Knowledge-Based Conformer Generation Using the Cambridge Structural Database

被引：51

作者：

Cole, Jason C. ^{[1
]}

Korb, Oliver ^{[1
]}

McCabe, Patrick ^{[1
]}

Read, Murray G. ^{[1
]}

Taylor, Robin ^{[1
]}

机构：

[1] Cambridge Crystallog Data Ctr, 12 Union Rd, Cambridge CB1 1EZ, England

来源：

JOURNAL OF CHEMICAL INFORMATION AND MODELING | 2018年 / 58卷 / 03期

关键词：

CRYSTAL-STRUCTURES; VALIDATION; PREFERENCES; ALGORITHM; MOLECULES; SPACE; ANGLE;

D O I：

10.1021/acs.jcim.7b00697

中图分类号：

R914 [药物化学];

学科分类号：

100701 ;

摘要：

Fast generation of plausible molecular conformations is central to molecular modeling. This paper presents an approach to conformer generation that makes extensive use of the information available in the Cambridge Structural Database. By using geometric distributions derived from the Cambridge Structural Database, it is possible to create biologically relevant conformations in the majority of cases analyzed. The paper compares the performance of the approach with previously published evaluations, and presents some cases where the method fails. The method appears to show significantly improved performance in reproduction of the conformations of structures observed in the Cambridge Structural Database and the Protein Data Bank as compared to other published methods of a similar speed.

引用

页码：615 / 629

页数：15

共 40 条

[11] Conformational Sampling for Large-Scale Virtual Screening: Accuracy versus Ensemble Size [J].

Griewel, Axel ;

Kayser, Ole ;

Schlosser, Jochen ;

Rarey, Matthias .

JOURNAL OF CHEMICAL INFORMATION AND MODELING, 2009, 49 (10) :2303-2311

[12] The Cambridge Structural Database [J].

Groom, Colin R. ;

Bruno, Ian J. ;

Lightfoot, Matthew P. ;

Ward, Suzanna C. .

ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE CRYSTAL ENGINEERING AND MATERIALS, 2016, 72 :171-179

[13] Conformer Generation with OMEGA: Learning from the Data Set and the Analysis of Failures [J].

Hawkins, Paul C. D. ;

Nicholls, Anthony .

JOURNAL OF CHEMICAL INFORMATION AND MODELING, 2012, 52 (11) :2919-2936

[14] Conformer Generation with OMEGA: Algorithm and Validation Using High Quality Structures from the Protein Databank and Cambridge Structural Database [J].

Hawkins, Paul C. D. ;

Skillman, A. Geoffrey ;

Warren, Gregory L. ;

Ellingson, Benjamin A. ;

Stahl, Matthew T. .

JOURNAL OF CHEMICAL INFORMATION AND MODELING, 2010, 50 (04) :572-584

[15] ZINC: A Free Tool to Discover Chemistry for Biology [J].

Irwin, John J. ;

Sterling, Teague ;

Mysinger, Michael M. ;

Bolstad, Erin S. ;

Coleman, Ryan G. .

JOURNAL OF CHEMICAL INFORMATION AND MODELING, 2012, 52 (07) :1757-1768

[16] Use of Crystal Structure Informatics for Defining the Conformational Space Needed for Predicting Crystal Structures of Pharmaceutical Molecules [J].

Iuzzolino, Luca ;

Reilly, Anthony M. ;

McCabe, Patrick ;

Price, Sarah L. .

JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2017, 13 (10) :5163-5171

[17] The PDB_REDO server for macromolecular structure model optimization [J].

Joosten, Robbie P. ;

Long, Fei ;

Murshudov, Garib N. ;

Perrakis, Anastassis .

IUCRJ, 2014, 1 :213-220

[18] PDB_REDO: constructive validation, more than just looking for errors [J].

Joosten, Robbie P. ;

Joosten, Krista ;

Murshudov, Garib N. ;

Perrakis, Anastassis .

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2012, 68 :484-496

[19] Re-refinement from deposited X-ray data can deliver improved models for most PDB entries [J].

Joosten, Robbie P. ;

Womack, Thomas ;

Vriend, Gert ;

Bricogne, Gerard .

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2009, 65 :176-185

[20] BCL::CONF: small molecule conformational sampling using a knowledge based rotamer library [J].

Kothiwale, Sandeepkumar ;

Mendenhall, Jeffrey L. ;

Meiler, Jens .

JOURNAL OF CHEMINFORMATICS, 2015, 7

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