Molecular docking is an efficient method to predict the conformations adopted by the ligand within the target binding site. Usually, standard docking protocol involves only one structure to represent the receptor, overlooking the changes in the binding pocket geometry induced by ligand binding. In our previous work, we observed that different conformations of the same target show different volu...

This paper proposes an integrated network design model for a post-distribution cross-docking strategy, comprising multi product production facilities with shared production resources, capacitated cross docks with setup cost and customer zones with time windows constraints. The model is dynamic in terms of time-varying uncertain demands, whereas uncertainty is expressed with scenario approach an...

We compared the performance of template-free (docking) and template-based methods for the prediction of protein-protein complex structures. We found similar performance for a template-based method based on threading (COTH) and another template-based method based on structural alignment (PRISM). The template-based methods showed similar performance to a docking method (ZDOCK) when the latter was...

We present an evaluation of our protein-protein docking approach using the ZDOCK and ZRANK algorithms, in combination with structural clustering and filtering, utilizing biological data in Rounds 6-11 of the CAPRI docking experiment. We achieved at least one prediction of acceptable accuracy for five of six targets submitted. In addition, two targets resulted in medium-accuracy predictions. In ...

Docking simulates molecular interactions. Protein protein docking, owing to the sizes of molecules, is a very challenging problem. As the number of degrees of freedom in the molecular structure of proteins is huge, docking algorithms consider the molecules as relatively rigid bodies. Shape matching of two protein molecules is computationally difficult because the possibilities of matching the m...

Near-native selections from docking decoys have proved challenging especially when unbound proteins are used in the molecular docking. One reason is that significant atomic clashes in docking decoys lead to poor predictions of binding affinities of near native decoys. Atomic clashes can be removed by structural refinement through energy minimization. Such an energy minimization, however, will l...

A message passing interface (MPI)-based implementation (Autodock4.lga.MPI) of the grid-based docking program Autodock4 has been developed to allow simultaneous and independent docking of multiple compounds on up to thousands of central processing units (CPUs) using the Lamarkian genetic algorithm. The MPI version reads a single binary file containing precalculated grids that represent the prote...

Microelectromechanical system (MEMS) technology promises to improve performance of future spacecraft components while reducing mass, cost, and manufacturing time. Arrays of microcilia actuators offer a lightweight alternative to conventional docking systems for miniature satellites. Instead of mechanical guiding structures, such a system uses a surface tiled with MEMS cilia actuators to guide t...

We present a new strategy, called dual-template docking oriented molecular imprinting (DTD-OMI), for facile and highly efficient imprinting within mesoporous materials. As compared with bulk imprinting, which is a widely used strategy, DTD-OMI did not require additional steps, but provided significantly improved imprinting efficiency and binding properties.

human immunodeficiency virus infection / acquired immunodeficiency syndrome (hiv/aids) is a disease pertained to the human immune system. given its crucial role in viral replication, hiv-1 protease (hiv-1 pr) is a prime therapeutic target in aids therapy. in this regard, the dynamic aspects of ligand-enzyme interactions may indicate an important role of conformational variability in hiv-1 pr in...