biskit -
9999 (This is a sample skeleton ebuild file)
ce -
20040716 (3-D protein structure comparison and alignment using the Combinatorial Extension (CE) method)
foldx-bin -
2.5.2 (A force field for energy calculations in proteins)
jalview -
2.3 (This is a sample skeleton ebuild file)
mmult -
1.0 (MAtching Molecular Models Obtained from THeory)
probalign -
1.3_beta (Probalign uses partition function posterior probability estimates to compute maximum expected accuracy multiple sequence alignments)
sap -
1.0.0 (Pairwise protein structure alignment via double dynamic programming)
surfaceracer -
5.0 (Calculates exact accessible surface area, molecular surface area and average curvature of molecular surface for macromolecules)
openbabel -
2.2.1-r1 (interconverts file formats used in molecular modeling)
pmb -
20060606 (Automated structure refinement tools for CNS)
prekin -
6.42.060120 (Prepares molecular kinemages (input files for Mage and KiNG) from PDB-format coordinate files)
profit -
2.5.3.1 (Designed to be the ultimate protein least squares fitting program)
pymss -
0.8.4 (Multiple superposition of proteins, using a genetic algorithm for optimization)
pyrx -
0.3 (GUI for Virtual Screening with AutoDock)
qutemol -
0.4 (High quality molecular visualization system that exploits GPU capabilites through OpenGL shaders)
rasmol -
2.7.4.2 (Free program that displays molecular structure.)
shelx -
20060317-r1 (Programs for crystal structure determination from single-crystal diffraction data)
solve-resolve-bin -
2.13 (Automated crystallographic structure solution for MIR, SAD, and MAD)
theseus -
1.4.3 (Maximum likelihood superpositioning and analysis of macromolecular structures)
tinker -
4.2-r1 (TINKER is a molecular modeling package that includes force fields for handing large molecules and large systems, such as AMBER and CHARMM. A Java based visualization front end is included.)
usf-rave-bin -
0.1 (The tools package from USF for macromolecular crystallography)
usf-voidoo-bin -
0.1 (The tools package from USF for macromolecular crystallography)
zodiac -
0.5 (Software for molecular modelling - computer-aided drug design)
abinit -
5.7.3 (Find total energy, charge density and electronic structure using density functional theory)
ape -
1.0.1 (DFT atomic program and pseudo-potential generator)
campos-asap -
2.14 (ASAP is a calculator for campos-ase, implementing the Effective Medium Potential)
campos-ase -
3.0.0.657 (The Atomistic Simulation Environment is the core of the CampOS simulation software. There are Python modules for: building atomic structures, molecular dynamics, structure optimization, analysis and much more.)
campos-dacapo -
2.7.7 (Dacapo is a plane-wave based Density Functional Theory program)
campos-gridpaw -
0.4.2734 (Real-spaced implementation of Density Functional Theory with Projector-Augmented Waves)
exciting -
0.9.74 (A full-potential linearised augmented-plane wave (FP-LAPW) code with many advanced features)
octopus -
3.0.0 (A first principles, electronic structure, excited states, time-dependent density functional theory program)