| 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 |
|---|
| 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 |
|---|
| clashlist | Build lists of van der Waals clashes from an input PDB file |
|---|
| cluster | Build lists of collections of interacting items |
|---|
| dssp | The protein secondary structure standard |
|---|
| easychem | Chemical structure drawing program - focused on presentation |
|---|
| elem | periodic table of the elements |
|---|
| gelemental | Periodic table viewer with detailed information on the chemical elements |
|---|
| gnome-chemistry-utils | Programs and library containing GTK widgets and C++ classes related to chemistry |
|---|
| gperiodic | Periodic table application for Linux |
|---|
| gromacs | The ultimate molecular dynamics simulation package |
|---|
| GromacsWrapper | Python framework for Gromacs |
|---|
| ksdssp | An open source implementation of sci-chemistry/dssp |
|---|
| MDAnalysis | A python library to analyze and manipulate molecular dynamics trajectories |
|---|
| mdtraj | Read, write and analyze MD trajectories with only a few lines of Python code |
|---|
| modeller | Homology or comparative modeling of protein three-dimensional structures |
|---|
| moldy | Molecular dynamics simulations platform |
|---|
| molequeue | Abstract, manage and coordinate execution of tasks |
|---|
| molmol | Publication-quality molecular visualization package |
|---|
| molsketch | Drawing tool for 2D molecular structures |
|---|
| mpqc | The Massively Parallel Quantum Chemistry Program |
|---|
| msms-bin | MSMS very efficiently computes triangulations of Solvent Excluded Surfaces |
|---|
| mustang | MUltiple STructural AligNment AlGorithm |
|---|
| openbabel | Interconverts file formats used in molecular modeling |
|---|
| ParmEd | Parameter and topology file editor and molecular mechanical simulator engine |
|---|
| pdbcat | Manipulate and process PDB files using tools such as Perl, awk, etc |
|---|
| pdbcns | Convert atom names for amino acids/nucleic acid bases between PDB and CNS format |
|---|
| pdbmat | Calculate Tirion's model from pdb structures |
|---|
| probe | Evaluates atomic packing within or between molecules |
|---|
| propka | pKa-value prediction of ionizable groups in protein and protein-ligand complexes |
|---|
| psi | Suite for ab initio quantum chemistry computing various molecular properties |
|---|
| pymol | A Python-extensible molecular graphics system |
|---|
| raster3d | Generation high quality raster images of proteins or other molecules |
|---|
| suitename | The ROC RNA Ontology nomenclature and conformer-list development |
|---|
| surf | Solvent accesible Surface calculator |
|---|
| theseus | Maximum likelihood superpositioning and analysis of macromolecular structures |
|---|
| threeV | 3V: Voss Volume Voxelator |
|---|
| tinker | Molecular modeling package that includes force fields, such as AMBER and CHARMM |
|---|
| tm-align | Quick & Accurate Structural Alignment |
|---|
| vmd | Visual Molecular Dynamics |
|---|
| votca | Versatile Object-oriented Toolkit for Coarse-graining Applications |
|---|
| wxmacmolplt | Chemical 3D graphics program with GAMESS input builder |
|---|
| xds-bin | Software for processing single-crystal X-ray monochromatic diffraction data |
|---|
Packages