(Q30494222)

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Conformer generation with OMEGA: algorithm and validation using high quality structures from the Protein Databank and Cambridge Structural Database

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scholarly article

1 reference

Europe PubMed Central

PMC publication ID

18 September 2017

Conformer generation with OMEGA: algorithm and validation using high quality structures from the Protein Databank and Cambridge Structural Database (English)

1 reference

Europe PubMed Central

PMC publication ID

18 September 2017

0 references

Cambridge Structural Database

0 references

Paul C. D. Hawkins

1

object named as

Paul C D Hawkins

1 reference

Europe PubMed Central

PMC publication ID

18 September 2017

author name string

A Geoffrey Skillman

2

1 reference

Europe PubMed Central

PMC publication ID

18 September 2017

Gregory L Warren

3

1 reference

Europe PubMed Central

PMC publication ID

18 September 2017

Benjamin A Ellingson

4

1 reference

Europe PubMed Central

PMC publication ID

18 September 2017

Matthew T Stahl

5

1 reference

Europe PubMed Central

PMC publication ID

18 September 2017

publication date

1 April 2010

1 reference

Europe PubMed Central

PMC publication ID

18 September 2017

Journal of Chemical Information and Modeling

1 reference

Europe PubMed Central

PMC publication ID

18 September 2017

50

1 reference

Europe PubMed Central

PMC publication ID

18 September 2017

4

1 reference

Europe PubMed Central

PMC publication ID

18 September 2017

572-584

1 reference

Europe PubMed Central

PMC publication ID

18 September 2017

Conformational sampling of druglike molecules with MOE and catalyst: implications for pharmacophore modeling and virtual screening

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859685

20 June 2018

Free R value: a novel statistical quantity for assessing the accuracy of crystal structures

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859685

20 June 2018

How to do an evaluation: pitfalls and traps

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859685

20 June 2018

Small molecule conformational preferences derived from crystal structure data. A medicinal chemistry focused analysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859685

20 June 2018

Frog: a FRee Online druG 3D conformation generator.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859685

20 June 2018

Conformational sampling of bioactive molecules: a comparative study

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859685

20 June 2018

A critical assessment of docking programs and scoring functions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859685

20 June 2018

The PDBbind database: methodologies and updates

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859685

20 June 2018

Comparing protein-ligand docking programs is difficult.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859685

20 June 2018

Refinement of macromolecular structures by the maximum-likelihood method

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859685

20 June 2018

Comparison of knowledge-based and distance geometry approaches for generation of molecular conformations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859685

20 June 2018

Validation of protein crystal structures

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859685

20 June 2018

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859685

20 June 2018

Remarks about protein structure precision

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859685

20 June 2018

Distributed torsion angle grid search in high dimensions: a systematic approach to NMR structure determination

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859685

20 June 2018

Contact area difference (CAD): a robust measure to evaluate accuracy of protein models

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859685

20 June 2018

Flexibases: a way to enhance the use of molecular docking methods

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859685

20 June 2018

Improved methods for building protein models in electron density maps and the location of errors in these models

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859685

20 June 2018

ASEDock-docking based on alpha spheres and excluded volumes.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859685

26 November 2018

Generating conformer ensembles using a multiobjective genetic algorithm

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859685

26 November 2018

CAESAR: a new conformer generation algorithm based on recursive buildup and local rotational symmetry consideration

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859685

26 November 2018

Diverse, high-quality test set for the validation of protein-ligand docking performance.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859685

26 November 2018

Lingos, finite state machines, and fast similarity searching.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859685

26 November 2018

Comparative performance assessment of the conformational model generators omega and catalyst: a large-scale survey on the retrieval of protein-bound ligand conformations.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859685

26 November 2018

Ph4Dock: pharmacophore-based protein-ligand docking

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859685

26 November 2018

Conformational analysis of drug-like molecules bound to proteins: an extensive study of ligand reorganization upon binding

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859685

26 November 2018

Conformational analysis by intersection: CONAN.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859685

26 November 2018

Rearrangement of Cruickshank's formulae for the diffraction-component precision index.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859685

26 November 2018

An Alternative Method for the Evaluation of Docking Performance: RSR vs RMSD

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859685

26 November 2018

MIMUMBA revisited: torsion angle rules for conformer generation derived from X-ray structures

1 reference

https://pubmed.ncbi.nlm.nih.gov/20235588

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Assessing the performance of OMEGA with respect to retrieving bioactive conformations

1 reference

https://pubmed.ncbi.nlm.nih.gov/20235588

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Comparison of Conformational Analysis Techniques To Generate Pharmacophore Hypotheses Using Catalyst

1 reference

https://pubmed.ncbi.nlm.nih.gov/20235588

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Torsion angle preference and energetics of small-molecule ligands bound to proteins

1 reference

https://pubmed.ncbi.nlm.nih.gov/20235588

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1021/CI100031X

1 reference

Europe PubMed Central

PMC publication ID

18 September 2017

DBLP publication ID

journals/jcisd/HawkinsSWES10

1 reference

DBLP Dataset 2021-01-02

28 January 2021

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

18 September 2017

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

18 September 2017

ResearchGate publication ID

0 references

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