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List of works by Martin Karplus

"New View" of Protein Folding Reconciled with the Old Through Multiple Unfolding Simulations ⬇️

scientific article published on December 12, 1997

10 Neural networks for protein structure prediction

scientific article published on January 1, 1991

1H NMR aromatic spectrum of the operator binding domain of the lambda repressor: resonance assignment with application to structure and dynamics

scientific article published on 01 February 1987

1H-NMR study of the λ operator siteOL1: assignment of the imino and adenine H2 resonances ⬇️

scientific article published on May 11, 1984

2 His Nobel Lecture and his speculative commentary on "What does the Future Hold"?

scientific article

9 Modeling of side chains, loops, and insertions in proteins

scientific article published on January 1, 1991

A CRITERION FOR ORBITAL HYBRIDIZATION AND CHARGE DISTRIBUTION IN CHEMICAL BONDS

scientific article

A Simple and Accurate Method To Calculate Free Energy Profiles and Reaction Rates from Restrained Molecular Simulations of Diffusive Processes

scientific article published on 26 May 2016

A Src-like inactive conformation in the abl tyrosine kinase domain

scientific article

A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations

scientific article (publication date: July 1990)

A comparative study of ligand-receptor complex binding affinity prediction methods based on glycogen phosphorylase inhibitors

scientific article published on 01 May 1999

A comparison between molecular dynamics and X-ray results for dissociated CO in myoglobin

scientific article published in March 1997

A comparison of the dynamic behavior of monomeric and dimeric insulin shows structural rearrangements in the active monomer

scientific article published on 01 September 2004

A comparison of the restrained molecular dynamics and distance geometry methods for determining three-dimensional structures of proteins on the basis of interproton distances

article

A conformational isomer of bovine pancreatic trypsin inhibitor protein produced by refolding

scientific article

A conformational transition in the myosin VI converter contributes to the variable step size

scientific article published on 15 November 2011

A differential fluctuation theorem

scientific article published on 11 March 2008

A dynamic analysis of the rotation mechanism for conformational change in F(1)-ATPase

scientific article published on 01 July 2002

A dynamic model for the allosteric mechanism of GroEL

scientific article (publication date: 15 September 2000)

A gating mechanism of pentameric ligand-gated ion channels

scientific article published on 16 September 2013

A hierarchy of timescales in protein dynamics is linked to enzyme catalysis

scientific article (publication date: 6 December 2007)

A kinetic model of coordinated myosin V

scientific article published on 08 May 2007

A lattice protein with an amyloidogenic latent state: stability and folding kinetics

scientific article published on 22 February 2007

A mathematical model for structure-function relations in hemoglobin ⬇️

scientific article published on December 14, 1972

A mathematical model for structure-function relationships in hemoglobin

scientific article published in January 1972

A mechanism for rotamase catalysis by the FK506 binding protein (FKBP)

scientific article published on 01 December 1993

A metastable state in folding simulations of a protein model

scientific article published on 01 March 1998

A model for the cooperative free energy transduction and kinetics of ATP hydrolysis by F 1 -ATPase ⬇️

scientific article published on September 18, 2003

A molecular dynamics analysis of protein structural elements

scientific article published on 01 January 1989

A new two-disulphide intermediate in the refolding of reduced bovine pancreatic trypsin inhibitor ⬇️

scientific article published on April 5, 1984

A normal mode analysis of structural plasticity in the biomolecular motor F(1)-ATPase

scientific article published in July 2004

A restrained locally enhanced sampling method (RLES) for finding free energy minima in complex systems

scientific article published on 01 September 2020

A simplified confinement method for calculating absolute free energies and free energy and entropy differences

scientific article published on 10 January 2013

A structure-based model for the synthesis and hydrolysis of ATP by F1-ATPase

scientific article

Absolute Binding Free Energies: A Quantitative Approach for Their Calculation

Acid and thermal denaturation of barnase investigated by molecular dynamics simulations

scientific article published on 01 October 1995

Active site dynamics in protein molecules: a stochastic boundary molecular-dynamics approach

scientific article published in May 1985

Active site dynamics of acyl-chymotrypsin

scientific article published on June 1993

Active site dynamics of ribonuclease

scientific article published on December 1985

Adaptive umbrella sampling of the potential energy: modified updating procedure of the umbrella potential and application to peptide folding

All-atom empirical potential for molecular modeling and dynamics studies of proteins

scientific article (publication date: 30 April 1998)

Allosteric communication in myosin V: from small conformational changes to large directed movements

scientific article (publication date: 2008)

Allostery and cooperativity revisited

scientific article

Amino-terminal arm of the lambda repressor: a 1H NMR study

scientific article published in October 1984

An analysis of incorrectly folded protein models. Implications for structure predictions

scientific article published in August 1984

An automated method for dynamic ligand design

scientific article published in December 1995

An improved method for nonbonded list generation: rapid determination of near-neighbor pairs

scientific article published in January 2003

Analysis and Elimination of a Bias in Targeted Molecular Dynamics Simulations of Conformational Transitions: Application to Calmodulin ⬇️

scientific article published on March 28, 2012

Analysis of an anomalous mutant of MutM DNA glycosylase leads to new insights into the catalytic mechanism

scientific article

Analysis of proton release in oxygen binding by hemoglobin: implications for the cooperative mechanism

scientific article published in February 1988

Analysis of side-chain orientations in homologous proteins

scientific article published on 01 July 1987

Analysis of the interaction of organic phosphates with hemoglobin ⬇️

scientific article published on June 29, 1976

Analysis of two-residue turns in proteins

scientific article published on 01 May 1994

Anatomy of a conformational change: hinged "lid" motion of the triosephosphate isomerase loop.

