The modeling of large biomolecular assemblies frequently requires a combination of multi-resolution data from a variety of biophysical sources. Several algorithmic solutions to this docking problem have been proposed which are usually based on the spatial cross correlation. In [1] it was shown that Laplace-filtering techniques can improve the docking performance of these algorithms. This note p...

Trajectory information can be analysed in both the time and space dimensions via a new metric called the M-metric. The M-metric is a measurement definition which quantifies the allocation of control across multiple degrees of freedom. Allocation of control is defined as the product of two components, the simultaneity of control and the efficiency of control, corresponding to the time and space ...

Rescoring is a simple approach that theoretically could improve the original docking results. In this study AutoDock Vina was used as a docked engine and three other scoring functions besides the original scoring function, Vina, as well as their combinations as consensus scoring functions were employed to explore the effect of rescoring on virtual screenings that had been done on diverse target...

Molecular docking studies were carried out against γ-amino butyric acid (GABA) molecular target using Molegro Virtual Docker v 5.0 to accomplish preliminary confirmation of the observed in-vivo anticonvulsant activity. Docking studies have shown that the title compound interact and bind efficiently with 1OHY subunits of γ-amino butyric acid (GABA) enzyme which resulted in anticonvulsant activit...

Accurately ranking docking poses remains a great challenge in computer-aided drug design. In this study, we present an integrated approach called MIEC-SVM that combines structure modeling and statistical learning to characterize protein-ligand binding based on the complex structure generated from docking. Using the HIV-1 protease as a model system, we showed that MIEC-SVM can successfully rank ...

GPCRs are key components of signal transduction pathways and are important drug targets. Recently determined GPCR structures provide opportunities for advancements in GPCR modeling. This review focuses on the choice of experimental templates, the treatment of extracellular loops and the description of ligand-binding sites in GPCR modeling. Four important conclusions are reached in this review: ...

Intermolecular binding underlies every metabolic and regulatory processes of the cell, and the therapeutic and pharmacological properties of drugs. Molecular docking systems model and simulate these interactions in silico and allow us to study the binding process. Haptic-based docking provides an immersive virtual docking environment where the user can interact with and guide the molecules to t...

The success of ligand docking calculations typically depends on the quality of the receptor structure. Given improvements in protein structure prediction approaches, approximate protein models now can be routinely obtained for the majority of gene products in a given proteome. Structure-based virtual screening of large combinatorial libraries of lead candidates against theoretically modeled rec...

The papain/CLIK-148 coordinate system was employed as a model to study the interactions of a nonpeptide thiocarbazate inhibitor of cathepsin L ( 1). This small molecule inhibitor, a thiol ester containing a diacyl hydrazine functionality and one stereogenic center, was most active as the S-enantiomer, with an IC 50 of 56 nM; the R-enantiomer ( 2) displayed only weak activity (33 microM). Corres...

Molecular docking is a simulation technique that aims to predict the binding pose between a ligand and a receptor. The resulting multidimensional continuous optimization problem is practically unsolvable in an exact way. One possible approach is the combination of an optimization algorithm and an objective function that describes the interaction. The software ParaDockS is designed to hold diffe...