(Q33988409)

30 July 2017

title

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

1 reference

30 July 2017

Brian D Weitzner

3

0 references

Jeffrey J. Gray

object named as

Jeffrey J Gray

6

0 references

author name string

Sidhartha Chaudhury

1

1 reference

30 July 2017

Monica Berrondo

2

1 reference

30 July 2017

Pravin Muthu

4

1 reference

30 July 2017

Hannah Bergman

5

1 reference

30 July 2017

language of work or name

English

0 references

publication date

2 August 2011

1 reference

30 July 2017

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30 July 2017

volume

6

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30 July 2017

issue

8

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30 July 2017

page(s)

e22477

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Creative Commons Attribution 4.0 International

30 July 2017

copyright license

start time

2 August 2011

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149062

RosettaScripts: a scripting language interface to the Rosetta macromolecular modeling suite

5 July 2018

1 reference

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149062

Mechanism of polyubiquitin chain recognition by the human ubiquitin conjugating enzyme Ube2g2

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149062

Rosetta in CAPRI rounds 13-19.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149062

A generalized approach to sampling backbone conformations with RosettaDock for CAPRI rounds 13-19

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149062

Computational predictions of the mutant behavior of AraC.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149062

SnugDock: paratope structural optimization during antibody-antigen docking compensates for errors in antibody homology models

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149062

PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta

5 July 2018

1 reference

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Identification of structural mechanisms of HIV-1 protease specificity using computational peptide docking: implications for drug resistance

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149062

Emergence of symmetry in homooligomeric biological assemblies.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149062

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149062

Protein-protein docking benchmark version 3.0.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149062

A combination of rescoring and refinement significantly improves protein docking performance

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149062

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149062

Protein-Protein Docking Benchmark 2.0: an update

5 July 2018

1 reference

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CAPRI rounds 3-5 reveal promising successes and future challenges for RosettaDock

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149062

Improved side-chain modeling for protein-protein docking

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149062

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149062

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149062

Mechanism of coenzyme recognition and binding revealed by crystal structure analysis of ferredoxin-NADP+ reductase complexed with NADP+

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149062

Crystallographic studies of the interaction between the ferredoxin-NADP+ reductase and ferredoxin from the cyanobacterium Anabaena: looking for the elusive ferredoxin molecule

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149062

5 July 2018

The Protein Data Bank

1 reference

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Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149062

Blind predictions of protein interfaces by docking calculations in CAPRI.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149062

Docking and scoring protein interactions: CAPRI 2009

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149062

Sub-angstrom modeling of complexes between flexible peptides and globular proteins.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149062

RosettaLigand docking with full ligand and receptor flexibility.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149062

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

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149062

Protein-protein docking with backbone flexibility.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149062

Modeling the structure of mAb 14B7 bound to the anthrax protective antigen.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149062

Structural model of the mAb 806-EGFR complex using computational docking followed by computational and experimental mutagenesis.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149062

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

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149062

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

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149062

10.1371/JOURNAL.PONE.0022477

29 October 2018

Identifiers

DOI

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30 July 2017

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1 reference

30 July 2017

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