| aqua |
Program suite in this distribution calculates restraint violations |
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| 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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| modeller |
Homology or comparative modeling of protein three-dimensional structures |
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| molden |
Display molecular density from GAMESS-UK, GAMESS-US, GAUSSIAN and Mopac/Ampac |
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| moldy |
Molecular dynamics simulations platform |
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| molequeue |
Abstract, manage and coordinate execution of tasks |
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| molmol |
Publication-quality molecular visualization package |
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| molsketch |
A drawing tool for 2D molecular structures |
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| mopac7 |
Autotooled, updated version of a powerful, fast semi-empirical package |
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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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| namd |
A powerful and highly parallelized molecular dynamics code |
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| nmrglue |
A module for working with NMR data in Python |
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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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| procheck |
Checks the stereochemical quality of a protein structure |
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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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| xyza2pipe |
Cross conversion environment of NMR spectra |
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Packages