Motivation Large-scale computational docking will be increasingly used in future years to discriminate protein-protein interactions at the residue resolution. Complete cross-docking experiments make in silico reconstruction of protein-protein interaction networks a feasible goal. They ask for efficient and accurate screening of the millions structural conformations issued by the calculations. ...

This study details the separate analyses of binding specificity of HIV-1 integrase (IN) and viral B-DNA forms through ligand-receptor docking studies by means of a fast molecular docking method. The application of solvated electrostatics with the University of Houston Brownian Dynamics Program (UHBD) and configurational sampling by the Daughter of Turnip (DOT) docking program resulted in the co...

Multinational companies frequently work with manufacturers that receive large orders for different products (or product varieties: size, shape, color, texture, material), to serve thousands of final destinations (e.g., shops) requesting a combination quantities each product. It is not the manufacturers’ task create individual shipments destination. But can deliver part their production in so-ca...

This paper studies the integration of vehicle routing problem with cross-docking (VRPCD). The aim is to find a set routes deliver products from suppliers customers through cross-dock facility, such that operational and transportation costs are minimized, without violating capacity time horizon constraints. A two-phase matheuristic based on column generation proposed. first phase focuses generat...

MDM2 is a negative regulator of p53 activity and an important target for cancer therapeutics. The N-terminal lid region of MDM2 modulates interactions with p53 via competition for its binding cleft, exchanging slowly between docked and undocked conformations in the absence of p53. To better understand these dynamics, we constructed Markov State Models (MSMs) from large collections of unbiased s...

Cells are interactive living systems where proteins movements, interactions and regulation are substantially free from centralized management. How protein physico-chemical and geometrical properties determine who interact with whom remains far from fully understood. We show that characterizing how a protein behaves with many potential interactors in a complete cross-docking study leads to a sha...

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...