scientific article

Anaysis of cooperativity in hemoglobin. Valency hybrids, oxidation, and methemoglobin replacement reactions ⬇️

scientific article published on March 11, 1975

Anisotropy and anharmonicity of atomic fluctuations in proteins: analysis of a molecular dynamics simulation

scientific article published on 01 January 1987

Anisotropy and anharmonicity of atomic fluctuations in proteins: implications for X-ray analysis

scientific article

Aplasia cutis congenita in one of monozygotic twins

scientific article published on 01 November 1986

Application of molecular dynamics with interproton distance restraints to three-dimensional protein structure determination. A model study of crambin

scientific article

Application of the diffusion-collision model to the folding of three-helix bundle proteins

scientific article published in April 2002

Aspects of protein dynamics

scientific article published on 01 January 1981

Asymmetric synthesis of pochonin E and F, revision of their proposed structure, and their conversion to potent Hsp90 inhibitors

scientific article published on 13 June 2012

Backbone-dependent rotamer library for proteins. Application to side-chain prediction

scientific article

Bayesian estimates of free energies from nonequilibrium work data in the presence of instrument noise

scientific article

Behind the folding funnel diagram ⬇️

scientific article published on June 17, 2011

Beta-sheet coil transitions in a simple polypeptide model

scientific article

Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase

scientific article

Binding free energy differences in a TCR-peptide-MHC complex induced by a peptide mutation: a simulation analysis

scientific article published in November 2002

Biomolecular motors: the F1-ATPase paradigm

scientific article published on April 2004

Brownian dynamics simulation of protein folding: a study of the diffusion-collision model

scientific article published on 01 April 1987

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

scientific article published in 1983

CHARMM: the biomolecular simulation program

scientific article

Calculation of free-energy differences by confinement simulations. Application to peptide conformers

scientific article published on July 2009

Calculation of one-electron properties for the formaldehyde molecule with the LCAO MO SCF function of Foster and Boys

scientific article published in October 1966

Calculation of pi-pi excited state conformations and vibronic structure of retinal and related molecules

scientific article

Calculation of the aqueous solvation energy and entropy, as well as free energy, of simple polar solutes

scientific article published on 01 November 2004

Catalysis and specificity in enzymes: a study of triosephosphate isomerase and comparison with methyl glyoxal synthase

scientific article published on January 2003

Chaperoned alchemical free energy simulations: a general method for QM, MM, and QM/MM potentials

scientific article

Characterization of flexible molecules in solution: the RGDW peptide.

scientific article

Chromophore-protein interactions and the function of the photosynthetic reaction center: a molecular dynamics study.

scientific article

Coexisting origins of subdiffusion in internal dynamics of proteins

scientific article published on 6 June 2017

Collective motions in proteins: A covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations ⬇️

scientific article published on January 1, 1991

Comment on a "fluctuation and cross correlation analysis of protein motions observed in nanosecond molecular dynamics simulations"

scientific article published on 01 October 1996

Comment on the Communication "The Key to Solving the Protein-Folding Problem Lies in an Accurate Description of the Denatured State" by van Gunsteren et al. We thank Eugene Shakhnovich (Harvard University) for pointing out the references on lattice

Comment on: 'The entropy cost of protein association'

scientific article published on 01 March 1999

Comparison of the transition state ensembles for folding of Im7 and Im9 determined using all-atom molecular dynamics simulations with phi value restraints

scientific article (publication date: 15 February 2004)

Computer simulation and analysis of the reaction pathway of triosephosphate isomerase

scientific article published on 01 June 1991

Computer simulations of the OmpF porin from the outer membrane of Escherichia coli

scientific article

Configurational entropy of native proteins

scientific article

Conformation of retinal isomers

scientific article published in February 1974

Conformational Free-Energy Difference of a Miniprotein from Nonequilibrium Simulations

Conformational analysis of a stereochemically complete set of cis-enediol peptide analogues

scientific article published on 01 September 2002

Conformational analysis of the backbone-dependent rotamer preferences of protein sidechains ⬇️

scientific article published on May 1, 1994

Conformational sampling using high-temperature molecular dynamics

scientific article published on 01 December 1990

Conformational sampling via a self-regulating effective energy surface

scientific article published in May 2006

Conformations of intermediates in the folding of the pancreatic trypsin inhibitor

scientific article

Constrained Molecular Wavefunctions: HF Molecule

article by A. Mukherji & Martin Karplus published January 1963 in Journal of Chemical Physics

Construction of a model for the three-dimensional structure of human renal renin

scientific article published on 01 January 1985

Construction of side-chains in homology modelling. Application to the C-terminal lobe of rhizopuspepsin

scientific article published on 01 December 1989

Contact Electron‐Spin Coupling of Nuclear Magnetic Moments

Contribution of the hydrophobic effect to protein stability: analysis based on simulations of the Ile-96----Ala mutation in barnase

scientific article published on December 1991

Cooperativity in Scapharca Dimeric Hemoglobin: Simulation of Binding Intermediates and Elucidation of the Role of Interfacial Water

scientific article published on 01 February 2003

Cooperativity inScapharca dimeric hemoglobin: Simulation of binding intermediates and elucidation of the role of interfacial water

Correlation effects in the spectra of polyenes

Crystal structures of two closely related but antigenically distinct HLA-A2/melanocyte-melanoma tumor-antigen peptide complexes

scientific article

Crystallographic R factor refinement by molecular dynamics

scientific article (publication date: 23 January 1987)

