We have developed a geometry-based suite of processes for molecular docking. The suite consists of a molecular surface representation, a docking algorithm, and a surface inter-penetration and contact filter. The surface representation is composed of a sparse set of critical points (with their associated normals) positioned at the face centers of the molecular surface, providing a concise yet re...

Many proteins of widely differing functionality and structure are capable of binding heparin and heparan sulfate. Since crystallizing protein-heparin complexes for structure determination is generally difficult, computational docking can be a useful approach for understanding specific interactions. Previous studies used programs originally developed for docking small molecules to well-defined p...

In order to improve docking score correction, we developed several structure-based quantitative structure activity relationship (QSAR) models by protein-drug docking simulations and applied these models to public affinity data. The prediction models used descriptor-based regression, and the compound descriptor was a set of docking scores against multiple (∼600) proteins including nontargets. Th...

Histone deacetylase inhibitors have gained a great deal of attention recently for the treatment of cancers and inflammatory diseases. So design of new inhibitors is of great importance in pharmaceutical industries and labs. Creating pharmacophor models in order to design new molecules or search a library for finding lead compounds is of great interest. This approach reduces the overall cost ass...

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...

cholera is an acute intestinal infection caused by consuming food or water contaminated with the bacterium vibrio cholerae. two main epidemiological characteristic of disease is tendency for create of sudden outbreaks and the ability to causing a pandemic. the objective of this study is to describe the epidemiology of the disease. this survey is a descriptive cross-sectional study based on repo...

Existing flexible docking approaches model the ligand and receptor flexibility either separately or in a loosely coupled manner, which captures the conformational changes inefficiently. Here, we propose a flexible docking approach, MedusaDock, which models both ligand and receptor flexibility simultaneously with sets of discrete rotamers. We developed an algorithm to build the ligand rotamer li...

The goal of this work was to determine if it is feasible to use Mir/Shuttle docking data to perform Mir damage detection. A time-domain technique called a Remote Sensing System was proposed as an approach. The method uses inverse structural dynamics to identify physical characteristics of a structure which can subsequently be used for damage detection. The RSS method was demonstrated for a nume...

Supply chains are going to evolve by a new technology, which is called the Electronic Product Code (EPC) technology, based on radio frequency identification (RFID). This provides new opportunities in automatic identification that none of previous technologies offered. It also appears to have the potential to enhance Efficient Consumer Response (ECR), which is a grocery industry supply chain man...

This paper presents a multi-objective model for location-transportation problem under uncertainty that has been developed to respond to crisis. In the proposed model, humanitarian aid distribution centers (HADC), the number and location of them, the amount of relief goods stored in distribution centers, the amount of relief goods sent to the disaster zone, the number of injured people transferr...