| ksdssp |
An open source implementation of sci-chemistry/dssp |
| mdtraj |
Read, write and analyze MD trajectories with only a few lines of Python code |
| pdbcat |
Manipulate and process PDB files using tools such as Perl, awk, etc |
| mars |
Robust automatic backbone assignment of proteins |
| p3d |
Python module for structural bioinformatics |
| mm-align |
Protein Complex Structural Alignment |
| tm-align |
Quick & Accurate Structural Alignment |
| suitename |
The ROC RNA Ontology nomenclature and conformer-list development |
| nmrglue |
A module for working with NMR data in Python |
| relax |
Molecular dynamics by NMR data analysis |
| MDAnalysis |
A python library to analyze and manipulate molecular dynamics trajectories |
| ParmEd |
Parameter/topology editor and molecular simulator |
| apbs |
Evaluation of electrostatic properties of nanoscale biomolecular systems |
| 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 |
| elem |
periodic table of the elements |
| gnome-chemistry-utils |
Programs and library containing GTK widgets and C++ classes related to chemistry |
| gperiodic |
Periodic table application for Linux |
| clashlist |
Build lists of van der Waals clashes from an input PDB file |
| gromacs |
The ultimate molecular dynamics simulation package |
| tinker |
Molecular modeling package that includes force fields, such as AMBER and CHARMM |
| votca-csgapps |
Extra applications for votca-csg |
| votca-ctp |
Votca charge transport module |
| wxmacmolplt |
Chemical 3D graphics program with GAMESS input builder |
| xyza2pipe |
Cross conversion environment of NMR spectra |
| votca-xtp |
Votca excitation and charge properties module |
| aqua |
Program suite in this distribution calculates restraint violations |
| 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 |
| pdb2pqr |
Automated pipeline for performing Poisson-Boltzmann electrostatics calculations |
| xds-bin |
Software for processing single-crystal X-ray monochromatic diffraction data |
| 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-emovie |
PyMOL plugin for convinient movie creation |
| pymol-plugins-promol |
Fast and accurate regognition of active sites |
| pymol |
A Python-extensible molecular graphics system |
| rasmol |
Molecular Graphics Visualisation Tool |
| bkchem |
Chemical drawing program |
| 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 |
| probe |
Evaluates atomic packing within or between molecules |
| procheck |
Checks the stereochemical quality of a protein structure |
| numbat |
new user-friendly method built for automatic dX-tensor determination |
| ortep3 |
Thermal ellipsoid plot program for crystal structure illustrations |
| pdb-tools |
Tools for manipulating and calculations on wwPDB macromolecule structure files |
| povscript+ |
Modified molscript that uses POV-Ray, does thermal ellipsoids, and more |
| prekin |
Prepares molecular kinemages from PDB-format coordinate files |
| prodecomp |
Decomposition-based analysis of NMR projections |
| propka |
pKa-value prediction of ionizable groups in protein and protein-ligand complexes |
| psi |
Suite for ab initio quantum chemistry computing various molecular properties |
| GromacsWrapper |
Python framework for Gromacs |
| cluster |
Build lists of collections of interacting items |
| dssp |
The protein secondary structure standard |
| easychem |
Chemical structure drawing program - focused on presentation |
| eden |
A crystallographic real-space electron-density refinement & optimization program |
| freeon |
An experimental suite of programs for linear scaling quantum chemistry |
| gelemental |
Periodic table viewer with detailed information on the chemical elements |
| gmxapi |
Gromacs API bindings |
| 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 |
| openbabel-perl |
Perl bindings for OpenBabel |
| openbabel-python |
Python bindings for OpenBabel (including Pybel) |
| openbabel |
Interconverts file formats used in molecular modeling |
| pdbcns |
Convert atom names for amino acids/nucleic acid bases between PDB and CNS format |
| pdbmat |
Calculate Tirion's model from pdb structures |
| raster3d |
Generation high quality raster images of proteins or other molecules |
| sparky |
Graphical NMR assignment and integration program for large polymers |
| surf |
Solvent accesible Surface calculator |
| theseus |
Maximum likelihood superpositioning and analysis of macromolecular structures |
| threeV |
3V: Voss Volume Voxelator |
| viewmol |
Open-source graphical front end for computational chemistry programs |
| vmd |
Visual Molecular Dynamics |
| votca-csg |
Votca coarse-graining engine |
Packages