Journal ArticleDOI
Evaluation of the CASP2 docking section
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TLDR
The docking section of CASP2 is reviewed, finding no single docking method seemed to consistently perform best and the predictions closest to the experimental results were not always those ranked the highest, pointing out that the evaluation of potential solutions is still an area that needs improvement.Abstract:
The docking section of CASP2 is reviewed. Seven small molecule ligand–protein targets and one protein–protein target were available for predictions. Many of the small molecule ligand complexes involved serine proteases. Overall results for the small molecule targets were good, with at least one prediction for each target being within 3 A root-mean-square deviation (RMSD) for nearly all targets and within 2 A RMSD for over half the targets. However, no single docking method seemed to consistently perform best. In addition, the predictions closest to the experimental results were not always those ranked the highest, pointing out that the evaluation (scoring) of potential solutions is still an area that needs improvement. The protein–protein target proved more difficult. None of the predictions did well in reproducing the geometry of the complex, although in many cases the interacting surfaces of the two proteins were predicted with reasonable accuracy. This target consisted of two large proteins and, therefore was a demanding target for docking methods. Proteins, Suppl. 1:198–204, 1997. © 1998 Wiley-Liss, Inc.read more
Citations
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Journal ArticleDOI
Knowledge-based scoring function to predict protein-ligand interactions
TL;DR: The development and validation of a new knowledge-based scoring function (DrugScore) to describe the binding geometry of ligands in proteins is presented and is superior to the "chemical scoring" implemented into this tool, while comparable results are obtained using the "energy scoring" in DOCK.
Journal ArticleDOI
Evaluation of the FLEXX incremental construction algorithm for protein-ligand docking.
TL;DR: A test of FLEXX, a fully automatic docking tool for flexible ligands, on a highly diverse data set of 200 protein–ligand complexes from the Protein Data Bank, finds that 46.5% of the complexes of the data set can be reproduced by a FLE XX docking solution at rank 1 with an rms deviation from the observed structure.
Journal ArticleDOI
Software for molecular docking: a review
TL;DR: Docking against homology-modeled targets also becomes possible for proteins whose structures are not known, and the druggability of the compounds and their specificity against a particular target can be calculated for further lead optimization processes.
Journal ArticleDOI
Protein-based virtual screening of chemical databases. 1. Evaluation of different docking/scoring combinations.
TL;DR: A two-step protocol for screening large databases is proposed: screening of a reduced dataset containing a few known ligands for deriving the optimal docking/consensus scoring scheme and applying the latter parameters to the screening of the entire database.
Journal ArticleDOI
CAPRI: A Critical Assessment of PRedicted Interactions
Joël Janin,Kim Henrick,John Moult,Lynn F. Ten Eyck,Michael J.E. Sternberg,Sandor Vajda,Ilya A. Vakser,Shoshana J. Wodak +7 more
TL;DR: The motivations for launching CAPRI, the rules that were applied to select targets and run the experiment, the results stress the need for new scoring functions and for methods handling the conformation changes that were observed in some of the target systems, and some conclusions can already be drawn.
References
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Journal ArticleDOI
A Fast Flexible Docking Method using an Incremental Construction Algorithm
TL;DR: This work presents an automatic method for docking organic ligands into protein binding sites that combines an appropriate model of the physico-chemical properties of the docked molecules with efficient methods for sampling the conformational space of the ligand.
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ICM—a new method for protein modeling and design: applications to docking and structure prediction from the distorted native conformation
TL;DR: It is concluded that the most promising detailed approach to the protein‐folding problem would consist of some coarse global sampling strategy combined with the local energy minimization in the torsion coordinate space.
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Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques.
Ephraim Katchalski-Katzir,I. Shariv,Miriam Eisenstein,Asher A. Friesem,Claude Aflalo,Ilya A. Vakser +5 more
TL;DR: A geometric recognition algorithm was developed to identify molecular surface complementarity and was tested and validated by using five known complexes for which the correct relative position of the molecules in the respective adducts was successfully predicted.
Journal ArticleDOI
Modelling protein docking using shape complementarity, electrostatics and biochemical information
TL;DR: A protein docking study was performed for two classes of biomolecular complexes: six enzyme/inhibitor and four antibody/antigen and tested the native rather than the complexed forms of the proteins to address the more scientifically interesting problem of predictive docking.
Journal ArticleDOI
Computational methods for biomolecular docking
Thomas Lengauer,Matthias Rarey +1 more
TL;DR: Methods for computer-aided molecular docking have to include a reasonably accurate model of energy and must be able to deal with the combinatorial complexity incurred by the molecular flexibility of the docking partners.