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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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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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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