Cytosolic expression, solution structures, and molecular dynamics simulation of genetically encodable disulfide-rich de novo designed peptides

scientific article published on 01 September 2018

DNA polymorphism: a comparison of force fields for nucleic acids

scientific article

Demonstration by NMR of folding domains in lysozyme

scientific article

Dependence of DNA polymerase replication rate on external forces: a model based on molecular dynamics simulations

scientific article

Design of dimerization inhibitors of HIV-1 aspartic proteinase: a computer-based combinatorial approach

scientific article published on 01 February 2000

Design, synthesis, and biological evaluation of HSP90 inhibitors based on conformational analysis of radicicol and its analogues

scientific article published in May 2005

Determination of a transition state at atomic resolution from protein engineering data

scientific article published in November 2002

Determination of equilibrium properties of biomolecular systems using multidimensional adaptive umbrella sampling

Determining the Conformational Change that Accompanies Donor–Acceptor Distance Fluctuations: An Umbrella Sampling Analysis ⬇️

scientific article published on May 27, 2011

Development of Multiscale Models for Complex Chemical Systems: From H+H2to Biomolecules (Nobel Lecture)

scientific article (publication date: 27 July 2014)

Diffusion-collision model for the folding kinetics of myoglobin

scientific article published on 01 January 1988

Diffusion-collision model for the folding kinetics of the lambda-repressor operator-binding domain

scientific article published on 01 March 1984

Diffusive reaction dynamics on invariant free energy profiles

scholarly article

Dimerization of the operator binding domain of phage lambda repressor.

scientific article

Dipolar NMR relaxation of nonprotonated aromatic carbons in proteins. Structural and dynamical effects ⬇️

scientific article published on July 1, 1982

Discordant Hirschsprung's disease in monozygotic twins

scientific article published on 01 October 1983

Discrimination of the native from misfolded protein models with an energy function including implicit solvation

scientific article (publication date: 7 May 1999)

Domain association in immunoglobulin molecules. The packing of variable domains

scientific article

Dynamic distance disorder in proteins is caused by trapping

scientific article published in May 2006

Dynamic ligand design and combinatorial optimization: designing inhibitors to endothiapepsin

scientific article published in August 2000

Dynamical aspects of molecular recognition

scientific article published on 01 March 2010

Dynamical search for bis-penicillamine enkephalin conformations ⬇️

scientific article published on December 1, 1991

Dynamical theory of activated processes in globular proteins

scientific article

Dynamics of DNA oligomers

scientific article published on 01 October 1983

Dynamics of activated processes in globular proteins ⬇️

scientific article published on August 1, 1979

Dynamics of folded proteins ⬇️

scientific article published on June 16, 1977

Dynamics of ligand binding to heme proteins ⬇️

scientific article published on August 15, 1979

Dynamics of myoglobin: comparison of simulation results with neutron scattering spectra

scientific article published on February 1990

Dynamics of proteins ⬇️

scientific article published on January 1, 1984

Dynamics of proteins: elements and function

scientific article published on January 1983

Effect of anisotropy and anharmonicity on protein crystallographic refinement. An evaluation by molecular dynamics

scientific article published on 01 July 1986

Effect of constraints, solvent and crystal environment on protein dynamics ⬇️

scientific article published on October 22, 1981

Effective atom volumes for implicit solvent models: comparison between Voronoi volumes and minimum fluctuation volumes

article

Effective coupling in biological electron transfer: exponential or complex distance dependence?

scientific article published in November 1993

Effective energy function for proteins in solution

scientific article (publication date: May 1999)

Electronic structure of cyanide complexes of hemes and heme proteins ⬇️

scientific article published on April 14, 1971

Electrostatic contributions to molecular free energies in solution

scientific article

Electrostatic effects and hydrogen exchange behaviour in proteins. The pH dependence of exchange rates in lysozyme

scientific article published in September 1987

Electrostatic effects of charge perturbations introduced by metal oxidation in proteins. A theoretical analysis

article

Electrostatic energies and forces computed without explicit interparticle interactions: a linear time complexity formulation

scientific article published in June 2005

Encounter and extrusion of an intrahelical lesion by a DNA repair enzyme

scientific article

Enforced presentation of an extrahelical guanine to the lesion recognition pocket of human 8-oxoguanine glycosylase, hOGG1.

scientific article

Enhanced Chemical Synthesis at Soft Interfaces: A Universal Reaction-Adsorption Mechanism in Microcompartments

scientific article published in Physical Review Letters

Enthalpic contribution to protein stability: insights from atom-based calculations and statistical mechanics.

scientific article published on January 1995

Entrapment and Structure of an Extrahelical Guanine Attempting to Enter the Active Site of a Bacterial DNA Glycosylase, MutM

scientific article

Erythrocyte Li+i-Na+o countertransport in the newborn

scientific article published on 01 January 1993

Estimation of the breadth of CD4bs targeting HIV antibodies by molecular modeling and machine learning

article

Estimation of uncertainties in X-ray refinement results by use of perturbed structures

scientific article published on 01 January 1987

Evaluation of comparative protein modeling by MODELLER

scientific article (publication date: November 1995)

