List of works - Ruth Nussinov

"Similarity trap" in protein-protein interactions could be carcinogenic: simulations of p53 core domain complexed with 53BP1 and BRCA1 BRCT domains

scientific article published on December 2006

'Latent drivers' expand the cancer mutational landscape

scientific article published on 05 February 2015

'Pathway drug cocktail': targeting Ras signaling based on structural pathways

scientific article published on 15 August 2013

(A)GGG(A), (A)CCC(A) and other potential 3' splice signals in primate nuclear pre-mRNA sequences

scientific article published in December 1987

1-amino-2-phenylcyclopentane-1-carboxylic acid: a conformationally restricted phenylalanine analogue

scientific article

A 3D sequence-independent representation of the protein data bank

scientific article

A Future Vision for PLOS Computational Biology

scholarly article

A New View of Pathway-Driven Drug Resistance in Tumor Proliferation

scientific article published on 25 February 2017

A New View of Ras Isoforms in Cancers

scientific article

A Protocol for the Design of Protein and Peptide Nanostructure Self-Assemblies Exploiting Synthetic Amino Acids

scientific article

A Review of 2010 for PLoS Computational Biology

scientific article

A Review of 2011 for PLoS Computational Biology

scientific article (publication date: 26 January 2012)

A Structural View of Negative Regulation of the Toll-like Receptor-Mediated Inflammatory Pathway.

scientific article

A Systems Pharmacology Approach Uncovers Wogonoside as an Angiogenesis Inhibitor of Triple-Negative Breast Cancer by Targeting Hedgehog Signaling

scientific article published on 06 June 2019

A broad view of scaffolding suggests that scaffolding proteins can actively control regulation and signaling of multienzyme complexes through allostery

scientific article published on 03 January 2013

A comparative study of amyloid fibril formation by residues 15-19 of the human calcitonin hormone: a single beta-sheet model with a small hydrophobic core

scientific article

A component overlapping attribute clustering (COAC) algorithm for single-cell RNA sequencing data analysis and potential pathobiological implications

scientific article published on 19 February 2019

A computer vision based technique for 3-D sequence-independent structural comparison of proteins

scientific article published in April 1993

A dataset of protein-protein interfaces generated with a sequence-order-independent comparison technique

scientific article published on July 1996

A disulphide-reinforced structural scaffold shared by small proteins with diverse functions

scientific article published on October 1995

A fixed-point alignment technique for detection of recurrent and common sequence motifs associated with biological features.

scientific article published in March 1988

A formal MIM specification and tools for the common exchange of MIM diagrams: an XML-Based format, an API, and a validation method

article

A geometry-based suite of molecular docking processes

scientific article

A hierarchical protein folding scheme based on the building block folding model.

scientific article

A mechanistic view of the role of E3 in sumoylation

scientific article

A method for biomolecular structural recognition and docking allowing conformational flexibility

scientific article

A method for simultaneous alignment of multiple protein structures

scientific article

A new, structurally nonredundant, diverse data set of protein-protein interfaces and its implications

scientific article

A permissive secondary structure-guided superposition tool for clustering of protein fragments toward protein structure prediction via fragment assembly.

scientific article

A proposed structural model for amyloid fibril elongation: domain swapping forms an interdigitating beta-structure polymer

scientific article

A second molecular biology revolution? The energy landscapes of biomolecular function

scientific article

A sequence analysis system encompassing rules for DNA helical distortion

scientific article

A set of van der Waals and coulombic radii of protein atoms for molecular and solvent-accessible surface calculation, packing evaluation, and docking

scientific article

A simulation strategy for the atomistic modeling of flexible molecules covalently tethered to rigid surfaces: application to peptides

scientific article published on 30 August 2010

A strategy based on protein-protein interface motifs may help in identifying drug off-targets

scientific article published on 31 July 2012

A study of four-helix bundles: investigating protein folding via similar architectural motifs in protein cores and in subunit interfaces

scientific article

A survey of available tools and web servers for analysis of protein-protein interactions and interfaces

scientific article published on 24 February 2009

A systematic study of the vibrational free energies of polypeptides in folded and random states

scientific article

A unified convention for biological assemblies with helical symmetry

scientific article

A unified view of "how allostery works"

scientific article (publication date: February 2014)

ARTS: alignment of RNA tertiary structures

scientific article published on 01 September 2005

Activity and architecture of pyroglutamate-modified amyloid-β (AβpE3-42) pores

scientific article

Advancements and challenges in computational biology

scientific article

Algorithms for multiple protein structure alignment and structure-derived multiple sequence alignment.

scientific article

Alignment of flexible protein structures.

scientific article

All-d-Enantiomer of β-Amyloid Peptide Forms Ion Channels in Lipid Bilayers

scientific article

Allo-network drugs: extension of the allosteric drug concept to protein- protein interaction and signaling networks

scientific article published on January 2013

Allo-network drugs: harnessing allostery in cellular networks

scientific article published on 16 September 2011

Allosteric KRas4B Can Modulate SOS1 Fast and Slow Ras Activation Cycles

scientific article published on 24 July 2018

Allosteric activation of RAF in the MAPK signaling pathway

scientific article published on 27 July 2018

Allosteric conformational barcodes direct signaling in the cell

scientific article published on September 2013

Allosteric control of antibody-prion recognition through oxidation of a disulfide bond between the CH and CL chains

scientific article published on 29 November 2016

Allosteric effects in the marginally stable von Hippel-Lindau tumor suppressor protein and allostery-based rescue mutant design

scholarly article

Allosteric effects of the oncogenic RasQ61L mutant on Raf-RBD

scientific article

Allosteric modulators can restore function in an amino acid neurotransmitter receptor by slightly altering intra‐molecular communication pathways ⬇️

scientific article published on April 1, 2012

Allosteric post-translational modification codes

scientific article published on 08 August 2012

Allosteric regulation of glycogen synthase kinase 3β: a theoretical study

scientific article

Allosteric stabilization of the amyloid-β peptide hairpin by the fluctuating N-terminal

scientific article

Allostery and population shift in drug discovery

scientific article published on 29 September 2010

Allostery in Its Many Disguises: From Theory to Applications

scientific article published on 07 February 2019

Allostery in disease and in drug discovery

scientific article

Allostery modulates the beat rate of a cardiac pacemaker

scientific article

Allostery without a conformational change? Revisiting the paradigm.

