FiberDock: Flexible induced-fit backbone refinement in molecular docking (Q34909306)

5 August 2017

title

FiberDock: Flexible induced-fit backbone refinement in molecular docking (English)

1 reference

5 August 2017

2

Ruth Nussinov

1 reference

5 August 2017

3

Haim J Wolfson

1 reference

5 August 2017

1

Efrat Mashiach

1 reference

5 August 2017

language of work or name

English

0 references

publication date

1 May 2010

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5 August 2017

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5 August 2017

volume

78

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5 August 2017

issue

6

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5 August 2017

page(s)

1503-1519

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

5 August 2017

cites work

1 reference

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The role of dynamic conformational ensembles in biomolecular recognition

8 July 2018

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Principles of flexible protein-protein docking

8 July 2018

1 reference

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

8 July 2018

1 reference

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Conformer selection and induced fit in flexible backbone protein-protein docking using computational and NMR ensembles

8 July 2018

1 reference

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Docking and scoring protein complexes: CAPRI 3rd Edition

8 July 2018

1 reference

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HingeProt: automated prediction of hinges in protein structures

8 July 2018

1 reference

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HADDOCK versus HADDOCK: new features and performance of HADDOCK2.0 on the CAPRI targets

8 July 2018

1 reference

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Application of a Theory of Enzyme Specificity to Protein Synthesis

8 July 2018

1 reference

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4290165

Progress in modeling of protein structures and interactions

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4290165

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4290165

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4290165

Docking essential dynamics eigenstructures

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4290165

Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4290165

Progress in protein-protein docking: atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4290165

PatchDock and SymmDock: servers for rigid and symmetric docking

8 July 2018

1 reference

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8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4290165

Conformational changes associated with protein-protein interactions

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4290165

New advances in normal mode analysis of supermolecular complexes and applications to structural refinement

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4290165

Docking macromolecules with flexible segments.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4290165

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4290165

Cyclic coordinate descent: A robotics algorithm for protein loop closure.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4290165

Antibody multispecificity mediated by conformational diversity

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4290165

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4290165

Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4290165

Structured disorder and conformational selection

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4290165

Conformational change of proteins arising from normal mode calculations

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4290165

Anisotropy of fluctuation dynamics of proteins with an elastic network model

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4290165

Folding and binding cascades: dynamic landscapes and population shifts

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4290165

Folding funnels and binding mechanisms

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4290165

Incorporating biochemical information and backbone flexibility in RosettaDock for CAPRI rounds 6-12.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4290165

Automatic prediction of protein interactions with large scale motion

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4290165

Protein-protein docking with backbone flexibility.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4290165

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

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4290165

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

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4290165

The third CAPRI assessment meeting Toronto, Canada, April 20-21, 2007.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4290165

FireDock: fast interaction refinement in molecular docking

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4290165

Accounting for loop flexibility during protein-protein docking.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4290165

Representing receptor flexibility in ligand docking through relevant normal modes.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4290165

Incorporation of flexibility into rigid-body docking: applications in rounds 3-5 of CAPRI.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4290165

Taking geometry to its edge: fast unbound rigid (and hinge-bent) docking

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4290165

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

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4290165

Guided docking: first step to locate potential binding sites.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4290165

Analysis of domain motions by approximate normal mode calculations

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4290165

Complementarity of Structure Ensembles in Protein-Protein Binding

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4290165

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

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4290165

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

9 December 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20077569

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Flexible relaxation of rigid-body docking solutions

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20077569

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1002/PROT.22668

1 reference

5 August 2017

1 reference

5 August 2017

1 reference