Evaluation of designed ligands by a multiple screening method: application to glycogen phosphorylase inhibitors constructed with a variety of approaches

scientific article published on July 1, 2001

Evolutionary optimization in quantitative structure-activity relationship: an application of genetic neural networks

scientific article published on March 1996

Exploration of disorder in protein structures by X-ray restrained molecular dynamics

article

Exploration of partially unfolded states of human alpha-lactalbumin by molecular dynamics simulation

scientific article

Exploratory search during directed navigation in C. elegans and Drosophila larva ⬇️

scientific article published on 30 October 2017

Factors that affect the folding ability of proteins

scientific article published on 01 April 1999

First passage analysis of the folding of a β-sheet miniprotein: is it more realistic than the standard equilibrium approach?

scientific article published on 09 April 2014

First-Order Disorder-to-Order Transition in an Isolated Homopolymer Model

scientific article published on 01 September 1996

Fluctuations and averaging of proton chemical shifts in the bovine pancreatic trypsin inhibitor ⬇️

scientific article published on March 16, 1982

Fluorescence depolarization of tryptophan residues in proteins: a molecular dynamics study

scientific article published on June 1983

Folding of a SH3 domain: standard and "hydrodynamic" analyses

scientific article

Folding of a model three-helix bundle protein: a thermodynamic and kinetic analysis

scientific article published in November 1999

Folding of ubiquitin: a simple model describes the strange kinetics

scientific article published in May 2006

Folding thermodynamics of a model three-helix-bundle protein.

scientific article published on December 1997

Folding time distributions as an approach to protein folding kinetics

scientific article published in March 2005

Force generation in kinesin hinges on cover-neck bundle formation

scientific article

Forced unfolding of fibronectin type 3 modules: an analysis by biased molecular dynamics simulations

scientific article

Forces and energetics of hapten-antibody dissociation: a biased molecular dynamics simulation study

scientific article published in November 2001

Free energy of conformational transition paths in biomolecules: The string method and its application to myosin VI ⬇️

scientific article published on February 28, 2011

Free energy of sickling: A simulation analysis

scientific article

Free energy simulations come of age: protein-ligand recognition

scientific article

Free energy simulations: the meaning of the individual contributions from a component analysis

scientific article published in September 1994

Free energy simulations: use of reverse cumulative averaging to determine the equilibrated region and the time required for convergence

scientific article published on 01 February 2004

Frontier Bonds in QM/MM Methods: A Comparison of Different Approaches

Functional group placement in protein binding sites: a comparison of GRID and MCSS.

scientific article

Functionality map analysis of the active site cleft of human thrombin

scientific article published on 01 February 1996

Functionality maps of binding sites: a multiple copy simultaneous search method

scientific article published in January 1991

Gaussian-mixture umbrella sampling

scientific article

Genetic neural networks for quantitative structure-activity relationships: improvements and application of benzodiazepine affinity for benzodiazepine/GABAA receptors

scientific article

Gestational diabetes among Bedouins in southern Israel: comparison of prevalence and neonatal outcomes with the Jewish population

scientific article

Glycogen phosphorylase inhibitors: a free energy perturbation analysis of glucopyranose spirohydantoin analogues

scientific article published in December 2005

HOOK: a program for finding novel molecular architectures that satisfy the chemical and steric requirements of a macromolecule binding site

scientific article

Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor

scientific article

Heat capacity and compactness of denatured proteins

scientific article published on 01 April 1999

Hemoglobin Bohr effects: atomic origin of the histidine residue contributions

scientific article published on 13 November 2013

Hemoglobin tertiary structural change on ligand binding. Its role in the co-operative mechanism

scientific article published on 01 December 1983

Hemolytic disease of the newborn due to anti-PP1 P k (anti-Tj a) ⬇️

scientific article published on 01 November 1977

Hidden complexity of free energy surfaces for peptide (protein) folding

scholarly article

Hidden thermodynamics of mutant proteins: a molecular dynamics analysis

scientific article published on 01 June 1989

How does a protein fold?

scientific article

How enzymes work: analysis by modern rate theory and computer simulations

scientific article (publication date: 9 January 2004)

How subunit coupling produces the gamma-subunit rotary motion in F1-ATPase

scientific article

Hydrodynamic description of protein folding

scientific article published on 11 January 2008

Hydrogen Bond Energetics: A Simulation and Statistical Analysis ofN-Methyl Acetamide (NMA), Water, and Human Lysozyme†

article

Implications of Torsional Potential of Retinal Isomers for Visual Excitation ⬇️

scientific article published on February 19, 1971

Implications of alternative substrate binding modes for catalysis by uracil-DNA glycosylase: an apparent discrepancy resolved

scientific article published on 01 November 2006

Implications of the quaternary twist allosteric model for the physiology and pathology of nicotinic acetylcholine receptors

scholarly article

Importance of metastable states in the free energy landscapes of polypeptide chains

scientific article published on 26 October 2007

Improving the accuracy of protein pKa calculations: conformational averaging versus the average structure

scientific article published in November 1998

Inelastic neutron scattering analysis of picosecond internal protein dynamics

article

Insights into the origin of the high energy-conversion efficiency of F1-ATPase

scientific article published on 24 July 2019

Interdomain motion in liver alcohol dehydrogenase. Structural and energetic analysis of the hinge bending mode

scientific article

Internal and Overall Peptide Group Motion in Proteins: Molecular Dynamics Simulations for Lysozyme Compared with Results from X-ray and NMR Spectroscopy

article

Internal dynamics of proteins

scientific article published on 01 January 1986

Internal dynamics of proteins. Short time and long time motions of aromatic sidechains in PTI.

scientific article

Internal mobility of ferrocytochrome c.