scientific article

Allostery: An Overview of Its History, Concepts, Methods, and Applications

scientific article

Allostery: absence of a change in shape does not imply that allostery is not at play

scientific article published on 29 February 2008

Alternative allosteric mechanisms can regulate the substrate and E2 in SUMO conjugation

scientific article published on 7 January 2011

Alzheimer's disease: which type of amyloid-preventing drug agents to employ?

scientific article

Alzheimer's β-Amyloid All-D-Enantiomers and Native All-L-Enantiomers Exhibit Similar Pore Structures in Lipid Bilayers: Atomic Force Microscopy

Amino acid pair interchanges at spatially conserved locations

scientific article

Amplification of signaling via cellular allosteric relay and protein disorder

scholarly article

Amylin-Aβ oligomers at atomic resolution using molecular dynamics simulations: a link between Type 2 diabetes and Alzheimer's disease

scientific article

Amyloid β Ion Channels in a Membrane Comprising Brain Total Lipid Extracts

scientific article

An accelerated algorithm for calculating the secondary structure of single stranded RNAs

scientific article published on January 1984

An automated computer vision and robotics-based technique for 3-D flexible biomolecular docking and matching.

scientific article

An efficient automated computer vision based technique for detection of three dimensional structural motifs in proteins

scientific article published in February 1992

An efficient code searching for sequence homology and DNA duplication ⬇️

scientific article published on January 21, 1983

An efficient string matching algorithm with K substitutions for nucleotide and amino acid sequences

scientific article published in June 1987

An efficient string matching algorithm with k differences for nucleotide and amino acid sequences

scientific article published on January 1986

An improved secondary structure computation method and its application to intervening sequence in the human alpha-like globin mRNA precursors

scientific article published in August 1988

An integrated suite of fast docking algorithms

scientific article

An interactive dot matrix system for locating potentially significant features in nucleic acid molecules

scientific article published in April 1987

An overview of recent advances in structural bioinformatics of protein-protein interactions and a guide to their principles

scientific article

Analysis and classification of RNA tertiary structures

scientific article published on 29 September 2008

Analysis of ordered and disordered protein complexes reveals structural features discriminating between stable and unstable monomers

scientific article

Anatomy of protein structures: visualizing how a one-dimensional protein chain folds into a three-dimensional shape

scientific article

Annular structures as intermediates in fibril formation of Alzheimer Abeta17-42

scientific article published on 06 May 2008

Antigen binding allosterically promotes Fc receptor recognition

scientific article published on 05 October 2018

Antimicrobial properties of amyloid peptides

scientific article published on 29 November 2011

Antimicrobial protegrin-1 forms amyloid-like fibrils with rapid kinetics suggesting a functional link

scientific article

Antimicrobial protegrin-1 forms ion channels: molecular dynamic simulation, atomic force microscopy, and electrical conductance studies

scientific article

Application of 1-aminocyclohexane carboxylic acid to protein nanostructure computer design

scientific article published on 17 January 2008

Approaching the CAPRI challenge with an efficient geometry-based docking

scientific article

Architectures and functional coverage of protein-protein interfaces

scientific article published on 06 May 2008

Are Parallel Proliferation Pathways Redundant?

scientific article published on 25 April 2020

Arl2-Mediated Allosteric Release of Farnesylated KRas4B from Shuttling Factor PDEδ

scientific article published on 18 July 2018

Artificial intelligence in COVID-19 drug repurposing

scientific article published on 18 September 2020

Association of putative concave protein-binding sites with the fluctuation behavior of residues

scientific article

Asymmetry in the distributions of the four nucleotides at mRNA initiation and 3' termini sites: some geometrical implications

scientific article published in February 1987

Atomic force microscopy and MD simulations reveal pore-like structures of all-D-enantiomer of Alzheimer's β-amyloid peptide: relevance to the ion channel mechanism of AD pathology

scientific article

Atomic-level description of amyloid beta-dimer formation

scientific article

Atomic-scale simulations confirm that soluble beta-sheet-rich peptide self-assemblies provide amyloid mimics presenting similar conformational properties

scientific article

Atomistic-level study of the interactions between hIAPP protofibrils and membranes: Influence of pH and lipid composition.

scientific article published on 8 February 2018

Attractor Structures of Signaling Networks: Consequences of Different Conformational Barcode Dynamics and Their Relations to Network-Based Drug Design

scientific article

Author Correction: In vivo tropism of Salmonella Typhi toxin to cells expressing a multiantennal glycan receptor

scientific article published on 01 July 2019

Autoinhibition can identify rare driver mutations and advise pharmacology

scientific article published on 22 November 2019

Autoinhibition in Ras effectors Raf, PI3Kα, and RASSF5: a comprehensive review underscoring the challenges in pharmacological intervention

scientific article published on 29 September 2018

Automated multiple structure alignment and detection of a common substructural motif

scientific article

Automatic prediction of protein interactions with large scale motion

scientific article

Aβ(1-42) fibril structure illuminates self-recognition and replication of amyloid in Alzheimer's disease

scientific article published on 4 May 2015

Backbone conformational preferences and pseudorotational ring puckering of 1-aminocyclopentane-1-carboxylic acid

scientific article

Bacteriophage lambda int protein may recognize structural features of the attachment sites

scientific article published in June 1986

Beta2-microglobulin amyloid fragment organization and morphology and its comparison to Abeta suggests that amyloid aggregation pathways are sequence specific

scientific article

Beta2-microglobulin amyloidosis: insights from conservation analysis and fibril modelling by protein docking techniques

scientific article

Binding and folding: in search of intramolecular chaperone-like building block fragments.

