Integrative computational modeling of protein interactions (Q38192759)

30 August 2017

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title

Integrative computational modeling of protein interactions (English)

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30 August 2017

computational biology

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1

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24588898%20AND%20SRC:MED&resulttype=core&format=json

8 June 2020

Alexandre Bonvin

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24588898%20AND%20SRC:MED&resulttype=core&format=json

8 June 2020

author name string

João P G L M Rodrigues

series ordinal

1

1 reference

30 August 2017

Alexandre M J J Bonvin

series ordinal

2

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30 August 2017

language of work or name

English

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publication date

26 March 2014

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30 August 2017

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24588898%20AND%20SRC:MED&resulttype=core&format=json

8 June 2020

volume

281

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24588898%20AND%20SRC:MED&resulttype=core&format=json

8 June 2020

page(s)

1988-2003

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24588898%20AND%20SRC:MED&resulttype=core&format=json

8 June 2020

issue

8

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24588898%20AND%20SRC:MED&resulttype=core&format=json

Interactome networks and human disease

8 June 2020

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Defining the limits of homology modeling in information-driven protein docking.

21 January 2018

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A multidomain flexible docking approach to deal with large conformational changes in the modeling of biomolecular complexes.

21 January 2018

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Molecular origins of binding affinity: seeking the Archimedean point

21 January 2018

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On the binding affinity of macromolecular interactions: daring to ask why proteins interact

21 January 2018

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Convergence and combination of methods in protein-protein docking

21 January 2018

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

21 January 2018

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ClusPro: performance in CAPRI rounds 6-11 and the new server.

21 January 2018

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pyDockWEB: a web server for rigid-body protein-protein docking using electrostatics and desolvation scoring.

21 January 2018

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Accelerating protein docking in ZDOCK using an advanced 3D convolution library

21 January 2018

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

21 January 2018

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An integrated suite of fast docking algorithms

21 January 2018

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HexServer: an FFT-based protein docking server powered by graphics processors.

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12771

ZDOCK: an initial-stage protein-docking algorithm.

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12771

PIPER: an FFT-based protein docking program with pairwise potentials.

21 January 2018

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Integrating atom-based and residue-based scoring functions for protein-protein docking

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12771

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

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12771

SwarmDock and the use of normal modes in protein-protein docking

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12771

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

Application of a Theory of Enzyme Specificity to Protein Synthesis

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

Flexible protein-protein docking

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

Accounting for conformational changes during protein-protein docking

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

The RosettaDock server for local protein-protein docking

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

ATTRACT: protein-protein docking in CAPRI using a reduced protein model.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

Flexible docking and refinement with a coarse-grained protein model using ATTRACT.

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12771

Scoring functions for protein-protein interactions

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12771

Benchmarking and analysis of protein docking performance in Rosetta v3.2.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

PatchDock and SymmDock: servers for rigid and symmetric docking

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

FastContact: a free energy scoring tool for protein-protein complex structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

Identification of protein-protein interaction sites from docking energy landscapes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

FireDock: fast interaction refinement in molecular docking.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

The scoring of poses in protein-protein docking: current capabilities and future directions

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

DECK: Distance and environment-dependent, coarse-grained, knowledge-based potentials for protein-protein docking

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

Improving ranking of models for protein complexes with side chain modeling and atomic potentials

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

ZRANK: reranking protein docking predictions with an optimized energy function.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

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/10.1111%2FFEBS.12771

Scoring protein interaction decoys using exposed residues (SPIDER): a novel multibody interaction scoring function based on frequent geometric patterns of interfacial residues

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12771

InterEvScore: a novel coarse-grained interface scoring function using a multi-body statistical potential coupled to evolution.

21 January 2018

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Scoring docking models with evolutionary information.

21 January 2018

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Using a consensus approach based on the conservation of inter-residue contacts to rank CAPRI models.

21 January 2018

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Ab initio folding of terminal segments with secondary structures reveals the fine difference between two closely related all-atom statistical energy functions

21 January 2018

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Clustering of low-energy conformations near the native structures of small proteins

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12771

Free energy landscapes of encounter complexes in protein-protein association

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

ClusPro: a fully automated algorithm for protein-protein docking

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12771

Performance of ZDOCK in CAPRI rounds 20-26.

