All packages

ksdssp An open source implementation of sci-chemistry/dssp
mdtraj Read, write and analyze MD trajectories with only a few lines of Python code
pdbcat Manipulate and process PDB files using tools such as Perl, awk, etc
mars Robust automatic backbone assignment of proteins
p3d Python module for structural bioinformatics
mm-align Protein Complex Structural Alignment
tm-align Quick & Accurate Structural Alignment
suitename The ROC RNA Ontology nomenclature and conformer-list development
nmrglue A module for working with NMR data in Python
relax Molecular dynamics by NMR data analysis
MDAnalysis A python library to analyze and manipulate molecular dynamics trajectories
ParmEd Parameter/topology editor and molecular simulator
apbs Evaluation of electrostatic properties of nanoscale biomolecular systems
autodock A suite of automated docking tools
autodock_vina Program for drug discovery, molecular docking and virtual screening
avogadro2 Advanced molecule editor and visualizer 2
elem periodic table of the elements
gnome-chemistry-utils Programs and library containing GTK widgets and C++ classes related to chemistry
gperiodic Periodic table application for Linux
clashlist Build lists of van der Waals clashes from an input PDB file
gromacs The ultimate molecular dynamics simulation package
tinker Molecular modeling package that includes force fields, such as AMBER and CHARMM
votca-csgapps Extra applications for votca-csg
votca-ctp Votca charge transport module
wxmacmolplt Chemical 3D graphics program with GAMESS input builder
xyza2pipe Cross conversion environment of NMR spectra
votca-xtp Votca excitation and charge properties module
aqua Program suite in this distribution calculates restraint violations
molden Display molecular density from GAMESS-UK, GAMESS-US, GAUSSIAN and Mopac/Ampac
moldy Molecular dynamics simulations platform
molequeue Abstract, manage and coordinate execution of tasks
molmol Publication-quality molecular visualization package
pdb2pqr Automated pipeline for performing Poisson-Boltzmann electrostatics calculations
xds-bin Software for processing single-crystal X-ray monochromatic diffraction data
pymol-plugins-bni-tools Gives Pymol additional functionalities and presets to the PyMOL GUI
pymol-plugins-caver Calculation of pathways of proteins from buried cavities to outside solvent
pymol-plugins-dssp DSSP Plugin for PyMOL
pymol-plugins-emovie PyMOL plugin for convinient movie creation
pymol-plugins-promol Fast and accurate regognition of active sites
pymol A Python-extensible molecular graphics system
rasmol Molecular Graphics Visualisation Tool
bkchem Chemical drawing program
bodr The Blue Obelisk Data Repository listing element and isotope properties
cara-bin Analysis of NMR spectra and Computer Aided Resonance Assignment
chemex Program to fit chemical exchange induced shift and relaxation data
chemical-mime-data A collection of data files to add support for chemical MIME types
chemtool A GTK program for drawing organic molecules
probe Evaluates atomic packing within or between molecules
procheck Checks the stereochemical quality of a protein structure
numbat new user-friendly method built for automatic dX-tensor determination
ortep3 Thermal ellipsoid plot program for crystal structure illustrations
pdb-tools Tools for manipulating and calculations on wwPDB macromolecule structure files
povscript+ Modified molscript that uses POV-Ray, does thermal ellipsoids, and more
prekin Prepares molecular kinemages from PDB-format coordinate files
prodecomp Decomposition-based analysis of NMR projections
propka pKa-value prediction of ionizable groups in protein and protein-ligand complexes
psi Suite for ab initio quantum chemistry computing various molecular properties
GromacsWrapper Python framework for Gromacs
cluster Build lists of collections of interacting items
dssp The protein secondary structure standard
easychem Chemical structure drawing program - focused on presentation
eden A crystallographic real-space electron-density refinement & optimization program
freeon An experimental suite of programs for linear scaling quantum chemistry
gelemental Periodic table viewer with detailed information on the chemical elements
gmxapi Gromacs API bindings
molscript Display 3D molecules (e.g., proteins) in schematic and detailed representations
molsketch A drawing tool for 2D molecular structures
mopac7 Autotooled, updated version of a powerful, fast semi-empirical package
mpqc The Massively Parallel Quantum Chemistry Program
msms-bin MSMS very efficiently computes triangulations of Solvent Excluded Surfaces
mustang MUltiple STructural AligNment AlGorithm
namd A powerful and highly parallelized molecular dynamics code
openbabel-perl Perl bindings for OpenBabel
openbabel-python Python bindings for OpenBabel (including Pybel)
openbabel Interconverts file formats used in molecular modeling
pdbcns Convert atom names for amino acids/nucleic acid bases between PDB and CNS format
pdbmat Calculate Tirion's model from pdb structures
raster3d Generation high quality raster images of proteins or other molecules
sparky Graphical NMR assignment and integration program for large polymers
surf Solvent accesible Surface calculator
theseus Maximum likelihood superpositioning and analysis of macromolecular structures
threeV 3V: Voss Volume Voxelator
viewmol Open-source graphical front end for computational chemistry programs
vmd Visual Molecular Dynamics
votca-csg Votca coarse-graining engine