scientific article

Binding of a C-end rule peptide to the neuropilin-1 receptor: a molecular modeling approach

scientific article

Binding of protofibrillar Aβ trimers to lipid bilayer surface enhances Aβ structural stability and causes membrane thinning

scientific article published on 5 October 2017

Bio-geometry

BioInfo3D: a suite of tools for structural bioinformatics

scientific article published on July 2004

Bioinformatics study of cancer-related mutations within p53 phosphorylation site motifs

scientific article

Building blocks, hinge-bending motions and protein topology

scientific article

CCRXP: exploring clusters of conserved residues in protein structures

scientific article

CD4 binding partially locks the bridging sheet in gp120 but leaves the beta2/3 strands flexible

scientific article

Ca2+-Dependent Switch of Calmodulin Interaction Mode with Tandem IQ Motifs in the Scaffolding Protein IQGAP1

scientific article published on 26 November 2019

Calmodulin (CaM) Activates PI3Kα by Targeting the "Soft" CaM-Binding Motifs in Both the nSH2 and cSH2 Domains of p85α

scientific article published on 08 August 2018

Calmodulin and IQGAP1 activation of PI3Kα and Akt in KRAS, HRAS and NRAS-driven cancers

scientific article published on 30 October 2017

Calmodulin and PI3K Signaling in KRAS Cancers

scientific article published on 18 February 2017

Cataloging and organizing p73 interactions in cell cycle arrest and apoptosis

scientific article published on 26 July 2008

Changing the charge distribution of beta-helical-based nanostructures can provide the conditions for charge transfer

scientific article published on 6 April 2007

Characterization of the conformational state and flexibility of HIV-1 glycoprotein gp120 core domain

scientific article

ChemInform Abstract: Application of 1-Aminocycohexane Carboxylic Acid to Protein Nanostructure Computer Design

Close-range electrostatic interactions in proteins

scientific article (publication date: 2 July 2002)

Coarse-grained representation of beta-helical protein building blocks

scientific article

Coarse-graining the self-assembly of beta-helical protein building blocks

scientific article

Combinatorial docking approach for structure prediction of large proteins and multi-molecular assemblies

scientific article

Comparing interfacial dynamics in protein-protein complexes: an elastic network approach

scientific article

Comparison of protein fragments identified by limited proteolysis and by computational cutting of proteins

scientific article published on July 2002

Comparison of the Conformations of KRAS Isoforms, K-Ras4A and K-Ras4B, Points to Similarities and Significant Differences

scientific article

Comparison of the human and worm p53 structures suggests a way for enhancing stability

scientific article

Comparison of the protein-protein interfaces in the p53-DNA crystal structures: towards elucidation of the biological interface

scientific article

Compilation of eukaryotic sequences around transcription initiation sites

scientific article published in June 1986

Compositional variations in DNA sequences

scientific article published in July 1991

Comprehensive analysis of co-occurring domain sets in yeast proteins

scientific article

Computational Investigation of Gantenerumab and Crenezumab's Recognition of Aβ Fibrils in Alzheimer's Disease Brain Tissue

scientific article published on 29 September 2020

Computational Methods for Exploration and Analysis of Macromolecular Structure and Dynamics

scientific article published on 27 October 2015

Computational Methods for Structural and Functional Studies of Alzheimer's Amyloid Ion Channels.

scientific article

Computational Structural Biology: Successes, Future Directions, and Challenges

Computational Tools for Allosteric Drug Discovery: Site Identification and Focus Library Design

scientific article

Computational study of the fibril organization of polyglutamine repeats reveals a common motif identified in beta-helices

scientific article published on 9 February 2006

Computational validation of protein nanotubes

scientific article published on March 2009

Computing Biology

scientific article published on 12 July 2016

Computing the Dynamic Supramolecular Structural Proteome

scientific article published on 19 January 2017

Concepts and schemes for the re-engineering of physical protein modules: generating nanodevices via targeted replacements with constrained amino acids

scientific article

Conformational Control of Ubiquitination in the Cullin-Ring E3 Ligase Machinery

Conformational basis for asymmetric seeding barrier in filaments of three- and four-repeat tau.

scientific article

Conformational control of the binding of the transactivation domain of the MLL protein and c-Myb to the KIX domain of CREB

scientific article

Conformational distribution and α-helix to β-sheet transition of human amylin fragment dimer

scientific article published on 16 December 2013

Conformational dynamics of cancer-associated MyD88-TIR domain mutant L252P (L265P) allosterically tilts the landscape toward homo-dimerization

scientific article published on 8 August 2016

Conformational ensembles, signal transduction and residue hot spots: application to drug discovery.

scientific article published on September 2010

Conformational exploration of two peptides and their hybrid polymer conjugates: potentialities as self-aggregating materials

scientific article published on 27 November 2012

Conformational preferences of 1-amino-2-phenylcyclohexanecarboxylic acid, a phenylalanine cyclohexane analogue

scientific article published on October 2009

Conformational preferences of alpha-substituted proline analogues

scientific article published on 20 March 2008

Conformational preferences of beta- and gamma-aminated proline analogues

scientific article

Conformational profile of a proline-arginine hybrid

scientific article

Conformational selection in amyloid-based immunotherapy: Survey of crystal structures of antibody-amyloid complexes

scientific article published on 3 June 2016

Conformational stability and dynamics of the cancer-associated isoform Δ133p53β are modulated by p53 peptides and p53-specific DNA

scientific article published on 12 December 2018

Conformational study of the protegrin-1 (PG-1) dimer interaction with lipid bilayers and its effect

scientific article

Conformations of proline analogues having double bonds in the ring

scientific article

Consensus features in amyloid fibrils: sheet-sheet recognition via a (polar or nonpolar) zipper structure

scientific article

Conservation and amyloid formation: a study of the gelsolin-like family

scientific article published in May 2003

Conservation of polar residues as hot spots at protein interfaces

scholarly article by Zengjian Hu published in June 2000

Conservation of polar residues as hot spots at protein interfaces

scientific article

Conserved putative signals in 3' intron junctions in rodents

scientific article published in June 1987

Conserved quartets near 5' intron junctions in primate nuclear pre-mRNA.

