Search Results for "protein"

A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) for Unix, Linux, MacOSX and MS Windows.

PSICOV (Protein Sparse Inverse Covariance estimation program) is a coevoultion algorithm applied to very large (typically >=1000 sequences) multiple sequence alignments for precise protein structural contact prediction. This is the unofficial precompiled Windows binary for PSICOV compiled by Chengxin Zhang at Fudan University. The source code is copyrighted by David T. Jones, University College London.

MDcons is a tool to analyze conserved contacts during Molecular Dynamics (MD) simulations of Protein, Rna, Dna & Ligand based complexes. The input is either a Molecular Dynamics trajectory or a set of snapshots. The input can also be a single snapshot. The outputs are (1) map of most/less frequently conserved contacts during MD (2) a list of most/less frequently conserved contacts during MD.

These are programs from the old BNL Protein Data Bank program tape, reissued under the GPL with the permission of DOE, NIH and NSF and the original authors. Programs will be made visible here only after conversion to modern Fortran.

SMMP (Simple Molecular Mechanics for Proteins) is a program library for protein simulations with an emphasis on advanced Monte Carlo algorithms. It includes various force fields to calculate the energy of a protein and protein-protein interactions.

ProgPorts is an administrative and easy user interface to hundreds of proteomics, molecular dynamics, and protein crystallography programs. It is a hybrid of the prog/setup system, developed at Johns Hopkins University, and GNU-Darwin ports system.

The program consgen takes multiple protein structures in PDB format and aligns them using a modified Procrustes method that aims to maximize residue similarity. The principal result is a consensus structure showing residue conservation.