Modeling Complexes of Transmembrane Proteins: Systematic Analysis of ProteinProtein Docking Tools (Q39537387)

12 September 2017

title

Modeling Complexes of Transmembrane Proteins: Systematic Analysis of ProteinProtein Docking Tools (English)

1 reference

12 September 2017

main subject

transmembrane protein

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Jana Selent

2

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Agnieszka Kaczor

object named as

Agnieszka A Kaczor

series ordinal

1

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Manuel Pastor

object named as

Manuel Pastor

series ordinal

4

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Ferran Sanz

object named as

Ferran Sanz

series ordinal

3

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publication date

6 August 2013

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12 September 2017

published in

Molecular Informatics

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12 September 2017

volume

32

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12 September 2017

issue

8

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12 September 2017

page(s)

717-733

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

12 September 2017

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Organization of the G protein-coupled receptors rhodopsin and opsin in native membranes

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Structures of the CXCR4 chemokine GPCR with small-molecule and cyclic peptide antagonists

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Dimerization of G-protein-coupled receptors.

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Prediction of interfaces for oligomerizations of G-protein coupled receptors.

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Protein-protein interactions: modeling the hepatitis C virus ion channel p7.

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Modelling of full-length human alpha4beta2 nicotinic receptor by fragmental approach and analysis of its binding modes

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Homodimerization of neurotensin 1 receptor involves helices 1, 2, and 4: insights from quaternary structure predictions and dimerization free energy estimations

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Computational study of the heterodimerization between mu and delta receptors.

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Molecular dynamics simulation of the heterodimeric mGluR2/5HT(2A) complex. An atomistic resolution study of a potential new target in psychiatric conditions.

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Computer analysis of protein-protein interaction

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Reaction pathway for the quaternary structure change in hemoglobin

21 January 2018

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3D-Garden: a system for modelling protein-protein complexes based on conformational refinement of ensembles generated with the marching cubes algorithm.

21 January 2018

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

21 January 2018

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Recent Progress and Future Directions in Protein-Protein Docking

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

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Quaternary structure predictions of transmembrane proteins starting from the monomer: a docking-based approach

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Dimerization and ligand binding affect the structure network of A(2A) adenosine receptor

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Classification of protein complexes based on docking difficulty.

21 January 2018

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ClusPro: a fully automated algorithm for protein-protein docking

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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Evaluation of protein docking predictions using Hex 3.1 in CAPRI rounds 1 and 2.

21 January 2018

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

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

21 January 2018

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Inference of macromolecular assemblies from crystalline state

21 January 2018

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VMD: visual molecular dynamics

21 January 2018

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The RosettaDock server for local protein-protein docking

21 January 2018

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X-ray structure of a ClC chloride channel at 3.0 A reveals the molecular basis of anion selectivity

21 January 2018

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The E. coli BtuCD structure: a framework for ABC transporter architecture and mechanism

21 January 2018

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Crystal structure of a photoactivated deprotonated intermediate of rhodopsin

21 January 2018

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Crystal structure of the ligand-free G-protein-coupled receptor opsin

21 January 2018

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Structure of the human κ-opioid receptor in complex with JDTic

21 January 2018

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Lipid patches in membrane protein oligomers: crystal structure of the bacteriorhodopsin-lipid complex

21 January 2018

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The Structure of the Potassium Channel: Molecular Basis of K+ Conduction and Selectivity

21 January 2018

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Refined structure of the nicotinic acetylcholine receptor at 4A resolution

21 January 2018

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Structure of the connexin 26 gap junction channel at 3.5 A resolution

21 January 2018

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21 January 2018

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21 January 2018

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21 January 2018

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21 January 2018

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A protein–protein docking algorithm dependent on the type of complexes

21 January 2018

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Achieving reliability and high accuracy in automated protein docking: ClusPro, PIPER, SDU, and stability analysis in CAPRI rounds 13-19

21 January 2018

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https://api.crossref.org/works/10.1002%2FMINF.201200150

The ConSurf-DB: pre-calculated evolutionary conservation profiles of protein structures

21 January 2018

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Structural changes in the L photointermediate of bacteriorhodopsin

21 January 2018

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https://api.crossref.org/works/10.1002%2FMINF.201200150

Principles of docking: An overview of search algorithms and a guide to scoring functions

21 January 2018

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Rhodopsin dimers in native disc membranes

21 January 2018

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21 January 2018

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https://opencitations.net/index/coci/api/v1/references/10.1002/MINF.201200150

G Protein-Coupled Receptors Self-Assemble in Dynamics Simulations of Model Bilayers

8 April 2023

1 reference

https://opencitations.net/index/coci/api/v1/references/10.1002/MINF.201200150

Scoring protein-protein docked structures based on the balance and tightness of binding

8 April 2023

1 reference

https://opencitations.net/index/coci/api/v1/references/10.1002/MINF.201200150

8 April 2023

1 reference

https://opencitations.net/index/coci/api/v1/references/10.1002/MINF.201200150

ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5

8 April 2023

1 reference

https://opencitations.net/index/coci/api/v1/references/10.1002/MINF.201200150

8 April 2023

Identifiers

DOI

10.1002/MINF.201200150

1 reference

12 September 2017

1 reference