scientific article published in July 1988

Conserved signals around the 5' splice sites in eukaryotic nuclear precursor mRNAs: G-runs are frequent in the introns and C in the exons near both 5' and 3' splice sites

scientific article published in April 1989

Constructing structural networks of signaling pathways on the proteome scale

scientific article published on 09 May 2012

Constructing templates for protein structure prediction by simulation of protein folding pathways.

scientific article

Contribution of salt bridges toward protein thermostability

scientific article

Cooperativity dominates the genomic organization of p53-response elements: a mechanistic view

scientific article

Correction to Familial Mutations May Switch Conformational Preferences in α-Synuclein Fibrils

scientific article published on 01 June 2018

Correction: Review: Precision medicine and driver mutations: Computational methods, functional assays and conformational principles for interpreting cancer drivers

scientific article published on 12 June 2019

Correlated mutations: advances and limitations. A study on fusion proteins and on the Cohesin-Dockerin families

scientific article

Coupling of Zinc-Binding and Secondary Structure in Nonfibrillar Aβ40 Peptide Oligomerization.

scientific article

Coupling of the non-amyloid-component (NAC) domain and the KTK(E/Q)GV repeats stabilize the α-synuclein fibrils

scientific article

Critical Nucleus Structure and Aggregation Mechanism of the C-terminal Fragment of Copper-Zinc Superoxide Dismutase Protein

scientific article

Cross-seeding and conformational selection between three- and four-repeat human Tau proteins

scientific article published on 5 March 2012

Cullin neddylation may allosterically tune polyubiquitin chain length and topology

scientific article published on 12 January 2017

DNA sequences at and between the GC and TATA boxes: potential DNA looping and spatial juxtapositioning of the protein factors

scientific article published in June 1992

DNA spatial considerations in the arrangement of G/C and A/T blocks

scientific article published on January 1, 1992

DNA-binding protects p53 from interactions with cofactors involved in transcription-independent functions

scientific article

DNAase I hypersensitive sites may be correlated with genomic regions of large structural variation

scientific article published in August 1984

De novo tubular nanostructure design based on self-assembly of beta-helical protein motifs

scientific article

Defining the Domain Arrangement of the Mammalian Target of Rapamycin Complex Component Rictor Protein

scientific article

Designing a nanotube using naturally occurring protein building blocks

scientific article published on 28 April 2006

Detection of non-topological motifs in protein structures

scientific article

Deterministic pharmacophore detection via multiple flexible alignment of drug-like molecules

scientific article published on September 2008

Developments in integrative modeling with dynamical interfaces

scientific article published on 12 November 2018

Different roles of electrostatics in heat and in cold: adaptation by citrate synthase

scientific article published in March 2004

Dimerization of the SP1 Region of HIV-1 Gag Induces a Helical Conformation and Association into Helical Bundles: Implications for Particle Assembly

scientific article published on 4 December 2015

Dipeptide analysis of p53 mutations and evolution of p53 family proteins.

scientific article published on 10 April 2013

Disordered amyloidogenic peptides may insert into the membrane and assemble into common cyclic structural motifs

scientific article

Disordered proteins and network disorder in network descriptions of protein structure, dynamics and function: hypotheses and a comprehensive review

scientific article

Distinct patterns in homooligomer tract sequence context in prokaryotic and eukaryotic DNA.

scientific article published in August 1989

Distinct patterns in the dinucleotide nearest neighbors to G/C and A/T oligomers in eukaryotic sequences

scientific article published in September 1991

Distinguishing between sequential and nonsequentially folded proteins: implications for folding and misfolding

scientific article

Does Ras Activate Raf and PI3K Allosterically?

scientific article published on 15 November 2019

Doublet frequencies in evolutionary distinct groups

scientific article

Druggable Orthosteric and Allosteric Hot Spots to Target Protein-protein Interactions ⬇️

scientific article published on January 1, 2014

Drugging Ras GTPase: a comprehensive mechanistic and signaling structural view

scientific article

Dynamic Protein Allosteric Regulation and Disease

scientific article published on 01 January 2019

Dynamic allostery: linkers are not merely flexible

scientific article published on July 2011

Dynamic multiprotein assemblies shape the spatial structure of cell signaling

scientific article

Dynamics differentiate between active and inactive inteins

scientific article

EMatch: an efficient method for aligning atomic resolution subunits into intermediate-resolution cryo-EM maps of large macromolecular assemblies

scientific article published on 13 December 2006

EMatch: discovery of high resolution structural homologues of protein domains in intermediate resolution cryo-EM maps

scientific article

Editorial overview: Folding and binding: Dynamic conformational heterogeneity is pivotal to cell life

scientific article

Effects of point substitutions on the structure of toxic Alzheimer's β-amyloid channels: atomic force microscopy and molecular dynamics simulations

scientific article published on 28 March 2012

Effects of secondary structures in RNA on interlocking probabilities ⬇️

scientific article published on January 1, 1984

Effects of the C-Terminal Tail on the Conformational Dynamics of Human Neuronal Calcium Sensor-1 Protein.

scientific article published on 8 October 2015

Efficient algorithms for searching for exact repetition of nucleotide sequences

scientific article published in January 1983

Efficient computational algorithms for docking and for generating and matching a library of functional epitopes I. Rigid and flexible hinge-bending docking algorithms.

