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The sci-chemistry category contains software that can be used in chemistral scientific environments.

All packages

acpype AnteChamber PYthon Parser interfacE
ambertools A suite for carrying out complete molecular mechanics investigations
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
arp-warp-bin Improvement and interpretation of crystallographic electron density maps
autodock A suite of automated docking tools
autodock_vina Program for drug discovery, molecular docking and virtual screening
avogadro Advanced molecular editor that uses Qt4 and OpenGL
azara A suite of programmes to process and view NMR data
babel Interconvert file formats used in molecular modeling
balbes Automated molecular replacement (MR) pipeline
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
ccp4 Protein X-ray crystallography toolkit -- meta package
ccp4-apps Protein X-ray crystallography toolkit
ccp4i Protein X-ray crystallography toolkit -- graphical interface
ccpn The Collaborative Computing Project for NMR
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 for model building, completion and validation
cyana Combined assignment and dynamics algorithm for NMR applications
dssp The protein secondary structure standard
easychem Chemical structure drawing program - focused on presentation
eden A crystallographic real-space electron-density refinement and 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
gamess A powerful quantum chemistry package
gamessq Simple job manager for GAMESS-US
gelemental Periodic table viewer that provides detailed information on the chemical elements
ghemical Chemical quantum mechanics and molecular mechanics
gopenmol Tool for the visualization and analysis of molecular structures
gperiodic Periodic table application for Linux
gromacs The ultimate molecular dynamics simulation package
GromacsWrapper Python framework for Gromacs
gsim Programm for visualisation and processing of experimental and simulated NMR spectra
gtk-gamess GUI for GAMESS, a General Atomic and Molecular Electronic Structure System
hollow Production of surface images of proteins
icm MolSoft LCC ICM Pro
icm-browser MolSoft LCC ICM Browser
imosflm A new GUI for the Mosflm crystallographic data processing tool
jmol Java molecular viever for 3-D chemical structures
ksdssp An open source implementation of sci-chemistry/dssp
makecif PDB --> CIF convertor
mars Robust automatic backbone assignment of proteins
massxpert Software suite to predict/analyze mass spectrometric data on (bio)polymers
mdanalysis A python library to analyze and manipulate molecular dynamics trajectories
mead Macroscopic Electrostatics with Atomic Detail
mm-align Protein Complex Structural Alignment
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
molrep molecular replacement program
molscript Display molecular 3D structures, such as proteins, in both schematic and detailed representations
molsketch A drawing tool for 2D molecular structures
mongochem Application for managing large collections of chemical data
mopac7 Autotooled, updated version of a powerful, fast semi-empirical package
mosflm A program for integrating single crystal diffraction data from area detectors
mpqc The Massively Parallel Quantum Chemistry Program
mrbump An automated scheme for Molecular Replacement
msms-bin MSMS allows to compute very efficiently triangulations of Solvent Excluded Surfaces
mustang MUltiple STructural AligNment AlGorithm
namd A powerful and highly parallelized molecular dynamics code
nmrglue A module for working with NMR data in Python
numbat new user-friendly method built for automatic dX-tensor determination
oasis A direct-method program for SAD/SIR phasing
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)
pdb-extract Tools for extracting mmCIF data from structure determination applications
pdb-tools Tools for manipulating and doing calculations on wwPDB macromolecule structure files
pdb2pqr An automated pipeline for performing Poisson-Boltzmann electrostatics calculations
pdbcat Manipulate and process PDB files using commonly available tools such as Perl, awk, etc
pdbcns Convert atom names for common amino acids and nucleic acid bases from PDB format to CNS or back
pdbmat Calculate Tirion's model from pdb structures
phaser A program for phasing macromolecular crystal structures
platon Versatile, SHELX-97 compatible, multipurpose crystallographic tool
pointless Scores crystallographic Laue and space groups
povscript+ Modified molscript that uses POV-Ray, does thermal ellipsoids, and more
prekin Prepares molecular kinemages (input files for Mage & KiNG) 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
propka Prediction of the pKa values of ionizable groups in proteins and protein-ligand complexes
psi Suite of ab initio quantum chemistry programs to compute various molecular properties
PyMca X-ray Fluorescence Toolkit
pymol A Python-extensible molecular graphics system
pymol-apbs-plugin APBS plugin for pymol
pymol-plugins-bni-tools Gives Pymol additional functionalities and presets to the PyMOL GUI
pymol-plugins-caver Calculation of pathways from buried cavities to outside solvent in protein structures
pymol-plugins-dssp DSSP Plugin for PyMOL
pymol-plugins-dynamics Molecular dynamics in Pymol
pymol-plugins-emovie eMovie is a plug-in tool for the molecular visualization program PyMOL
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
refmac Macromolecular crystallographic refinement program
relax Molecular dynamics by NMR data analysis
scala Scale together multiple observations of reflections
sfcheck Program for assessing the agreement between the atomic model and X-ray data or EM map
shelx Programs for crystal structure determination from single-crystal diffraction data
solve-resolve-bin Automated crystallographic structure solution for MIR, SAD, and MAD
sparky Graphical NMR assignment and integration program for proteins, nucleic acids, and other polymers
suitename The ROC RNA Ontology Consortium consensus RNA backbone 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
wxmacmolplt Chemical 3D graphics program with GAMESS input builder
xds-bin X-ray Detector Software for processing single-crystal monochromatic diffraction data
xdsgui GUI for XDS that is supposed to help both novice and experienced users
xdsi A crude interface for running the XDS
xdsstat-bin Prints various statistics (that are not available from XDS itself)
xia2 An automated data reduction system for crystallography
xyza2pipe Cross conversion environment of NMR spectra


134 Packages