scientific article published in October 1980

Internal motion of proteins: nuclear magnetic resonance measurements and dynamic simulations

scientific article published on 01 January 1986

Internal motions of antibody molecules

scientific article published on 01 August 1977

Interpretation of the Binding of Carbon Monoxide to Hemoglobin Under Photodissociating Conditions ⬇️

scientific article published on March 1, 1973

Interpreting the folding kinetics of helical proteins

scientific article published in Nature

Intrinsic motions along an enzymatic reaction trajectory

scientific article

Investigation of glucose binding sites on insulin

scientific article published in May 2004

Investigations of α-helix↔β-sheet transition pathways in a miniprotein using the finite-temperature string method

scientific article

Ion transport in a model gramicidin channel. Structure and thermodynamics ⬇️

scientific article published on May 1, 1991

Ion transport in the gramicidin channel: molecular dynamics study of single and double occupancy

scientific article

Is protein unfolding the reverse of protein folding? A lattice simulation analysis

scientific article published on 01 September 1999

Kinesin motility is driven by subdomain dynamics

scientific article published on 7 November 2017

Kinesin's cover-neck bundle folds forward to generate force

scientific article

Kinetic control of dimer structure formation in amyloid fibrillogenesis

scientific article

Kinetics of protein folding

Kinetics of protein folding. A lattice model study of the requirements for folding to the native state

scientific article published in February 1994

Lagrangian formulation with dissipation of Born-Oppenheimer molecular dynamics using the density-functional tight-binding method

scientific article

Large amplitude conformational change in proteins explored with a plastic network model: adenylate kinase

scientific article published on September 2005

Ligand binding and protein relaxation in heme proteins: a room temperature analysis of NO geminate recombination

scientific article published in April 1991

Ligand design by a combinatorial approach based on modeling and experiment: application to HLA-DR4.

scientific article

Ligand-induced conformational changes in ras p21: a normal mode and energy minimization analysis ⬇️

scientific article published on November 21, 1997

Local and collective motions in protein dynamics

scientific article published on 01 January 1983

Low-frequency modes in proteins: Use of the effective-medium approximation to interpret the fractal dimension observed in electron-spin relaxation measurements

scientific article published on 01 January 1986

MCSS functionality maps for a flexible protein

scientific article published in December 1999

Mechanical coupling in myosin V: a simulation study

scientific article

Mechanical unfolding of a titin Ig domain: structure of unfolding intermediate revealed by combining AFM, molecular dynamics simulations, NMR and protein engineering

scientific article (publication date: 27 September 2002)

Mechanism of tertiary structural change in hemoglobin ⬇️

scientific article published on March 1, 1977

Microsecond Molecular Dynamics Simulations of Proteins Using a Quasi-Equilibrium Solvation Shell Model

scientific article published on 11 February 2020

Minimum free energy pathways and free energy profiles for conformational transitions based on atomistic molecular dynamics simulations

scientific article published in April 2007

Model for the structure of the lipid bilayer

scientific article published on February 1991

Modeling of globular proteins. A distance-based data search procedure for the construction of insertion/deletion regions and Pro----non-Pro mutations

scientific article

Modeling of the TCR-MHC-peptide complex

scientific article published on 01 July 2000

Modeling zinc in biomolecules with the self consistent charge-density functional tight binding (SCC-DFTB) method: applications to structural and energetic analysis

scientific article published in April 2003

Models for the three-dimensional structure of renin inhibitors bound in the active site of human renin: an analysis of the properties that produce tight binding

scientific article published on 01 January 1987

Molecular Dynamics Simulations of the Gramicidin Channel ⬇️

scientific article published on January 1, 1994

Molecular anatomy of the antibody binding site

scientific article published in Journal of Biological Chemistry

Molecular and stochastic dynamics of proteins

scientific article

Molecular dynamics and protein function

scientific article

Molecular dynamics of an alpha-helical polypeptide: Temperature dependence and deviation from harmonic behavior

scientific article

Molecular dynamics of biological macromolecules: a brief history and perspective

scientific article published on March 2003

Molecular dynamics of ferrocytochrome c ⬇️

scientific article published on July 17, 1980

Molecular dynamics of ferrocytochrome c. Magnitude and anisotropy of atomic displacements

scientific article published on 01 December 1981

Molecular dynamics of myoglobin at 298 degrees K. Results from a 300-ps computer simulation

scientific article

Molecular dynamics simulation of protein denaturation: solvation of the hydrophobic cores and secondary structure of barnase

scientific article

Molecular dynamics simulations in biology

scientific article

Molecular dynamics simulations of biomolecules

scientific article

Molecular dynamics simulations of biomolecules

scientific article published on 01 June 2002

Molecular dynamics simulations of native and substrate-bound lysozyme. A study of the average structures and atomic fluctuations

scientific article published on 01 August 1986

Molecular dynamics studies of NMR relaxation in proteins

scientific article

Molecular dynamics: applications to proteins

article

Molecular dynamics: applications to proteins

scientific article published on 01 January 1986

Molecular recognition in proteins. Simulation analysis of substrate binding by a tyrosyl-tRNA synthetase mutant

scientific article published in March 1994

Molecular switch in signal transduction: Reaction paths of the conformational changes in ras p21 ⬇️

scientific article published on October 28, 1997

Multidimensional adaptive umbrella sampling: Applications to main chain and side chain peptide conformations

Multiple conformational states of proteins: a molecular dynamics analysis of myoglobin

scientific article published on 01 January 1987

Multiple copy simultaneous search and construction of ligands in binding sites: application to inhibitors of HIV-1 aspartic proteinase

scientific article published on 01 July 1993

Multiple-site titration curves of proteins: an analysis of exact and approximate methods for their calculation

scientific article (publication date: November 1991)