scientific article

Efficient computational algorithms for docking and for generating and matching a library of functional epitopes II. Computer vision-based techniques for the generation and utilization of functional epitopes

scientific article

Efficient detection of three-dimensional structural motifs in biological macromolecules by computer vision techniques

scientific article published on December 1991

Electrostatic strengths of salt bridges in thermophilic and mesophilic glutamate dehydrogenase monomers.

scientific article

Electrostatics, allostery, and activity of the yeast chorismate mutase

scientific article

Emerging Allosteric Mechanism of EGFR Activation in Physiological and Pathological Contexts

scientific article published on 28 May 2019

Energetic determinants of protein binding specificity: insights into protein interaction networks

scientific article published in April 2009

Energetic redistribution in allostery to execute protein function

scientific article published on 10 July 2017

Energy landscape and dynamics of the beta-hairpin G peptide and its isomers: Topology and sequences

scientific article published on September 2003

Energy landscape of amyloidogenic peptide oligomerization by parallel-tempering molecular dynamics simulation: significant role of Asn ladder

scientific article

Engineering strategy to improve peptide analogs: from structure-based computational design to tumor homing

scientific article published on 14 December 2012

Enhancer elements share local homologous twist-angle variations with a helical periodicity

scientific article

Enriching the human apoptosis pathway by predicting the structures of protein-protein complexes

scientific article

Enzyme dynamics point to stepwise conformational selection in catalysis ⬇️

scientific article published on September 6, 2010

Erratum: The role of dynamic conformational ensembles in biomolecular recognition

scholarly article published in Nature Chemical Biology

Eukaryotic dinucleotide preference rules and their implications for degenerate codon usage ⬇️

scientific article published on June 15, 1981

Eukaryotic oligomer frequencies are correlated with certain DNA helical parameters

scientific article published in October 1985

Evolution of domain promiscuity in eukaryotic genomes--a perspective from the inferred ancestral domain architectures

scientific article published on 3 December 2010

Examination of shape complementarity in docking of unbound proteins

scientific article

Examination of shape complementarity in docking ofUnbound proteins

article by Raquel Norel et al published 15 August 1999 in Proteins

Expanding the conformational selection paradigm in protein-ligand docking

scientific article published on January 2012

Experiment-guided thermodynamic simulations on reversible two-state proteins: implications for protein thermostability

scientific article published in November 2004

Experimental and Computational Protocols for Studies of Cross-Seeding Amyloid Assemblies.

scientific article published in January 2018

Explicit and implicit water simulations of a ?-hairpin peptide

scholarly article by Buyong Ma published in October 1999

Explicit and implicit water simulations of a beta-hairpin peptide

scientific article

Exploiting conformational ensembles in modeling protein-protein interactions on the proteome scale

scientific article published on 30 April 2013

Exploring the energy landscape of a molecular engineered analog of a tumor-homing peptide

scientific article published on 24 January 2011

Extended disordered proteins: targeting function with less scaffold

scientific article (publication date: February 2003)

Factors enhancing protein thermostability

scientific article published in March 2000

Familial Alzheimer's disease Osaka mutant (ΔE22) β-barrels suggest an explanation for the different Aβ1-40/42 preferred conformational states observed by experiment

scientific article

Familial Mutations May Switch Conformational Preferences in α-Synuclein Fibrils

scientific article published on 11 January 2017

Fast algorithm for predicting the secondary structure of single-stranded RNA

scientific article

Fast alignment of DNA and protein sequences

scientific article

Fast and accurate modeling of protein-protein interactions by combining template-interface-based docking with flexible refinement

scientific article published on 31 January 2012

Fast protein fold recognition via sequence to structure alignment and contact capacity potentials

scientific article

Favorable domain size in proteins

scientific article

Favorable scaffolds: proteins with different sequence, structure and function may associate in similar ways

scientific article

Fewer Dimensions, More Structures for Improved Discrete Models of Dynamics of Free versus Antigen-Bound Antibody

scientific article published in 2022

FiberDock: Flexible induced-fit backbone refinement in molecular docking

scientific article

FiberDock: a web server for flexible induced-fit backbone refinement in molecular docking

scientific article

Fibril modelling by sequence and structure conservation analysis combined with protein docking techniques: beta(2)-microglobulin amyloidosis

scientific article

FireDock: a web server for fast interaction refinement in molecular docking

scientific article published on 19 April 2008

FireDock: fast interaction refinement in molecular docking

scientific article

FlexProt: alignment of flexible protein structures without a predefinition of hinge regions

scientific article

Flexible Cullins in Cullin-RING E3 Ligases Allosterically Regulate Ubiquitination ⬇️

scientific article published on September 20, 2011

Flexible docking allowing induced fit in proteins: insights from an open to closed conformational isomers

scientific article

Flexible protein alignment and hinge detection

scientific article

Flexible structural comparison allowing hinge-bending, swiveling motions

scientific article published in February 1999

Flexible-body motions of calmodulin and the farnesylated hypervariable region yield a high-affinity interaction enabling K-Ras4B membrane extraction.

scientific article published on 16 June 2017

Fluctuations between stabilizing and destabilizing electrostatic contributions of ion pairs in conformers of the c-Myc-Max leucine zipper

scientific article

Fluctuations in ion pairs and their stabilities in proteins

scientific article

Folding and binding cascades: dynamic landscapes and population shifts

scientific article

Folding and binding cascades: shifts in energy landscapes

scientific article

Folding funnels and binding mechanisms

scientific article

Folding funnels and conformational transitions via hinge-bending motions

scientific article (publication date: 1999)

