MOTIVATION Scoring functions provided by the docking software are still a major limiting factor in virtual screening (VS) process to classify compounds. Score analysis of the docking is not able to find out all active compounds. This is due to a bad estimation of the ligand binding energies. Making the assumption that active compounds should have specific contacts with their target to display a...

Based on the results of several groups using different docking methods, the key properties that determine the expected success rate in protein-protein docking calculations are measures of conformational change, interface area, and hydrophobicity. A classification of protein complexes in terms of these measures provides a prediction of docking difficulty. This classification is used to study the...

BACKGROUND Macromolecular complexes are the molecular machines of the cell. Knowledge at the atomic level is essential to understand and influence their function. However, their number is huge and a significant fraction is extremely difficult to study using classical structural methods such as NMR and X-ray crystallography. Therefore, the importance of large-scale computational approaches in st...

background: tubulin protein being the fundamental unit of microtubules is actively involved in cell division thus making them a potential anti-cancer drug target. in spite of many reported drugs against tubulin, few of them have started developing resistance in human β-tubulin due to amino acid substitutions. methods: in this study we generated three mutants (f270v, a364t and q292e) using model...

Fimbrial adhesion is a Virulence Determinant which is classified under Adhesins category of virulence factor of uropathogenic Escherichia coli. Afimbrial adhesin Protein with swissprot accession number P12730, of length 181 amino was selected for modeling using Bioinformatics tools. Modelled protein has been submitted to protein model database and has been assigned an accession number of PM0075...

Large-scale analyses of protein-protein interactions based on coarse-grain molecular docking simulations and binding site predictions resulting from evolutionary sequence analysis, are possible and realizable on hundreds of proteins with variate structures and interfaces. We demonstrated this on the 168 proteins of the Mintseris Benchmark 2.0. On the one hand, we evaluated the quality of the in...

Protein-protein interfaces (PPIs) are an important class of drug targets. We report on the first large-scale validation study on docking into PPIs. DrugScore-adapted AutoDock3 and Glide showed good success rates with a moderate drop-off compared to docking to "classical targets". An analysis of the binding energetics in a PPI allows identifying those interfaces that are amenable for docking. Th...

Results of a previous docking study are reanalyzed and extended to include results from the docking program FRED and a detailed statistical analysis of both structure reproduction and virtual screening results. FRED is run both in a traditional docking mode and in a hybrid mode that makes use of the structure of a bound ligand in addition to the protein structure to screen molecules. This analy...

We describe a novel method for predicting protein docking conformations using spectral analysis techniques. Rigid-body docking methods based on shape complementarity, particularly Fourier transform based techniques are successful for docking monomers with conformations adopted at binding (complexed conformations) [4]. This approach is very efficient because a complete search over all six degree...