NO rebinding to myoglobin: a reactive molecular dynamics study

scientific article published on 01 July 2002

Native and non-native interactions along protein folding and unfolding pathways

scientific article published on 01 May 2002

Native proteins are surface-molten solids: application of the Lindemann criterion for the solid versus liquid state

scientific article

Nature of the iron-oxygen bond in oxyhemoglobin

scientific article published on August 31, 1977

Neural networks for secondary structure and structural class predictions.

scientific article published on February 1995

New Insights into the Folding of a β-Sheet Miniprotein in a Reduced Space of Collective Hydrogen Bond Variables: Application to a Hydrodynamic Analysis of the Folding Flow ⬇️

scientific article published on May 15, 2013

New formulation for derivatives of torsion angles and improper torsion angles in molecular mechanics: Elimination of singularities

New methods for accurate prediction of protein secondary structure

scientific article published on May 1999

Nonexponential relaxation after ligand dissociation from myoglobin: a molecular dynamics simulation.

scientific article

Normal mode calculations of icosahedral viruses with full dihedral flexibility by use of molecular symmetry

scientific article published on 7 April 2005

Normal modes for specific motions of macromolecules: application to the hinge-bending mode of lysozyme

scientific article published on August 1985

Nuclear Magnetic Resonance Determination of the Angle Ψ in Peptides ⬇️

scientific article published on November 1, 1972

Nucleophilic attack on phosphate diesters: a density functional study of in-line reactivity in dianionic, monoanionic, and neutral systems

scientific article published on 01 June 2006

One-dimensional barrier-preserving free-energy projections of a beta-sheet miniprotein: new insights into the folding process

scientific article published on July 2008

One-dimensional free-energy profiles of complex systems: progress variables that preserve the barriers

scientific article published in June 2006

Optimal estimates of free energies from multistate nonequilibrium work data

scientific article published on 15 March 2006

PDB-based protein loop prediction: parameters for selection and methods for optimization

scientific article published in April 1997

PR65, the HEAT-repeat scaffold of phosphatase PP2A, is an elastic connector that links force and catalysis

scientific article

Packaging of proteases and proteoglycans in the granules of mast cells and other hematopoietic cells. A cluster of histidines on mouse mast cell protease 7 regulates its binding to heparin serglycin proteoglycans

scientific article published on August 1995

Pharmacokinetic aspects of caffeine in premature infants with apnoea

scientific article published on 01 January 1982

Pi release from myosin: a simulation analysis of possible pathways

scientific article

Picosecond dynamics of tyrosine side chains in proteins ⬇️

scientific article published on March 20, 1979

Polar hydrogen positions in proteins: Empirical energy placement and neutron diffraction comparison

scholarly article by Axel T. Brünger published in January 1988

Potential energy surface and molecular dynamics of MbNO: existence of an unsuspected FeON minimum

scientific article published on 01 November 2005

Potential energy surfaces and conformational transitions in biomolecules: a successive confinement approach applied to a solvated tetrapeptide

scientific article published on 02 January 2002

Prediction of optimal peptide mixtures to induce broadly neutralizing antibodies to human immunodeficiency virus type 1 ⬇️

scientific article published on August 1, 1991

Prediction of the folding of short polypeptide segments by uniform conformational sampling

scientific article published on 01 January 1987

Probability Distributions for Complex Systems: Adaptive Umbrella Sampling of the Potential Energy

Probing polar solvation dynamics in proteins: a molecular dynamics simulation analysis

scientific article published on 24 January 2007

Product-assisted catalysis in base-excision DNA repair

scientific article (publication date: March 2003)

Protein Folding: A Perspective from Theory and Experiment.

scientific article published in April 1998

Protein dynamics in solution and in a crystalline environment: a molecular dynamics study

scientific article published on 01 May 1982

Protein dynamics investigated by inherent structure analysis

scientific article

Protein folding bottlenecks: A lattice Monte Carlo simulation

scientific article published on 01 September 1991

Protein folding dynamics: the diffusion-collision model and experimental data

scientific article

Protein secondary structure prediction with a neural network

scientific article

Protein structural fluctuations during a period of 100 ps

scientific article published on 01 February 1979

Protein structural transitions and their functional role

scientific article

Protein-Protein Interactions in DNA Recognition: H-NMR Studies of Lambda cI Repressors Genetically Altered by Site-Directed Mutagenesis

scientific article

Protein-folding dynamics

scientific article published in Nature

Protein-ligand binding free energy estimation using molecular mechanics and continuum electrostatics. Application to HIV-1 protease inhibitors

scientific article published in December 2003

Proteins: dynamics and function

scientific article published on January 1988

Proton NMR studies of the association and folding of glucagon in solution

scientific article published on 01 October 1980

Proton and nitrogen sequential assignments and secondary structure determination of the human FK506 and rapamycin binding protein ⬇️

scientific article published on May 14, 1991

Pseudooutbreak of Candida guilliermondii fungemia in a neonatal intensive care unit

scientific article published on 01 December 1991

Quantum mechanics/molecular mechanics studies of triosephosphate isomerase-catalyzed reactions: effect of geometry and tunneling on proton-transfer rate constants

scientific article published on 01 March 2002

Quaternary structure and function in phage lambda repressor: 1H-NMR studies of genetically altered proteins

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Rare fluctuations of native proteins sampled by equilibrium hydrogen exchange

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Refinement of the solution structure of the DNA hexamer 5'd(GCATGC)2: combined use of nuclear magnetic resonance and restrained molecular dynamics

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Refolding of potato carboxypeptidase inhibitor by molecular dynamics simulations with disulfide bond constraints a aEdited by A. R. Fersht

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Relation between sequence and structure of HIV-1 protease inhibitor complexes: a model system for the analysis of protein flexibility11Edited by R. Huber ⬇️

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Response to comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'.

