Literature DB >> 18037925

Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go.

N Moitessier1, P Englebienne, D Lee, J Lawandi, C R Corbeil.   

Abstract

Accelerating the drug discovery process requires predictive computational protocols capable of reducing or simplifying the synthetic and/or combinatorial challenge. Docking-based virtual screening methods have been developed and successfully applied to a number of pharmaceutical targets. In this review, we first present the current status of docking and scoring methods, with exhaustive lists of these. We next discuss reported comparative studies, outlining criteria for their interpretation. In the final section, we describe some of the remaining developments that would potentially lead to a universally applicable docking/scoring method.

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Year:  2007        PMID: 18037925      PMCID: PMC2268060          DOI: 10.1038/sj.bjp.0707515

Source DB:  PubMed          Journal:  Br J Pharmacol        ISSN: 0007-1188            Impact factor:   8.739


  182 in total

1.  The consequences of translational and rotational entropy lost by small molecules on binding to proteins.

Authors:  Christopher W Murray; Marcel L Verdonk
Journal:  J Comput Aided Mol Des       Date:  2002-10       Impact factor: 3.686

2.  Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy.

Authors:  Richard A Friesner; Jay L Banks; Robert B Murphy; Thomas A Halgren; Jasna J Klicic; Daniel T Mainz; Matthew P Repasky; Eric H Knoll; Mee Shelley; Jason K Perry; David E Shaw; Perry Francis; Peter S Shenkin
Journal:  J Med Chem       Date:  2004-03-25       Impact factor: 7.446

3.  A method for induced-fit docking, scoring, and ranking of flexible ligands. Application to peptidic and pseudopeptidic beta-secretase (BACE 1) inhibitors.

Authors:  Nicolas Moitessier; Eric Therrien; Stephen Hanessian
Journal:  J Med Chem       Date:  2006-10-05       Impact factor: 7.446

4.  Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes.

Authors:  Richard A Friesner; Robert B Murphy; Matthew P Repasky; Leah L Frye; Jeremy R Greenwood; Thomas A Halgren; Paul C Sanschagrin; Daniel T Mainz
Journal:  J Med Chem       Date:  2006-10-19       Impact factor: 7.446

5.  A new implicit solvent model for protein-ligand docking.

Authors:  Antonio Morreale; Rubén Gil-Redondo; Angel R Ortiz
Journal:  Proteins       Date:  2007-05-15

6.  Docking ligands into flexible and solvated macromolecules. 1. Development and validation of FITTED 1.0.

Authors:  Christopher R Corbeil; Pablo Englebienne; Nicolas Moitessier
Journal:  J Chem Inf Model       Date:  2007-02-17       Impact factor: 4.956

7.  CH/pi interactions in DNA and proteins. A theoretical study.

Authors:  Adrià Gil; Vicenç Branchadell; Joan Bertran; Antoni Oliva
Journal:  J Phys Chem B       Date:  2007-07-11       Impact factor: 2.991

8.  Binding affinities for sulfonamide inhibitors with human thrombin using Monte Carlo simulations with a linear response method.

Authors:  D K Jones-Hertzog; W L Jorgensen
Journal:  J Med Chem       Date:  1997-05-09       Impact factor: 7.446

9.  Flexible ligand docking using a genetic algorithm.

Authors:  C M Oshiro; I D Kuntz; J S Dixon
Journal:  J Comput Aided Mol Des       Date:  1995-04       Impact factor: 3.686

10.  Solvated docking: introducing water into the modelling of biomolecular complexes.

Authors:  Aalt D J van Dijk; Alexandre M J J Bonvin
Journal:  Bioinformatics       Date:  2006-08-09       Impact factor: 6.937

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  101 in total

1.  Exhaustive search and solvated interaction energy (SIE) for virtual screening and affinity prediction.

Authors:  Traian Sulea; Hervé Hogues; Enrico O Purisima
Journal:  J Comput Aided Mol Des       Date:  2011-12-25       Impact factor: 3.686

2.  Substantial improvements in large-scale redocking and screening using the novel HYDE scoring function.

Authors:  Nadine Schneider; Sally Hindle; Gudrun Lange; Robert Klein; Jürgen Albrecht; Hans Briem; Kristin Beyer; Holger Claußen; Marcus Gastreich; Christian Lemmen; Matthias Rarey
Journal:  J Comput Aided Mol Des       Date:  2011-12-27       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

4.  Rapid prediction of solvation free energy. 3. Application to the SAMPL2 challenge.

Authors:  Enrico O Purisima; Christopher R Corbeil; Traian Sulea
Journal:  J Comput Aided Mol Des       Date:  2010-04-06       Impact factor: 3.686

5.  Computational molecular biology approaches to ligand-target interactions.

Authors:  Paola Lupieri; Chuong Ha Hung Nguyen; Zhaleh Ghaemi Bafghi; Alejandro Giorgetti; Paolo Carloni
Journal:  HFSP J       Date:  2009-03-10

6.  Improved ligand-protein binding affinity predictions using multiple binding modes.

Authors:  Eva Stjernschantz; Chris Oostenbrink
Journal:  Biophys J       Date:  2010-06-02       Impact factor: 4.033

7.  pK(a) based protonation states and microspecies for protein-ligand docking.

Authors:  Tim ten Brink; Thomas E Exner
Journal:  J Comput Aided Mol Des       Date:  2010-09-30       Impact factor: 3.686

8.  Lithocholic acid is an endogenous inhibitor of MDM4 and MDM2.

Authors:  Simon M Vogel; Matthias R Bauer; Andreas C Joerger; Rainer Wilcken; Tobias Brandt; Dmitry B Veprintsev; Trevor J Rutherford; Alan R Fersht; Frank M Boeckler
Journal:  Proc Natl Acad Sci U S A       Date:  2012-10-03       Impact factor: 11.205

9.  Rigid Body Energy Minimization on Manifolds for Molecular Docking.

Authors:  Hanieh Mirzaei; Dmitri Beglov; Ioannis Ch Paschalidis; Sandor Vajda; Pirooz Vakili; Dima Kozakov
Journal:  J Chem Theory Comput       Date:  2012-08-21       Impact factor: 6.006

10.  Structure-based predictions of activity cliffs.

Authors:  Jarmila Husby; Giovanni Bottegoni; Irina Kufareva; Ruben Abagyan; Andrea Cavalli
Journal:  J Chem Inf Model       Date:  2015-05-11       Impact factor: 4.956

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