(Q31109061)

16 October 2017

Using RosettaLigand for small molecule docking into comparative models (English)

1 reference

16 October 2017

2

1 reference

28 June 2017

Kristian W Kaufmann

1

1 reference

PMCID

3519832

16 October 2017

language of work or name

English

0 references

publication date

11 December 2012

1 reference

16 October 2017

1 reference

16 October 2017

7

1 reference

16 October 2017

12

1 reference

16 October 2017

e50769

1 reference

Creative Commons Attribution 4.0 International

16 October 2017

start time

11 December 2012

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

NNScore 2.0: a neural-network receptor-ligand scoring function

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3519832

Design and directed evolution of a dideoxy purine nucleoside phosphorylase

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3519832

A machine learning approach to predicting protein-ligand binding affinity with applications to molecular docking

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3519832

Practically useful: what the Rosetta protein modeling suite can do for you

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3519832

Molecular docking screens using comparative models of proteins

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3519832

Q-Dock(LHM): Low-resolution refinement for ligand comparative modeling.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3519832

I-TASSER: fully automated protein structure prediction in CASP8

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3519832

Assessment of the protein-structure refinement category in CASP8

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3519832

Structure prediction for CASP8 with all-atom refinement using Rosetta.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3519832

Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3519832

Target domain definition and classification in CASP8

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3519832

Computational fragment-based binding site identification by ligand competitive saturation

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3519832

Blind docking of pharmaceutically relevant compounds using RosettaLigand

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3519832

Identifying and characterizing binding sites and assessing druggability

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3519832

SITEHOUND-web: a server for ligand binding site identification in protein structures.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3519832

Structural determinants of species-selective substrate recognition in human and Drosophila serotonin transporters revealed through computational docking studies

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3519832

Q-Dock: Low-resolution flexible ligand docking with pocket-specific threading restraints

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3519832

Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3519832

Clustal W and Clustal X version 2.0

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3519832

Assessing the energy landscape of CAPRI targets by FunHunt

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3519832

Evaluation of the utility of homology models in high throughput docking

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3519832

A critical assessment of docking programs and scoring functions

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3519832

Protein-ligand docking: current status and future challenges

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3519832

MUSTANG: a multiple structural alignment algorithm.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3519832

A comparative study of available software for high-accuracy homology modeling: from sequence alignments to structural models

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3519832

Physically realistic homology models built with ROSETTA can be more accurate than their templates

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3519832

Screening drug-like compounds by docking to homology models: a systematic study.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3519832

Toward high-resolution de novo structure prediction for small proteins.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3519832

Announcing the worldwide Protein Data Bank

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3519832

Design of a Novel Globular Protein Fold with Atomic-Level Accuracy

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3519832

A review of protein-small molecule docking methods

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3519832

A geometric approach to macromolecule-ligand interactions

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3519832

The relation between the divergence of sequence and structure in proteins

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3519832

The Protein Data Bank. A computer-based archival file for macromolecular structures

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3519832

Protein-ligand docking against non-native protein conformers

14 July 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0050769

Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0050769

The basic concepts of molecular modeling.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0050769

ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0050769

RosettaLigand docking with full ligand and receptor flexibility.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0050769

Effects of protein conformation in docking: improved pose prediction through protein pocket adaptation

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0050769

Computational drug design accommodating receptor flexibility: the relaxed complex scheme

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0050769

Bio3d: an R package for the comparative analysis of protein structures.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0050769

10.1371/JOURNAL.PONE.0050769

21 January 2018

Identifiers

DOI

1 reference

16 October 2017

0 references

1 reference

16 October 2017

1 reference

PMCID

3519832