21 January 2018

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Data-driven docking for the study of biomolecular complexes

21 January 2018

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Strengths and weaknesses of data-driven docking in critical assessment of prediction of interactions.

21 January 2018

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How good is automated protein docking?

21 January 2018

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GRAMM-X public web server for protein-protein docking

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

Structural characterization of protein-protein complexes by integrating computational docking with small-angle scattering data

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

Efficient restraints for protein-protein docking by comparison of observed amino acid substitution patterns with those predicted from local environment.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

Various strategies of using residual dipolar couplings in NMR-driven protein docking: application to Lys48-linked di-ubiquitin and validation against 15N-relaxation data

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

Protein–protein HADDocking using exclusively pseudocontact shifts

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

On the usefulness of ion-mobility mass spectrometry and SAXS data in scoring docking decoys

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

Determination of three-dimensional structures of proteins by simulated annealing with interproton distance restraints. Application to crambin, potato carboxypeptidase inhibitor and barley serine proteinase inhibitor 2.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

Building macromolecular assemblies by information-driven docking: introducing the HADDOCK multibody docking server

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

A unified conformational selection and induced fit approach to protein-peptide docking

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

ATTRACT-EM: a new method for the computational assembly of large molecular machines using cryo-EM maps

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

Geometry-based flexible and symmetric protein docking.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

SymmRef: a flexible refinement method for symmetric multimers

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

MultiFit: a web server for fitting multiple protein structures into their electron microscopy density map.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

Subunit order of eukaryotic TRiC/CCT chaperonin by cross-linking, mass spectrometry, and combinatorial homology modeling

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

Mechanism of Nitric Oxide Synthase Regulation: Electron Transfer and Interdomain Interactions.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

Solution Structure of the 128 kDa Enzyme I Dimer from Escherichia coli and Its 146 kDa Complex with HPr Using Residual Dipolar Couplings and Small- and Wide-Angle X-ray Scattering

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

Combining NMR and small angle X-ray and neutron scattering in the structural analysis of a ternary protein-RNA complex

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

Ion mobility mass spectrometry of proteins and protein assemblies.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

WHISCY: what information does surface conservation yield? Application to data-driven docking.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

PredUs: a web server for predicting protein interfaces using structural neighbors

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

InterProSurf: a web server for predicting interacting sites on protein surfaces

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

Prediction-based fingerprints of protein-protein interactions.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

ProMate: a structure based prediction program to identify the location of protein-protein binding sites

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

CPORT: a consensus interface predictor and its performance in prediction-driven docking with HADDOCK.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

PresCont: predicting protein-protein interfaces utilizing four residue properties.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

meta-PPISP: a meta web server for protein-protein interaction site prediction.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

Partner-aware prediction of interacting residues in protein-protein complexes from sequence data

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

DockRank: Ranking docked conformations using partner-specific sequence homology-based protein interface prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

Structural basis of histidine kinase autophosphorylation deduced by integrating genomics, molecular dynamics, and mutagenesis

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

Binding interface prediction by combining protein-protein docking results

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

Putting the pieces together: integrative modeling platform software for structure determination of macromolecular assemblies

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

Prediction of protein-protein interactions by combining structure and sequence conservation in protein interfaces

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

Protein-protein complex structure predictions by multimeric threading and template recombination

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

Templates are available to model nearly all complexes of structurally characterized proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

Protein docking using case-based reasoning.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

Evaluating template-based and template-free protein-protein complex structure prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

The Relationship Between Sequence and Interaction Divergence in Proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

Dynamic control of selectivity in the ubiquitination pathway revealed by an ASP to GLU substitution in an intra-molecular salt-bridge network

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

Mechanism of activation of methyltransferases involved in translation by the Trm112 'hub' protein

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

Computer analysis of protein-protein interaction

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

The birth of computational structural biology

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

Next challenges in protein-protein docking: from proteome to interactome and beyond

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

Crystal structure of RlmAI: implications for understanding the 23S rRNA G745/G748-methylation at the macrolide antibiotic-binding site.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

HomPPI: a class of sequence homology based protein-protein interface prediction methods

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

How proteins get in touch: interface prediction in the study of biomolecular complexes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

Progress and challenges in predicting protein-protein interaction sites

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771

pyDock: electrostatics and desolvation for effective scoring of rigid-body protein-protein docking

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12771