GromacsWrapper : Python framework for Gromacs ( https://orbeckst.github.com/GromacsWrapper/ )
PyMca : X-ray Fluorescence Toolkit ( http://pymca.sourceforge.net/ )
acpype : AnteChamber PYthon Parser interfacE ( https://code.google.com/p/acpype/ )
ambertools : A suite for carrying out complete molecular mechanics investigations ( http://ambermd.org/#AmberTools" einfo "Go to ${HOMEPAGE} and get ${A} )
apbs : Evaluation of electrostatic properties of nanoscale biomolecular systems ( http://www.poissonboltzmann.org/apbs/ )
aqua : Program suite in this distribution calculates restraint violations ( http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html )
aria : Automated NOE assignment and NMR structure calculation ( http://aria.pasteur.fr/ )
arp-warp-bin : Improvement and interpretation of crystallographic electron density maps ( http://www.embl-hamburg.de/ARP/ )
autodock : A suite of automated docking tools ( http://autodock.scripps.edu/ )
autodock_vina : Program for drug discovery, molecular docking and virtual screening ( http://vina.scripps.edu/ )
avogadro : Advanced molecular editor that uses Qt4 and OpenGL ( http://avogadro.openmolecules.net/ )
azara : A suite of programmes to process and view NMR data ( http://www.bio.cam.ac.uk/azara/ )
babel : Interconvert file formats used in molecular modeling ( http://smog.com/chem/babel/ )
balbes : Automated molecular replacement (MR) pipeline ( http://www.ysbl.york.ac.uk/~fei/balbes/index.html )
ball : Biochemical Algorithms Library ( http://www.ball-project.org/ )
bkchem : Chemical drawing program ( http://bkchem.zirael.org/ )
bodr : The Blue Obelisk Data Repository listing element and isotope properties ( http://sourceforge.net/projects/bodr )
burrow-owl : Visualize multidimensional nuclear magnetic resonance (NMR) spectra ( http://burrow-owl.sourceforge.net/ )
cara-bin : Analysis of NMR spectra and Computer Aided Resonance Assignment ( http://www.nmr.ch )
ccp4 : Protein X-ray crystallography toolkit -- meta package ( http://www.ccp4.ac.uk/ )
ccp4-apps : Protein X-ray crystallography toolkit ( http://www.ccp4.ac.uk/ )
ccp4i : Protein X-ray crystallography toolkit -- graphical interface ( http://www.ccp4.ac.uk/ )
ccpn : The Collaborative Computing Project for NMR ( http://www.ccpn.ac.uk/ccpn )
chemical-mime-data : A collection of data files to add support for chemical MIME types ( http://chemical-mime.sourceforge.net/ )
chemtool : A GTK program for drawing organic molecules ( http://ruby.chemie.uni-freiburg.de/~martin/chemtool/ )
clashlist : Build lists of van der Waals clashes from an input PDB file ( http://kinemage.biochem.duke.edu/software/index.php )
cluster : Build lists of collections of interacting items ( http://kinemage.biochem.duke.edu/software/index.php )
cns : Crystallography and NMR System ( http://cns.csb.yale.edu/ )
coot : Crystallographic Object-Oriented Toolkit for model building, completion and validation ( https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/ )
cyana : Combined assignment and dynamics algorithm for NMR applications ( http://www.las.jp/english/products/cyana.html )
dssp : The protein secondary structure standard ( http://swift.cmbi.ru.nl/gv/dssp/ )
easychem : Chemical structure drawing program - focused on presentation ( http://easychem.sourceforge.net/ )
eden : A crystallographic real-space electron-density refinement and optimization program ( http://www.gromacs.org/pipermail/eden-users/ )
elem : periodic table of the elements ( http://elem.sourceforge.net/ )
freeon : An experimental suite of programs for linear scaling quantum chemistry ( http://www.freeon.org )
gabedit : GUI for computational chemistry packages ( http://gabedit.sourceforge.net/ )
gamess : A powerful quantum chemistry package ( http://www.msg.chem.iastate.edu/GAMESS/GAMESS.html )
gamessq : Simple job manager for GAMESS-US ( http://www.msg.chem.iastate.edu/GAMESS/GamessQ/ )
gelemental : Periodic table viewer that provides detailed information on the chemical elements ( http://freecode.com/projects/gelemental/ )
ghemical : Chemical quantum mechanics and molecular mechanics ( http://bioinformatics.org/ghemical/ )
gopenmol : Tool for the visualization and analysis of molecular structures ( http://www.csc.fi/gopenmol/" SRC_URI="${HOMEPAGE}/distribute/${P}-linux.tar.gz )
gperiodic : Periodic table application for Linux ( http://www.frantz.fi/software/gperiodic.php )
gromacs : The ultimate molecular dynamics simulation package ( http://www.gromacs.org/ )
gsim : Programm for visualisation and processing of experimental and simulated NMR spectra ( http://sourceforge.net/projects/gsim/ )