Folding funnels, binding funnels, and protein function

scientific article

Folding of two large nucleotide chains

scientific article published in February 1984

Free energy diagrams for protein function

scientific article published on 06 February 2014

From "What Is?" to "What Isn't?" Computational Biology

scientific article

From allosteric drugs to allo-network drugs: state of the art and trends of design, synthesis and computational methods

scientific article published in January 2013

From computational quantum chemistry to computational biology: experiments and computations are (full) partners

scientific article

From peptide-based material science to protein fibrils: discipline convergence in nanobiology

scientific article

From structure to function: methods and applications

scientific article

GOSSIP: a method for fast and accurate global alignment of protein structures

scientific article

GTP Binding and Oncogenic Mutations May Attenuate Hypervariable Region (HVR)-Catalytic Domain Interactions in Small GTPase K-Ras4B, Exposing the Effector Binding Site

scientific article

GTP-Dependent K-Ras Dimerization

scientific article published on 4 June 2015

Gene-specific transcription activation via long-range allosteric shape-shifting

scientific article published on October 2011

General nearest neighbor preferences in G/C oligomers interrupted by A/T: correlation with DNA structure

scientific article published in October 1990

Generation and analysis of a protein-protein interface data set with similar chemical and spatial patterns of interactions

scientific article

Genome Landscapes of Disease: Strategies to Predict the Phenotypic Consequences of Human Germline and Somatic Variation

scientific article published on 18 August 2016

Geometrical docking algorithms. A practical approach

scientific article

Geometry-based flexible and symmetric protein docking

scientific article

Graphite-Templated Amyloid Nanostructures Formed by a Potential Pentapeptide Inhibitor for Alzheimer's Disease: A Combined Study of Real-Time Atomic Force Microscopy and Molecular Dynamics Simulations

scientific article published on 12 June 2017

HMI-PRED: A Web Server for Structural Prediction of Host-Microbe Interactions Based on Interface Mimicry

scientific article published on 13 February 2020

Harnessing endophenotypes and network medicine for Alzheimer's drug repurposing

scientific article published on 13 July 2020

Head and Neck Cancers Promote an Inflammatory Transcriptome through Coactivation of Classic and Alternative NF-κB Pathways

scientific article published on 17 October 2019

Helix stability in prokaryotic promoter regions

scientific article

Hierarchical protein folding pathways: a computational study of protein fragments.

scientific article

High-Affinity Interaction of the K-Ras4B Hypervariable Region with the Ras Active Site

scientific article

High-Affinity Interactions of the nSH3/cSH3 Domains of Grb2 with the C-Terminal Proline-Rich Domain of SOS1

scientific article published on 04 February 2020

HingeProt: automated prediction of hinges in protein structures

scientific article

Hollow core of Alzheimer's Abeta42 amyloid observed by cryoEM is relevant at physiological pH.

scientific article

Homology modeling and molecular dynamics simulations of lymphotactin

scientific article

Homonyms, synonyms and mutations of the sequence/structure vocabulary

scientific article published in May 1984

Hot regions in protein--protein interactions: the organization and contribution of structurally conserved hot spot residues

scientific article

How Can PLoS Computational Biology help the biological sciences?

scientific article

How Does Hyperphopsphorylation Promote Tau Aggregation and Modulate Filament Structure and Stability?

scientific article published on 8 February 2016

How can computation advance microbiome research? ⬇️

scientific article published on 21 September 2017

How different are structurally flexible and rigid binding sites? Sequence and structural features discriminating proteins that do and do not undergo conformational change upon ligand binding

scientific article

How do dynamic cellular signals travel long distances?

scientific article published on 18 July 2011

How do thermophilic proteins deal with heat?

scientific article

How do transcription factors select specific binding sites in the genome?

scientific article published in November 2009

How does the reductase help to regulate the catalytic cycle of cytochrome P450 3A4 using the conserved water channel?

scientific article

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scientific article

The Key Role of Calmodulin in KRAS-Driven Adenocarcinomas

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The Mechanism of ATP-Dependent Allosteric Protection of Akt Kinase Phosphorylation

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The Mystery of Rap1 Suppression of Oncogenic Ras

scientific article published on 02 March 2020

The NRF2-related interactome and regulome contain multifunctional proteins and fine-tuned autoregulatory loops.

scientific article published on 26 May 2012

The Role of Allostery in the Termination of Second Messenger Signaling

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The Role of Protein Loops and Linkers in Conformational Dynamics and Allostery

scientific article published on 18 February 2016

The Structural Basis of Oncogenic Mutations G12, G13 and Q61 in Small GTPase K-Ras4B.

scientific article published on 23 February 2016

The Structural Basis of the Farnesylated and Methylated KRas4B Interaction with Calmodulin

scientific article published on 05 September 2019

The building block folding model and the kinetics of protein folding

scientific article published in October 2001

The contribution of the Trp/Met/Phe residues to physical interactions of p53 with cellular proteins

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The design of covalent allosteric drugs

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The different ways through which specificity works in orthosteric and allosteric drugs

scientific article published in January 2012

The disordered hypervariable region and the folded catalytic domain of oncogenic K-Ras4B partner in phospholipid binding

scientific article published on 19 December 2015

The distinct structural preferences of tau protein repeat domains

The distributions of nucleotides near bacterial transcription initiation and termination sites show distinct signals that may affect DNA geometry

scientific article published in January 1987

The dynamic mechanism of RASSF5 and MST kinase activation by Ras.

scientific article published on 15 February 2017

The energy landscape of a selective tumor-homing pentapeptide

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The eukaryotic CCAAT and TATA boxes, DNA spacer flexibility and looping

scientific article published on March 1992

The free energy landscape in translational science: how can somatic mutations result in constitutive oncogenic activation?

