A new program named "DARWIN" has been developed to perform docking calculations with proteins and other biological molecules. The program uses the Genetic Algorithm to optimize the molecule's conformation and orientation under the selective pressure of minimizing the potential energy of the complex. A unique feature of DARWIN is that it communicates with the molecular mechanics program CHARMM t...

Phthalate esters are ubiquitous environmental contaminants that interact with peroxisome proliferator-activated receptors (PPARs), a family of nuclear receptors. Molecular docking and free energy calculations were performed in an effort to identify novel phthalate ligands of PPARgamma, a subtype expressed in a wide range of human tissues. The method was validated using several agonists and part...

PVM and other distributed computing systems have enabled the use of networks of workstations for parallel computation, but their approach of treating all networks as collections of point-to-point connections does not promote e cient communication|particularly collective communication. The E cient Collective Operations package (ECO) contains programs which solve this problem by analyzing the net...

Intrinsically disordered proteins (IDPs) are notoriously challenging to study both experimentally and computationally. The structure of IDPs cannot be described by a single conformation but must instead be described as an ensemble of interconverting conformations. Atomistic simulations are increasingly used to obtain such IDP conformational ensembles. Here, we have compared the IDP ensembles ge...

Many signaling events require the binding of cytoplasmic proteins to cell membranes by recognition of specific charged lipids, such as phosphoinositol-phosphates. As a model for a protein-membrane binding site, we consider one charged phosphoinositol phosphate (PtdIns(3)P) embedded in a phosphatidylcholine bilayer. As the protein-membrane binding is driven by electrostatic interactions, continu...

A fast stable finite difference Poisson-Boltzmann (FDPB) model for implicit solvation in molecular dynamics simulations was developed using the smooth permittivity FDPB method implemented in the OpenEye ZAP libraries. This was interfaced with two widely used molecular dynamics packages, AMBER and CHARMM. Using the CHARMM-ZAP software combination, the implicit solvent model was tested on eight p...

In this paper, the second-order hydrophobic moment for fifteen globular proteins in 150 nonhomologous protein chains was performed in a comparative study involving two sets of hydrophobicity: one selected from the consensus scale and the other derived from the CHARMM partial atomic charges. These proteins were divided into three groups, based on their number of residues (N) and the asphericity ...