| autodock | A suite of automated docking tools |
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| autodock_vina | Program for drug discovery, molecular docking and virtual screening |
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| avogadro2 | Advanced molecule editor and visualizer 2 |
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| bodr | The Blue Obelisk Data Repository listing element and isotope properties |
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| cara-bin | Analysis of NMR spectra and Computer Aided Resonance Assignment |
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| chemex | Program to fit chemical exchange induced shift and relaxation data |
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| chemical-mime-data | A collection of data files to add support for chemical MIME types |
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| chemtool | A GTK program for drawing organic molecules |
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| clashlist | Build lists of van der Waals clashes from an input PDB file |
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| cluster | Build lists of collections of interacting items |
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| dssp | The protein secondary structure standard |
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| easychem | Chemical structure drawing program - focused on presentation |
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| elem | periodic table of the elements |
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| gelemental | Periodic table viewer with detailed information on the chemical elements |
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| gnome-chemistry-utils | Programs and library containing GTK widgets and C++ classes related to chemistry |
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| gperiodic | Periodic table application for Linux |
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| gromacs | The ultimate molecular dynamics simulation package |
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| GromacsWrapper | Python framework for Gromacs |
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| ksdssp | An open source implementation of sci-chemistry/dssp |
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| MDAnalysis | A python library to analyze and manipulate molecular dynamics trajectories |
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| mdtraj | Read, write and analyze MD trajectories with only a few lines of Python code |
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| moldy | Molecular dynamics simulations platform |
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| molmol | Publication-quality molecular visualization package |
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| molsketch | Drawing tool for 2D molecular structures |
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| mpqc | The Massively Parallel Quantum Chemistry Program |
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| msms-bin | MSMS very efficiently computes triangulations of Solvent Excluded Surfaces |
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| mustang | MUltiple STructural AligNment AlGorithm |
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| openbabel | Interconverts file formats used in molecular modeling |
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| ParmEd | Parameter and topology file editor and molecular mechanical simulator engine |
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| pdbcat | Manipulate and process PDB files using tools such as Perl, awk, etc |
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| pdbcns | Convert atom names for amino acids/nucleic acid bases between PDB and CNS format |
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| pdbmat | Calculate Tirion's model from pdb structures |
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| probe | Evaluates atomic packing within or between molecules |
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| propka | pKa-value prediction of ionizable groups in protein and protein-ligand complexes |
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| psi | Suite for ab initio quantum chemistry computing various molecular properties |
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| pymol | A Python-extensible molecular graphics system |
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| raster3d | Generation high quality raster images of proteins or other molecules |
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| suitename | The ROC RNA Ontology nomenclature and conformer-list development |
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| surf | Solvent accesible Surface calculator |
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| theseus | Maximum likelihood superpositioning and analysis of macromolecular structures |
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| threeV | 3V: Voss Volume Voxelator |
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| tinker | Molecular modeling package that includes force fields, such as AMBER and CHARMM |
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| tm-align | Quick & Accurate Structural Alignment |
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| vmd | Visual Molecular Dynamics |
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| votca | Versatile Object-oriented Toolkit for Coarse-graining Applications |
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| wxmacmolplt | Chemical 3D graphics program with GAMESS input builder |
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| xds-bin | Software for processing single-crystal X-ray monochromatic diffraction data |
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Packages