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The higher level of complexity of K-Ras4B activation at the membrane

scientific article published on 30 December 2015

The hydrophobic effect: a new insight from cold denaturation and a two-state water structure

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The implications of higher (or lower) success in secondary structure prediction of chain fragments

scientific article published on August 2005

The mechanism of PI3Kα activation at the atomic level

scientific article published on 20 February 2019

The mechanism of activation of MEK1 by B-Raf and KSR1

scientific article published on 04 May 2022

The mechanism of ubiquitination in the cullin-RING E3 ligase machinery: conformational control of substrate orientation

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The molecular basis of targeting protein kinases in cancer therapeutics

scientific article published on 04 May 2013

The multiple common point set problem and its application to molecule binding pattern detection

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The ordering of nucleotides in the DNA: strong pyrimidine-purine patterns near homooligomer tracts

scientific article published in March 1991

The ordering of the nucleotides in DNA: computational problems in molecular biology

scientific article published on January 1989

The origin of allosteric functional modulation: multiple pre-existing pathways

scientific article published on August 2009

The potential impact of recent developments in three-dimensional quantitative interaction proteomics on structural biology

scientific article published on 22 April 2016

The predicted presence of large helical structural variation in yeast HIS4 upstream region is correlated with general amino acid control on the CYC1 gene

scientific article published in October 1985

The quaternary assembly of KRas4B with Raf-1 at the membrane

scientific article published on 25 March 2020

The role of allostery in the ubiquitin-proteasome system

scientific article published on 13 December 2012

The role of dynamic conformational ensembles in biomolecular recognition

scientific article (publication date: November 2009)

The role of response elements organization in transcription factor selectivity: the IFN-β enhanceosome example

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The sequence dependence of fiber organization. A comparative molecular dynamics study of the islet amyloid polypeptide segments 22-27 and 22-29.

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The significance of the 2013 Nobel Prize in Chemistry and the challenges ahead

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The spatial structure of cell signaling systems ⬇️

scientific article published on 02 August 2013

The stability and dynamics of the human calcitonin amyloid peptide DFNKF

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The stability of monomeric intermediates controls amyloid formation: Abeta25-35 and its N27Q mutant

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The structural basis for Ras activation of PI3Kα lipid kinase

scientific article published on 01 June 2019

The structural basis for cancer treatment decisions

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The structural basis of ATP as an allosteric modulator

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The structural network of Interleukin-10 and its implications in inflammation and cancer

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The structural network of inflammation and cancer: merits and challenges.

scientific article published on 24 May 2013

The structural pathway of interleukin 1 (IL-1) initiated signaling reveals mechanisms of oncogenic mutations and SNPs in inflammation and cancer

scientific article (publication date: February 2014)

The underappreciated role of allostery in the cellular network.

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The unique Alzheimer's β-amyloid triangular fibril has a cavity along the fibril axis under physiological conditions

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The universal dinucleotide asymmetry rules in DNA and the amino acid codon choice

scientific article published in January 1981

Theoretical characterization of substrate access/exit channels in the human cytochrome P450 3A4 enzyme: involvement of phenylalanine residues in the gating mechanism

scientific article published on October 2009

Theoretical molecular biology: prospectives and perspectives

scientific article published in March 1987

Thermal unfolding molecular dynamics simulation of Escherichia coli dihydrofolate reductase: thermal stability of protein domains and unfolding pathway

scientific article published on February 2002

Thermodynamic differences among homologous thermophilic and mesophilic proteins

scientific article published in November 2001

Three dimensional structure and sequence homology determine splicing sites in eukaryotic precursor RNA.

scientific article published in April 1980

Three-dimensional, sequence order-independent structural comparison of a serine protease against the crystallographic database reveals active site similarities: potential implications to evolution and to protein folding

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Topological properties of protein interaction networks from a structural perspective

scientific article published on December 2008

Towards drugs targeting multiple proteins in a systems biology approach

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Towards inferring time dimensionality in protein-protein interaction networks by integrating structures: the p53 example ⬇️

scientific article published in December 2009

Transient, highly populated, building blocks folding model

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Transition-state ensemble in enzyme catalysis: possibility, reality, or necessity?

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Transmembrane β-Barrel Topology Model for Alzheimer's β-Amyloid (Aβ) Ion Channels

article published in 2011

Tree graphs of RNA secondary structures and their comparisons

scientific article published in October 1989

Trends in the 5' vs. 3' flanks of oligonucleotides in eukaryotic and prokaryotic genomes: the asymmetric roles played by cytosine and guanine

scientific article published in November 1991

Triggering loops and enzyme function: identification of loops that trigger and modulate movements

scientific article published in September 2003

Trp/Met/Phe hot spots in protein-protein interactions: potential targets in drug design

scientific article published on January 2007

Truncated beta-amyloid peptide channels provide an alternative mechanism for Alzheimer's Disease and Down syndrome

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Unraveling structural mechanisms of allosteric drug action

scientific article published on 14 April 2014

Unraveling the molecular mechanism of interactions of the Rho GTPases Cdc42 and Rac1 with the scaffolding protein IQGAP2.

scientific article published on 22 January 2018

Use of constrained synthetic amino acids in beta-helix proteins for conformational control

scientific article published on 8 March 2007

Using DelPhi to compute electrostatic potentials and assess their contribution to interactions

scientific article published in August 2003

What can we learn from highly connected beta-rich structures for structural interface design?

scientific article published on January 2008

What's in a name? Why these proteins are intrinsically disordered: Why these proteins are intrinsically disordered

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Why Are Some Driver Mutations Rare?

scientific article published on 05 November 2019

Why does binding of proteins to DNA or proteins to proteins not necessarily spell function?

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Zinc ions promote Alzheimer Abeta aggregation via population shift of polymorphic states

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deepDR: a network-based deep learning approach to in silico drug repositioning

scientific article published on 01 December 2019

p53-Induced DNA bending: the interplay between p53-DNA and p53-p53 interactions

scientific article published on 08 May 2008

β-Barrel topology of Alzheimer's β-amyloid ion channels

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List of works by Ruth Nussinov

"Similarity trap" in protein-protein interactions could be carcinogenic: simulations of p53 core domain complexed with 53BP1 and BRCA1 BRCT domains

'Latent drivers' expand the cancer mutational landscape

'Pathway drug cocktail': targeting Ras signaling based on structural pathways

(A)GGG(A), (A)CCC(A) and other potential 3' splice signals in primate nuclear pre-mRNA sequences

1-amino-2-phenylcyclopentane-1-carboxylic acid: a conformationally restricted phenylalanine analogue

A 3D sequence-independent representation of the protein data bank

A Future Vision for PLOS Computational Biology

A New View of Pathway-Driven Drug Resistance in Tumor Proliferation

A New View of Ras Isoforms in Cancers

A Protocol for the Design of Protein and Peptide Nanostructure Self-Assemblies Exploiting Synthetic Amino Acids

A Review of 2010 for PLoS Computational Biology

A Review of 2011 for PLoS Computational Biology

A Structural View of Negative Regulation of the Toll-like Receptor-Mediated Inflammatory Pathway.

