(Q41239235)

28 September 2017

SwarmDock and the use of normal modes in protein-protein docking (English)

1 reference

28 September 2017

1

1 reference

28 September 2017

2

1 reference

PMC publication ID

2996808

28 September 2017

language of work or name

English

0 references

publication date

28 September 2010

1 reference

International Journal of Molecular Sciences

28 September 2017

1 reference

28 September 2017

11

1 reference

28 September 2017

10

1 reference

28 September 2017

3623-3648

1 reference

Creative Commons Attribution 4.0 International

28 September 2017

start time

28 September 2010

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

FiberDock: Flexible induced-fit backbone refinement in molecular docking

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

The role of dynamic conformational ensembles in biomolecular recognition

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

The structural basis of Arf effector specificity: the crystal structure of ARF6 in a complex with JIP4

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

Alternating evolutionary pressure in a genetic algorithm facilitates protein model selection

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

Principles of flexible protein-protein docking

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

Insights into protein flexibility: The relationship between normal modes and conformational change upon protein-protein docking

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

Fast procedure for reconstruction of full-atom protein models from reduced representations.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

pso@autodock: a fast flexible molecular docking program based on Swarm intelligence

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

Insights into equilibrium dynamics of proteins from comparison of NMR and X-ray data with computational predictions

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

Flexible protein-protein docking

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

Can conformational change be described by only a few normal modes?

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

Accounting for global protein deformability during protein-protein and protein-ligand docking

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

Structural basis for the activation of cholera toxin by human ARF6-GTP

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

Refinement of docked protein-ligand and protein-DNA structures using low frequency normal mode amplitude optimization

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

Docking essential dynamics eigenstructures

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

PatchDock and SymmDock: servers for rigid and symmetric docking

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

A graph-theory algorithm for rapid protein side-chain prediction

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

HADDOCK: a protein-protein docking approach based on biochemical or biophysical information

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

A coarse-grained normal mode approach for macromolecules: an efficient implementation and application to Ca(2+)-ATPase

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

Hinge-bending motion of D-allose-binding protein from Escherichia coli: three open conformations

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

Anisotropy of fluctuation dynamics of proteins with an elastic network model

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

Rapid refinement of protein interfaces incorporating solvation: application to the docking problem

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

Episelection: novel Ki approximately nanomolar inhibitors of serine proteases selected by binding or chemistry on an enzyme surface

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

X-ray structure of the GCN4 leucine zipper, a two-stranded, parallel coiled coil

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

Consistent improvement of cross-docking results using binding site ensembles generated with elastic network normal modes

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

Protein-protein docking benchmark version 3.0.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

How well can we understand large-scale protein motions using normal modes of elastic network models?

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

Protein-protein docking with a reduced protein model accounting for side-chain flexibility

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

Conformational change of proteins arising from normal mode calculations

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

Protein hinge bending as seen in molecular dynamics simulations of native and M61 mutant T4 lysozymes

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

Protein-ligand docking accounting for receptor side chain and global flexibility in normal modes: evaluation on kinase inhibitor cross docking

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

Prediction of the receptor conformation for iGluR2 agonist binding: QM/MM docking to an extensive conformational ensemble generated using normal mode analysis

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

Context shapes: Efficient complementary shape matching for protein-protein docking.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

SOFTDOCK application to protein-protein interaction benchmark and CAPRI.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

Energy minimization in low-frequency normal modes to efficiently allow for global flexibility during systematic protein-protein docking.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

Implicit flexibility in protein docking: cross-docking and local refinement.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

FireDock: fast interaction refinement in molecular docking

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

SODOCK: swarm optimization for highly flexible protein-ligand docking.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

Loop motions of triosephosphate isomerase observed with elastic networks.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

Accounting for loop flexibility during protein-protein docking.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

Representing receptor flexibility in ligand docking through relevant normal modes.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

Geometry-based flexible and symmetric protein docking

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

Development and testing of an automated approach to protein docking.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

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

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

ClusPro: an automated docking and discrimination method for the prediction of protein complexes.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

Improved Hidden Markov Model training for multiple sequence alignment by a particle swarm optimization-evolutionary algorithm hybrid.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

ICM-DISCO docking by global energy optimization with fully flexible side-chains

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

Successful discrimination of protein interactions.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

A protein-protein docking benchmark.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

Assessment of blind predictions of protein-protein interactions: current status of docking methods

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

Docking unbound proteins using shape complementarity, desolvation, and electrostatics.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

Protein docking using a genetic algorithm.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

Building-block approach for determining low-frequency normal modes of macromolecules.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

Protein docking using spherical polar Fourier correlations.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

Hinge-bending motion in citrate synthase arising from normal mode calculations.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996808

Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis

19 August 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS11103623

Minimization by Random Search Techniques

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS11103623

Complementarity of Structure Ensembles in Protein-Protein Binding

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS11103623

Thorough Validation of Protein Normal Mode Analysis: A Comparative Study with Essential Dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS11103623

Normal mode analysis as a prerequisite for drug design: Application to matrix metalloproteinases inhibitors

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS11103623

The relationship between the flexibility of proteins and their conformational states on forming protein-protein complexes with an application to protein-protein docking

21 January 2018

1 reference

12 December 2020

RDOCK: Refinement of rigid‐body protein docking predictions

1 reference

12 December 2020

Detection and refinement of encounter complexes for protein-protein docking: taking account of macromolecular crowding

1 reference

12 December 2020

Protein docking using continuum electrostatics and geometric fit

1 reference

12 December 2020

Flexible relaxation of rigid-body docking solutions

1 reference

12 December 2020

Identifiers

DOI

10.3390/IJMS11103623

1 reference

28 September 2017

1 reference

PMC publication ID

2996808

28 September 2017

PubMed publication ID

21152290

1 reference

PMC publication ID

2996808