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Ring Orientation in βIonone and Retinals ⬇️

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Role of conformation transitions in adenylate kinase

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Role of conformational heterogeneity in domain swapping and adapter function of the Cks proteins

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Role of framework mutations and antibody flexibility in the evolution of broadly neutralizing antibodies.

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Role of structural flexibility in conformational calculations. Application to acetylcholine and .beta.-methylacetylcholine ⬇️

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Segmented transition pathway of the signaling protein nitrogen regulatory protein C

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Self-consistent determination of the transition state for protein folding: application to a fibronectin type III domain

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Side-chain torsional potentials: effect of dipeptide, protein, and solvent environment ⬇️

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Sidechain torsional potentials and motion of amino acids in porteins: bovine pancreatic trypsin inhibitor ⬇️

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Signaling pathways of PDZ2 domain: a molecular dynamics interaction correlation analysis

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Simulation analysis of the stability mutant R96H of T4 lysozyme

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Simulation analysis of the stability mutants R96H of bacteriophage T4 lysozyme and I96A of barnase

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Simulation analysis of triose phosphate isomerase: conformational transition and catalysis ⬇️

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Simulation of activation free energies in molecular systems

Simulation of conformational transitions by the restricted perturbation-targeted molecular dynamics method

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Simulations of enzymic reactions.

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Simulations of lysozyme: internal motions and the reaction mechanism

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Small-world view of the amino acids that play a key role in protein folding

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Solution NMR studies of intact lambda repressor

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Solution Structure of FKBP, a Rotamase Enzyme and Receptor for FK506 and Rapamycin ⬇️

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Solution conformation of a heptadecapeptide comprising the DNA binding helix F of the cyclic AMP receptor protein of Escherichia coli. Combined use of 1H nuclear magnetic resonance and restrained molecular dynamics

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Solution conformations and thermodynamics of structured peptides: molecular dynamics simulation with an implicit solvation model.

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Solution conformations of human growth hormone releasing factor: comparison of the restrained molecular dynamics and distance geometry methods for a system without long-range distance data

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Solution conformations of structured peptides: continuum electrostatics versus distance-dependent dielectric functions

Solution of a protein crystal structure with a model obtained from NMR interproton distance restraints

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Solvent effects on protein motion and protein effects on solvent motion. Dynamics of the active site region of lysozyme

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Solvent mobility and the protein 'glass' transition

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Spatially constrained minimization of macromolecules

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Specific amino acid recognition by aspartyl-tRNA synthetase studied by free energy simulations 1 1A. R. Fersht

Spinach on the ceiling: a theoretical chemist's return to biology

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Stereochemistry of carbon monoxide binding to myoglobin and hemoglobin

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Strandwise translocation of a DNA glycosylase on undamaged DNA

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Structural basis for power stroke vs. Brownian ratchet mechanisms of motor proteins

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Structural details of urea binding to barnase: a molecular dynamics analysis

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Structure activity relationship by NMR and by computer: a comparative study

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Structure and internal mobility of proteins: a molecular dynamics study of hen egg white lysozyme

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Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA.

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Structure of proteins with single-site mutations: a minimum perturbation approach

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Structure of the EmrE multidrug transporter and its use for inhibitor peptide design

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Structure of the triosephosphate isomerase-phosphoglycolohydroxamate complex: an analogue of the intermediate on the reaction pathway

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Structure refinement of oligonucleotides by molecular dynamics with nuclear Overhauser effect interproton distance restraints: application to 5' d(C-G-T-A-C-G)2.

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Structure-specific model of hemoglobin cooperativity

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Structures and relative free energies of partially folded states of proteins

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Structures of scrambled disulfide forms of the potato carboxypeptidase inhibitor predicted by molecular dynamics simulations with constraints

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Structures of scrambled disulfide forms of the potato carboxypeptidase inhibitor predicted by molecular dynamics simulations with constraints

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Study of the insulin dimerization: binding free energy calculations and per-residue free energy decomposition

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Subglottic laryngeal atresia associated with tracheoesophageal fistula. Long-term survival.

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Substrate conformational transitions in the active site of chorismate mutase: their role in the catalytic mechanism

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T cell recognition of hapten. Anatomy of T cell receptor binding of a H-2kd-associated photoreactive peptide derivative.

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Temperature dependence of the structure and dynamics of myoglobin. A simulation approach

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Temperature echoes in molecular dynamics simulations of proteins

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The HSP90 binding mode of a radicicol-like E-oxime determined by docking, binding free energy estimations, and NMR 15N chemical shifts

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The Levinthal paradox: yesterday and today ⬇️

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The Mechanism of the Translocation Step in DNA Replication by DNA Polymerase I: A Computer Simulation Analysis

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The allosteric mechanism of yeast chorismate mutase: a dynamic analysis

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The calorimetric criterion for a two-state process revisited

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The contribution of cross‐links to protein stability: A normal mode analysis of the configurational entropy of the native state ⬇️

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The contribution of vibrational entropy to molecular association. The dimerization of insulin.

