Literature DB >> 17696866

Structure-based drug design: docking and scoring.

Romano T Kroemer1.   

Abstract

This review gives an introduction into ligand - receptor docking and illustrates the basic underlying concepts. An overview of different approaches and algorithms is provided. Although the application of docking and scoring has led to some remarkable successes, there are still some major challenges ahead, which are outlined here as well. Approaches to address some of these challenges and the latest developments in the area are presented. Some aspects of the assessment of docking program performance are discussed. A number of successful applications of structure-based virtual screening are described.

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Year:  2007        PMID: 17696866     DOI: 10.2174/138920307781369382

Source DB:  PubMed          Journal:  Curr Protein Pept Sci        ISSN: 1389-2037            Impact factor:   3.272


  72 in total

1.  Conformational analysis of a polyconjugated protein-binding ligand by joint quantum chemistry and polarizable molecular mechanics. Addressing the issues of anisotropy, conjugation, polarization, and multipole transferability.

Authors:  Elodie Goldwaser; Benoit de Courcy; Luc Demange; Christiane Garbay; Françoise Raynaud; Reda Hadj-Slimane; Jean-Philip Piquemal; Nohad Gresh
Journal:  J Mol Model       Date:  2014-11-01       Impact factor: 1.810

2.  Can we really do computer-aided drug design?

Authors:  Matthew Segall
Journal:  J Comput Aided Mol Des       Date:  2011-12-11       Impact factor: 3.686

Review 3.  Flexibility and binding affinity in protein-ligand, protein-protein and multi-component protein interactions: limitations of current computational approaches.

Authors:  Pierre Tuffery; Philippe Derreumaux
Journal:  J R Soc Interface       Date:  2011-10-12       Impact factor: 4.118

Review 4.  From laptop to benchtop to bedside: structure-based drug design on protein targets.

Authors:  Lu Chen; John K Morrow; Hoang T Tran; Sharangdhar S Phatak; Lei Du-Cuny; Shuxing Zhang
Journal:  Curr Pharm Des       Date:  2012       Impact factor: 3.116

5.  Can we use docking and scoring for hit-to-lead optimization?

Authors:  Istvan J Enyedy; William J Egan
Journal:  J Comput Aided Mol Des       Date:  2008-01-09       Impact factor: 3.686

Review 6.  Biomolecular simulation and modelling: status, progress and prospects.

Authors:  Marc W van der Kamp; Katherine E Shaw; Christopher J Woods; Adrian J Mulholland
Journal:  J R Soc Interface       Date:  2008-12-06       Impact factor: 4.118

7.  Further analysis and comparative study of intermolecular interactions using dimers from the S22 database.

Authors:  Laszlo Fusti Molnar; Xiao He; Bing Wang; Kenneth M Merz
Journal:  J Chem Phys       Date:  2009-08-14       Impact factor: 3.488

8.  Docking to RNA via root-mean-square-deviation-driven energy minimization with flexible ligands and flexible targets.

Authors:  Christophe Guilbert; Thomas L James
Journal:  J Chem Inf Model       Date:  2008-05-30       Impact factor: 4.956

9.  Comparative evaluation of several docking tools for docking small molecule ligands to DC-SIGN.

Authors:  Gregor Jug; Marko Anderluh; Tihomir Tomašič
Journal:  J Mol Model       Date:  2015-06-04       Impact factor: 1.810

10.  FINDSITE(comb): a threading/structure-based, proteomic-scale virtual ligand screening approach.

Authors:  Hongyi Zhou; Jeffrey Skolnick
Journal:  J Chem Inf Model       Date:  2012-12-28       Impact factor: 4.956

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