(Q37684662)

22 August 2017

Performance of ZDOCK in CAPRI rounds 20-26. (English)

1 reference

22 August 2017

1

Thom Vreven

1 reference

22 August 2017

Brian G Pierce

2

1 reference

22 August 2017

Howook Hwang

series ordinal

3

1 reference

22 August 2017

Zhiping Weng

series ordinal

4

1 reference

22 August 2017

language of work or name

English

0 references

publication date

1 December 2013

1 reference

22 August 2017

1 reference

22 August 2017

81

1 reference

22 August 2017

12

1 reference

22 August 2017

2175-2182

1 reference

Blind prediction of interfacial water positions in CAPRI

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3975700

Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3975700

Exploring angular distance in protein-protein docking algorithms

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3975700

Community-wide assessment of protein-interface modeling suggests improvements to design methodology

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3975700

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3975700

Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3975700

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3975700

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3975700

A structure-based benchmark for protein-protein binding affinity

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3975700

ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3975700

Design, production and molecular structure of a new family of artificial alpha-helicoidal repeat proteins (αRep) based on thermostable HEAT-like repeats

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3975700

Structure of a fibronectin type III-like module fromClostridium thermocellum

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3975700

The structural and energetic basis for high selectivity in a high-affinity protein-protein interaction

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3975700

CHARMM: the biomolecular simulation program

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3975700

Antibody recognition of a highly conserved influenza virus epitope

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3975700

Protein structure prediction on the Web: a case study using the Phyre server

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3975700

Structural consequences of effector protein complex formation in a diiron hydroxylase

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3975700

Structure-based design of a T-cell receptor leads to nearly 100-fold improvement in binding affinity for pepMHC.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3975700

Structure and mode of action of a mosquitocidal holotoxin

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3975700

Data-driven docking: HADDOCK's adventures in CAPRI.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3975700

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3975700

CAPRI: a Critical Assessment of PRedicted Interactions

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3975700

A simple physical model for binding energy hot spots in protein-protein complexes

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3975700

High-resolution crystal structures of the lectin-like xylan binding domain from Streptomyces lividans xylanase 10A with bound substrates reveal a novel mode of xylan binding

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3975700

Enhancement of protein modeling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3975700

Comparative protein modelling by satisfaction of spatial restraints

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3975700

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3975700

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3975700

Binding interface prediction by combining protein-protein docking results

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3975700

Prediction of protein-protein binding free energies

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3975700

Performance of ZDOCK and ZRANK in CAPRI rounds 13-19.

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3975700

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

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3975700

Protein-protein docking benchmark version 3.0.

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3975700

A combination of rescoring and refinement significantly improves protein docking performance

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3975700

A holistic approach to protein docking.

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3975700

The performance of ZDOCK and ZRANK in rounds 6-11 of CAPRI.

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3975700

Integrating statistical pair potentials into protein complex prediction.

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3975700

Ranking multiple docking solutions based on the conservation of inter-residue contacts.

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3975700

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

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3975700

Structures of in vitro evolved binding sites on neocarzinostatin scaffold reveal unanticipated evolutionary pathways

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3975700

Prediction of multimolecular assemblies by multiple docking

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3975700

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

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3975700

ZDOCK: an initial-stage protein-docking algorithm.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3975700

ZDOCK predictions for the CAPRI challenge.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3975700

A novel shape complementarity scoring function for protein‐protein docking

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3975700

Prediction of protein interaction sites from sequence profile and residue neighbor list.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3975700

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

1 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24123140

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Structure of T4moC, the Rieske-type ferredoxin component of toluene 4-monooxygenase

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24123140

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Redox and functional analysis of the Rieske ferredoxin component of the toluene 4-monooxygenase

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24123140

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1002/PROT.24432

1 reference

22 August 2017

1 reference

22 August 2017

PubMed publication ID

24123140

1 reference