Software: Proteins - Energy and Properities

The software packages available here are capable of performing various energy-related calculations like single-point energy calculation or local minimization of energy function as well as determining other properties of polypeptides and proteins.  

ANALYZE processes files obtained from calculations using ECEPPAK. These functions include calculations of conformational characteristics (hydrogen bonds, turn position and types, RMS deviation from a reference conformation, interchromophore distances, interproton distances, etc.), calculation of Boltzmann-averaged properties of the conformational ensemble, calculation of the dihedral angles from supplied Cartesian coordinates, and cluster analysis of the conformational ensemble by the minimal spanning tree or minimum-variance method. The program can  also be used for NMR related calculations.
ECEPPAK performs the following calculations: Single Energy Evaluation, Single Energy Minimization, Energy evaluation of Multiple Input Conformations, Energy Minimization of Multiple Input Conformations, Monte Carlo Search using a generalized MCM (EDMC) algorithm, Produce an energy map for a pair of dihedral angles, Carry out an rms deviations analysis, Variable Target Function Procedure for structure determination

The MOIL modeling package can be used to simulate structure, dynamics, and function of biological molecules at the atomic level of detail.

The main application of the PROTARCH package is protein structure prediction. However, the package contains many useful tools for transforming structures to and from united-residue representation, carrying out local minimization of the united-residue energy function (with or without constraints) as well as performing cluster analysis of united-residue proteins.