The sci-chemistry category contains software that can be used in chemistral scientific environments.
| apbs | Evaluation of electrostatic properties of nanoscale biomolecular systems |
|---|---|
| aqua | Program suite in this distribution calculates restraint violations |
| aria | Automated NOE assignment and NMR structure calculation |
| 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 |
| azara | A suite of programmes to process and view NMR data |
| ball | Biochemical Algorithms Library |
| bkchem | Chemical drawing program |
| bodr | The Blue Obelisk Data Repository listing element and isotope properties |
| burrow-owl | Visualize multidimensional nuclear magnetic resonance (NMR) spectra |
| cara-bin | Analysis of NMR spectra and Computer Aided Resonance Assignment |
| ccpn | The Collaborative Computing Project for NMR |
| 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 |
| cns | Crystallography and NMR System |
| coot | Crystallographic Object-Oriented Toolkit |
| dssp | The protein secondary structure standard |
| easychem | Chemical structure drawing program - focused on presentation |
| eden | A crystallographic real-space electron-density refinement & optimization program |
| elem | periodic table of the elements |
| freeon | An experimental suite of programs for linear scaling quantum chemistry |
| gabedit | GUI for computational chemistry packages |
| gelemental | Periodic table viewer with detailed information on the chemical elements |
| ghemical | Chemical quantum mechanics and molecular mechanics |
| gperiodic | Periodic table application for Linux |
| gromacs | The ultimate molecular dynamics simulation package |
| GromacsWrapper | Python framework for Gromacs |
| hollow | Production of surface images of proteins |
| jmol | Java molecular viever for 3-D chemical structures |
| ksdssp | An open source implementation of sci-chemistry/dssp |
| mars | Robust automatic backbone assignment of proteins |
| 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 |
| mm-align | Protein Complex Structural Alignment |
| modeller | Homology or comparative modeling of protein three-dimensional structures |
| 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 |
| 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 |
| nmrdepaker | Program to perform NMR spectra 'De-Pake-ing' and moment calculation |
| nmrglue | A module for working with NMR data in Python |
| numbat | new user-friendly method built for automatic dX-tensor determination |
| openbabel | Interconverts file formats used in molecular modeling |
| openbabel-perl | Perl bindings for OpenBabel |
| openbabel-python | Python bindings for OpenBabel (including Pybel) |
| ortep3 | Thermal ellipsoid plot program for crystal structure illustrations |
| p3d | Python module for structural bioinformatics |
| parassign | Assign protein nuclei solely on the basis of pseudocontact shifts (PCS) |
| ParmEd | Parameter/topology editor and molecular simulator |
| pdb-tools | Tools for manipulating and calculations on wwPDB macromolecule structure files |
| pdb2pqr | Automated pipeline for performing Poisson-Boltzmann electrostatics calculations |
| 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 |
| povscript+ | Modified molscript that uses POV-Ray, does thermal ellipsoids, and more |
| prekin | Prepares molecular kinemages from PDB-format coordinate files |
| probe | Evaluates atomic packing within or between molecules |
| procheck | Checks the stereochemical quality of a protein structure |
| prodecomp | Decomposition-based analysis of NMR projections |
| prody | Protein Dynamics Analysis |
| 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 |
| 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-dynamics | Molecular dynamics in Pymol |
| pymol-plugins-emovie | PyMOL plugin for convinient movie creation |
| pymol-plugins-msms | GUI for MSMS and displaying its results in PyMOL |
| pymol-plugins-promol | Fast and accurate regognition of active sites |
| pymol-plugins-psico | Pymol ScrIpt COllection |
| rasmol | Molecular Graphics Visualisation Tool |
| raster3d | Generation high quality raster images of proteins or other molecules |
| reduce | Adds hydrogens to a Protein Data Bank (PDB) molecule structure file |
| relax | Molecular dynamics by NMR data analysis |
| shelx | Crystal structure determination from single-crystal diffraction data |
| sparky | Graphical NMR assignment and integration program for large polymers |
| 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 |
| viewmol | Open-source graphical front end for computational chemistry programs |
| vmd | Visual Molecular Dynamics |
| votca-csg | Votca coarse-graining engine |
| votca-csgapps | Extra applications for votca-csg |
| votca-ctp | Votca charge transport module |
| votca-xtp | Votca excitation and charge properties module |
| wxmacmolplt | Chemical 3D graphics program with GAMESS input builder |
| xds-bin | Software for processing single-crystal X-ray monochromatic diffraction data |
| xdsstat-bin | Prints various statistics (that are not available from XDS itself) |
| xyza2pipe | Cross conversion environment of NMR spectra |