A Systems Pharmacology Approach Uncovers Wogonoside as an Angiogenesis Inhibitor of Triple-Negative Breast Cancer by Targeting Hedgehog Signaling

A broad view of scaffolding suggests that scaffolding proteins can actively control regulation and signaling of multienzyme complexes through allostery

A comparative study of amyloid fibril formation by residues 15-19 of the human calcitonin hormone: a single beta-sheet model with a small hydrophobic core

A component overlapping attribute clustering (COAC) algorithm for single-cell RNA sequencing data analysis and potential pathobiological implications

A computer vision based technique for 3-D sequence-independent structural comparison of proteins

A dataset of protein-protein interfaces generated with a sequence-order-independent comparison technique

A disulphide-reinforced structural scaffold shared by small proteins with diverse functions

A fixed-point alignment technique for detection of recurrent and common sequence motifs associated with biological features.

A formal MIM specification and tools for the common exchange of MIM diagrams: an XML-Based format, an API, and a validation method

A geometry-based suite of molecular docking processes

A hierarchical protein folding scheme based on the building block folding model.

A mechanistic view of the role of E3 in sumoylation

A method for biomolecular structural recognition and docking allowing conformational flexibility

A method for simultaneous alignment of multiple protein structures

A new, structurally nonredundant, diverse data set of protein-protein interfaces and its implications

A permissive secondary structure-guided superposition tool for clustering of protein fragments toward protein structure prediction via fragment assembly.

A proposed structural model for amyloid fibril elongation: domain swapping forms an interdigitating beta-structure polymer

A second molecular biology revolution? The energy landscapes of biomolecular function

A sequence analysis system encompassing rules for DNA helical distortion

A set of van der Waals and coulombic radii of protein atoms for molecular and solvent-accessible surface calculation, packing evaluation, and docking

A simulation strategy for the atomistic modeling of flexible molecules covalently tethered to rigid surfaces: application to peptides

A strategy based on protein-protein interface motifs may help in identifying drug off-targets

A study of four-helix bundles: investigating protein folding via similar architectural motifs in protein cores and in subunit interfaces

A survey of available tools and web servers for analysis of protein-protein interactions and interfaces

A systematic study of the vibrational free energies of polypeptides in folded and random states

A unified convention for biological assemblies with helical symmetry

A unified view of "how allostery works"

ARTS: alignment of RNA tertiary structures

Activity and architecture of pyroglutamate-modified amyloid-β (AβpE3-42) pores

Advancements and challenges in computational biology

Algorithms for multiple protein structure alignment and structure-derived multiple sequence alignment.

Alignment of flexible protein structures.

All-d-Enantiomer of β-Amyloid Peptide Forms Ion Channels in Lipid Bilayers

Allo-network drugs: extension of the allosteric drug concept to protein- protein interaction and signaling networks

Allo-network drugs: harnessing allostery in cellular networks

Allosteric KRas4B Can Modulate SOS1 Fast and Slow Ras Activation Cycles

Allosteric activation of RAF in the MAPK signaling pathway

Allosteric conformational barcodes direct signaling in the cell

Allosteric control of antibody-prion recognition through oxidation of a disulfide bond between the CH and CL chains

Allosteric effects in the marginally stable von Hippel-Lindau tumor suppressor protein and allostery-based rescue mutant design

Allosteric effects of the oncogenic RasQ61L mutant on Raf-RBD

Allosteric modulators can restore function in an amino acid neurotransmitter receptor by slightly altering intra‐molecular communication pathways ⬇️

Allosteric post-translational modification codes

Allosteric regulation of glycogen synthase kinase 3β: a theoretical study

Allosteric stabilization of the amyloid-β peptide hairpin by the fluctuating N-terminal

Allostery and population shift in drug discovery

Allostery in Its Many Disguises: From Theory to Applications

Allostery in disease and in drug discovery

Allostery modulates the beat rate of a cardiac pacemaker

Allostery without a conformational change? Revisiting the paradigm.

Allostery: An Overview of Its History, Concepts, Methods, and Applications

Allostery: absence of a change in shape does not imply that allostery is not at play

Alternative allosteric mechanisms can regulate the substrate and E2 in SUMO conjugation

Alzheimer's disease: which type of amyloid-preventing drug agents to employ?

Alzheimer's β-Amyloid All-D-Enantiomers and Native All-L-Enantiomers Exhibit Similar Pore Structures in Lipid Bilayers: Atomic Force Microscopy

Amino acid pair interchanges at spatially conserved locations

Amplification of signaling via cellular allosteric relay and protein disorder

Amylin-Aβ oligomers at atomic resolution using molecular dynamics simulations: a link between Type 2 diabetes and Alzheimer's disease

Amyloid β Ion Channels in a Membrane Comprising Brain Total Lipid Extracts

An accelerated algorithm for calculating the secondary structure of single stranded RNAs

An automated computer vision and robotics-based technique for 3-D flexible biomolecular docking and matching.

An efficient automated computer vision based technique for detection of three dimensional structural motifs in proteins

An efficient code searching for sequence homology and DNA duplication ⬇️

An efficient string matching algorithm with K substitutions for nucleotide and amino acid sequences

An efficient string matching algorithm with k differences for nucleotide and amino acid sequences

An improved secondary structure computation method and its application to intervening sequence in the human alpha-like globin mRNA precursors