(Q34130178)

31 July 2017

Kinetic rate constant prediction supports the conformational selection mechanism of protein binding (English)

1 reference

31 July 2017

1

0 references

Paul A. Bates

series ordinal

2

0 references

publication date

12 January 2012

1 reference

PLOS Computational Biology

31 July 2017

1 reference

31 July 2017

8

1 reference

31 July 2017

1

1 reference

31 July 2017

e1002351

1 reference

Creative Commons Attribution 4.0 International

31 July 2017

start time

12 January 2012

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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A structure-based benchmark for protein-protein binding affinity

28 July 2018

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Induced fit, conformational selection and independent dynamic segments: an extended view of binding events

28 July 2018

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From induced fit to conformational selection: a continuum of binding mechanism controlled by the timescale of conformational transitions

28 July 2018

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Potentials 'R' Us web-server for protein energy estimations with coarse-grained knowledge-based potentials

28 July 2018

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PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta

28 July 2018

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The role of dynamic conformational ensembles in biomolecular recognition

28 July 2018

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Quantitative prediction of protein-protein binding affinity with a potential of mean force considering volume correction.

28 July 2018

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Pushing structural information into the yeast interactome by high-throughput protein docking experiments

28 July 2018

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CHARMM: the biomolecular simulation program

28 July 2018

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Fast predictions of thermodynamics and kinetics of protein-protein recognition from structures: from molecular design to systems biology

28 July 2018

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Fundamental aspects of protein-protein association kinetics

28 July 2018

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Dynamic energy landscape view of coupled binding and protein conformational change: induced-fit versus population-shift mechanisms

28 July 2018

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Targeting the human cancer pathway protein interaction network by structural genomics

28 July 2018

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Transition networks for modeling the kinetics of conformational change in macromolecules

28 July 2018

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OPUS-PSP: an orientation-dependent statistical all-atom potential derived from side-chain packing.

28 July 2018

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OPUS-Ca: a knowledge-based potential function requiring only Calpha positions

28 July 2018

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Structures in systems biology

28 July 2018

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Bridging from molecular simulation to biochemical networks.

28 July 2018

1 reference

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Do we underestimate the importance of water in cell biology?

28 July 2018

1 reference

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Application of a Theory of Enzyme Specificity to Protein Synthesis

28 July 2018

1 reference

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Structural systems biology: modelling protein interactions.

28 July 2018

1 reference

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Protein fragment reconstruction using various modeling techniques

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257286

Water and proteins: a love-hate relationship

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257286

Water in protein structure prediction

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257286

Antibody multispecificity mediated by conformational diversity

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257286

Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257286

Biomolecular diffusional association

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257286

Protein folding mediated by solvation: water expulsion and formation of the hydrophobic core occur after the structural collapse

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257286

Evaluation of a fast implicit solvent model for molecular dynamics simulations

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257286

Structure-based thermodynamic analysis of the dissociation of protein phosphatase-1 catalytic subunit and microcystin-LR docked complexes

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257286

Folding funnels and binding mechanisms

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257286

A systematic study of low-resolution recognition in protein--protein complexes

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257286

Folding funnels, binding funnels, and protein function

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257286

Effective energy function for proteins in solution

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257286

Energy functions that discriminate X-ray and near native folds from well-constructed decoys

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257286

Conformational isomerism and the diversity of antibodies

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257286

Analyzing protein interaction networks using structural information

28 July 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002351

Mathematical modeling identifies Smad nucleocytoplasmic shuttling as a dynamic signal-interpreting system

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002351

Protein-protein binding affinity prediction on a diverse set of structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002351

Selected-fit versus induced-fit protein binding: kinetic differences and mutational analysis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002351

Predicting kinetic constants of protein-protein interactions based on structural properties.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002351

A physical reference state unifies the structure-derived potential of mean force for protein folding and binding.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002351

Assembly and function of a quaternary signal transduction complex monitored by surface plasmon resonance

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002351

Specific interactions for ab initio folding of protein terminal regions with secondary structures.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002351

Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002351

Four-body contact potentials derived from two protein datasets to discriminate native structures from decoys.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002351

FireDock: fast interaction refinement in molecular docking

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002351

New measures for estimating surface complementarity and packing at protein-protein interfaces.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002351

Adhesive water networks facilitate binding of protein interfaces

21 January 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257286

28 October 2018

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002351

Binding of 125I-fasciculin to rat brain acetylcholinesterase. The complex still binds diisopropyl fluorophosphate.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257286

A Systematic Study of the Energetics Involved in Structural Changes upon Association and Connectivity in Protein Interaction Networks

28 October 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002351

Prediction of protein conformational freedom from distance constraints

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3257286

Loops in Proteins Can Be Modeled as Worm-Like Chains

28 October 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002351

Fasciculin 2 binds to the peripheral site on acetylcholinesterase and inhibits substrate hydrolysis by slowing a step involving proton transfer during enzyme acylation

21 January 2018

1 reference

12 December 2020

Refined models for computer simulation of protein folding. Applications to the study of conserved secondary structure and flexible hinge points during the folding of pancreatic trypsin inhibitor

1 reference

12 December 2020

Spectroscopic, calorimetric, and kinetic demonstration of conformational adaptation in peptide-antibody recognition

1 reference

12 December 2020

Lack of significant differences in association rates and affinities of antibodies from short-term and long-term responses to hen egg lysozyme

1 reference

12 December 2020

Antigen recognition by conformational selection

1 reference

12 December 2020

ProtorP: a protein-protein interaction analysis server

1 reference

12 December 2020

Kinetic analysis of macromolecular interactions using surface plasmon resonance biosensors

1 reference

12 December 2020

10.1371/JOURNAL.PCBI.1002351

Identifiers

DOI

1 reference

31 July 2017

journals/ploscb/MoalB12

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

31 July 2017

1 reference

PubMed ID

22253587