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The crystallographic structure of the aldose reductase-IDD552 complex shows direct proton donation from tyrosine 48

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The distance fluctuation criterion for melting: Comparison of square-well and Morse potential models for clusters and homopolymers

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The dynamics of proteins

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The elastic properties of the structurally characterized myosin II S2 subdomain: a molecular dynamics and normal mode analysis

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The folding mechanism of larger model proteins: role of native structure

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The fundamentals of protein folding: bringing together theory and experiment

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The hinge-bending mode in lysozyme

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The hinge-bending mode of a lysozyme-inhibitor complex

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The human cytomegalovirus UL44 C clamp wraps around DNA.

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The impact of prenatal care on the outcome of pregnancy

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The importance of larger data sets for protein secondary structure prediction with neural networks

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The internal dynamics of globular proteins.

scientific article published on January 1981

The interpretation of site-directed mutagenesis experiments by linear free energy relations

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The meaning of component analysis: decomposition of the free energy in terms of specific interactions

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The missing link between thermodynamics and structure in F1-ATPase

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The nature of the ion binding interactions in EF-hand peptide analogs: free energy simulation of Asp to Asn mutations

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The normal modes of the gramicidin-A dimer channel

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The origin of protein sidechain order parameter distributions

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The role of carbon-donor hydrogen bonds in stabilizing tryptophan conformations

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The role of sequence and structure in protein folding kinetics; the diffusion-collision model applied to proteins L and G

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The roles of stability and contact order in determining protein folding rates

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The signaling pathway of rhodopsin

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The three-dimensional structure of alpha1-purothionin in solution: combined use of nuclear magnetic resonance, distance geometry and restrained molecular dynamics

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The trajectory of intrahelical lesion recognition and extrusion by the human 8-oxoguanine DNA glycosylase

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The unfolding action of GroEL on a protein substrate

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Theoretical approaches to solvation of biopolymers

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Theoretical evaluation of pK(a) in phosphoranes: implications for phosphate ester hydrolysis

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Theoretical investigations of Ferredoxin I: the possible role of internal water molecules on the coupled electron proton transfer reaction

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Theoretical investigations on Azotobacter vinelandii ferredoxin I: effects of electron transfer on protein dynamics

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Theoretical studies of protein folding and unfolding

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Thermal expansion of a protein

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Thermodynamics of protein folding: a microscopic view

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Three key residues form a critical contact network in a protein folding transition state

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Three-Dimensional Quantitative Structure−Activity Relationships from Molecular Similarity Matrices and Genetic Neural Networks. 1. Method and Validations ⬇️

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Three-dimensional models of four mouse mast cell chymases. Identification of proteoglycan binding regions and protease-specific antigenic epitopes

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Three-dimensional structure of proteins determined by molecular dynamics with interproton distance restraints: application to crambin

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Time dependence of atomic fluctuations in proteins: analysis of local and collective motions in bovine pancreatic trypsin inhibitor

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Titration calculations of foot-and-mouth disease virus capsids and their stabilities as a function of pH.

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Transition from B to Z DNA: contribution of internal fluctuations to the configurational entropy difference

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Transition state contact orders correlate with protein folding rates

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Translocation mechanism of long sugar chains across the maltoporin membrane channel

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Trapping the ATP binding state leads to a detailed understanding of the F1-ATPase mechanism

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Triosephosphate isomerase: a theoretical comparison of alternative pathways

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Trypsinogen-trypsin transition: a molecular dynamics study of induced conformational change in the activation domain

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Two-dimensional 1H NMR study of the lambda operator site OL1: a sequential assignment strategy and its application ⬇️

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Two-dimensional NMR and photo-CIDNP studies of the insulin monomer: assignment of aromatic resonances with application to protein folding, structure, and dynamics

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Two-metal-ion mechanism for hammerhead-ribozyme catalysis

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Understanding beta-hairpin formation ⬇️

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Understanding protein folding via free-energy surfaces from theory and experiment

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Understanding the Role of Active‐Site Residues in Chorismate Mutase Catalysis from Molecular‐Dynamics Simulations ⬇️

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Unfolding proteins by external forces and temperature: the importance of topology and energetics

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Unsuspected pathway of the allosteric transition in hemoglobin

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Uracil-DNA glycosylase acts by substrate autocatalysis

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Use of MCSS to design small targeted libraries: application to picornavirus ligands.

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Use of a minimum perturbation approach to predict TIM mutant structures

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Use of a quantitative structure-property relationship to design larger model proteins that fold rapidly

scientific article published in November 1999

Use of quantitative structure-property relationships to predict the folding ability of model proteins

scientific article published in November 1998

Use of the multiple copy simultaneous search (MCSS) method to design a new class of picornavirus capsid binding drugs

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Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size

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Validity of Gō models: comparison with a solvent-shielded empirical energy decomposition

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Vicinal coupling constants and protein dynamics

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Water Dynamics Around Proteins: T- and R-States of Hemoglobin and Melittin

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What contributions to protein side-chain dynamics are probed by NMR experiments? A molecular dynamics simulation analysis

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Why protein R-factors are so large: a self-consistent analysis

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X-ray refinement of protein structures by simulated annealing: test of the method on myohemerythrin

scientific article published on 01 June 1989

X-ray structural and simulation analysis of a protein mutant: the value of a combined approach.

scientific article published in May 2004

X-ray structure and refinement of carbon-monoxy (Fe II)-myoglobin at 1.5 A resolution

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Yeast chorismate mutase in the R state: simulations of the active site

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Zinc binding in proteins and solution: a simple but accurate nonbonded representation

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pH Dependence of binding reactions from free energy simulations and macroscopic continuum electrostatic calculations: Application to 2′GMP/3′GMP binding to ribonuclease T1 and implications for catalysis

pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model

scientific article (publication date: November 1990)

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