Literature DB >> 12574069

Molecular recognition and docking algorithms.

Natasja Brooijmans1, Irwin D Kuntz.   

Abstract

Molecular docking is an invaluable tool in modern drug discovery. This review focuses on methodological developments relevant to the field of molecular docking. The forces important in molecular recognition are reviewed and followed by a discussion of how different scoring functions account for these forces. More recent applications of computational chemistry tools involve library design and database screening. Last, we summarize several critical methodological issues that must be addressed in future developments.

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Year:  2003        PMID: 12574069     DOI: 10.1146/annurev.biophys.32.110601.142532

Source DB:  PubMed          Journal:  Annu Rev Biophys Biomol Struct        ISSN: 1056-8700


  139 in total

1.  Robust scoring functions for protein-ligand interactions with quantum chemical charge models.

Authors:  Jui-Chih Wang; Jung-Hsin Lin; Chung-Ming Chen; Alex L Perryman; Arthur J Olson
Journal:  J Chem Inf Model       Date:  2011-10-07       Impact factor: 4.956

2.  Gaussian mapping of chemical fragments in ligand binding sites.

Authors:  Kun Wang; Marta Murcia; Pere Constans; Carlos Pérez; Angel R Ortiz
Journal:  J Comput Aided Mol Des       Date:  2004-02       Impact factor: 3.686

3.  Integrating computational and mixture-based screening of combinatorial libraries.

Authors:  Austin B Yongye; Clemencia Pinilla; Jose L Medina-Franco; Marc A Giulianotti; Colette T Dooley; Jon R Appel; Adel Nefzi; Thomas Scior; Richard A Houghten; Karina Martínez-Mayorga
Journal:  J Mol Model       Date:  2010-09-21       Impact factor: 1.810

4.  Chemical space sampling by different scoring functions and crystal structures.

Authors:  Natasja Brooijmans; Christine Humblet
Journal:  J Comput Aided Mol Des       Date:  2010-04-18       Impact factor: 3.686

5.  Scoring and lessons learned with the CSAR benchmark using an improved iterative knowledge-based scoring function.

Authors:  Sheng-You Huang; Xiaoqin Zou
Journal:  J Chem Inf Model       Date:  2011-08-31       Impact factor: 4.956

Review 6.  Asparagine synthetase chemotherapy.

Authors:  Nigel G J Richards; Michael S Kilberg
Journal:  Annu Rev Biochem       Date:  2006       Impact factor: 23.643

7.  Efficient molecular docking of NMR structures: application to HIV-1 protease.

Authors:  Sheng-You Huang; Xiaoqin Zou
Journal:  Protein Sci       Date:  2006-11-22       Impact factor: 6.725

8.  Benchmarking sets for molecular docking.

Authors:  Niu Huang; Brian K Shoichet; John J Irwin
Journal:  J Med Chem       Date:  2006-11-16       Impact factor: 7.446

9.  Iterative Knowledge-Based Scoring Functions Derived from Rigid and Flexible Decoy Structures: Evaluation with the 2013 and 2014 CSAR Benchmarks.

Authors:  Chengfei Yan; Sam Z Grinter; Benjamin Ryan Merideth; Zhiwei Ma; Xiaoqin Zou
Journal:  J Chem Inf Model       Date:  2015-10-01       Impact factor: 4.956

10.  Inclusion of solvation and entropy in the knowledge-based scoring function for protein-ligand interactions.

Authors:  Sheng-You Huang; Xiaoqin Zou
Journal:  J Chem Inf Model       Date:  2010-02-22       Impact factor: 4.956

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