Nuclear Overhauser Effect To Determine the Conformations of Ligands Bound to Proteins

article by Feng Ni & Harold A. Scheraga published September 1994 in Accounts of Chemical Research

Variable-target-function and build-up procedures for the calculation of protein conformation. Application to bovine pancreatic trypsin inhibitor using limited simulated nuclear magnetic resonance data

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Vibrational frequencies of water clusters

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Volume of the intersection of three spheres of unequal size: a simplified formula

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Water molecule interactions. Stability of cyclic polymers

WeFold: a coopetition for protein structure prediction

scientific article

What can we learn by computing 13Calpha chemical shifts for X-ray protein models?

scientific article

beta-hairpin-forming peptides; models of early stages of protein folding

scientific article

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