gtk-gamess : GUI for GAMESS, a General Atomic and Molecular Electronic Structure System ( http://sourceforge.net/projects/gtk-gamess/ )
hollow : Production of surface images of proteins ( http://hollow.sourceforge.net/ )
icm : MolSoft LCC ICM Pro ( http://www.molsoft.com/icm_pro.html" einfo "${HOMEPAGE} )
icm-browser : MolSoft LCC ICM Browser ( http://www.molsoft.com/icm_browser.html" einfo "${HOMEPAGE}" einfo "you should purchaise license from ${HOMEPAGE} and place it to )
imosflm : A new GUI for the Mosflm crystallographic data processing tool ( http://www.mrc-lmb.cam.ac.uk/harry/imosflm" SRC_URI="${HOMEPAGE}/ver${MY_PV}/downloads/${P}.zip )
jmol : Java molecular viever for 3-D chemical structures ( http://jmol.sourceforge.net/ )
ksdssp : An open source implementation of sci-chemistry/dssp ( http://www.cgl.ucsf.edu/Overview/software.html )
makecif : PDB -- CIF convertor ( http://www.ysbl.york.ac.uk/~alexei/makecif.html )
mars : Robust automatic backbone assignment of proteins ( http://www.mpibpc.mpg.de/groups/zweckstetter/_links/software_mars.htm )
massxpert : Software suite to predict/analyze mass spectrometric data on (bio)polymers ( http://massxpert.org )
mdanalysis : A python library to analyze and manipulate molecular dynamics trajectories ( http://www.mdanalysis.org/ )
mead : Macroscopic Electrostatics with Atomic Detail ( http://www.teokem.lu.se/~ulf/Methods/mead.html )
mm-align : Protein Complex Structural Alignment ( http://zhanglab.ccmb.med.umich.edu/MM-align/ )
molden : Display molecular density from GAMESS-UK, GAMESS-US, GAUSSIAN and Mopac/Ampac ( http://www.cmbi.kun.nl/~schaft/molden/molden.html )
moldy : Molecular dynamics simulations platform ( http://www.ccp5.ac.uk/moldy/moldy.html )
molequeue : Abstract, manage and coordinate execution of tasks ( http://www.openchemistry.org/OpenChemistry/project/molequeue.html )
molmol : Publication-quality molecular visualization package ( http://hugin.ethz.ch/wuthrich/software/molmol/index.html )
molrep : molecular replacement program ( http://www.ysbl.york.ac.uk/~alexei/molrep.html )
molscript : Display molecular 3D structures, such as proteins, in both schematic and detailed representations ( http://www.avatar.se/molscript/" elog "Please visit ${HOMEPAGE} )
molsketch : A drawing tool for 2D molecular structures ( http://molsketch.sourceforge.net/ )
mongochem : Application for managing large collections of chemical data ( http://www.openchemistry.org/ )
mopac7 : Autotooled, updated version of a powerful, fast semi-empirical package ( http://sourceforge.net/projects/mopac7/ )
mosflm : A program for integrating single crystal diffraction data from area detectors ( http://www.mrc-lmb.cam.ac.uk/harry/mosflm/" SRC_URI="${HOMEPAGE}ver${MY_PV}/build-it-yourself/${MY_P}.tgz )
mpqc : The Massively Parallel Quantum Chemistry Program ( http://www.mpqc.org/ )
mrbump : An automated scheme for Molecular Replacement ( http://www.ccp4.ac.uk/MrBUMP" SRC_URI="${HOMEPAGE}/release/${P}.tar.gz )
msms-bin : MSMS allows to compute very efficiently triangulations of Solvent Excluded Surfaces ( http://mgl.scripps.edu/people/sanner/html/msms_home.html )
mustang : MUltiple STructural AligNment AlGorithm ( http://www.csse.monash.edu.au/~karun/Site/mustang.html )
namd : A powerful and highly parallelized molecular dynamics code ( http://www.ks.uiuc.edu/Research/namd/ )
nmrglue : A module for working with NMR data in Python ( http://nmrglue.com/ )
numbat : new user-friendly method built for automatic dX-tensor determination ( http://www.nmr.chem.uu.nl/~christophe/numbat.html )
oasis : A direct-method program for SAD/SIR phasing ( http://cryst.iphy.ac.cn/Project/protein/protein-I.html )
openbabel : Interconverts file formats used in molecular modeling ( http://openbabel.sourceforge.net/ )
openbabel-perl : Perl bindings for OpenBabel ( http://openbabel.sourceforge.net/ )
openbabel-python : Python bindings for OpenBabel (including Pybel) ( http://openbabel.sourceforge.net/ )
ortep3 : Thermal ellipsoid plot program for crystal structure illustrations ( http://www.ornl.gov/sci/ortep/ )
p3d : Python module for structural bioinformatics ( http://p3d.fufezan.net/ )
parassign : Assign protein nuclei solely on the basis of pseudocontact shifts (PCS) ( http://protchem.lic.leidenuniv.nl/software/parassign/registration )
pdb-extract : Tools for extracting mmCIF data from structure determination applications ( http://sw-tools.pdb.org/apps/PDB_EXTRACT/index.html )
pdb-tools : Tools for manipulating and doing calculations on wwPDB macromolecule structure files ( https://github.com/harmslab/pdbtools )
pdb2pqr : An automated pipeline for performing Poisson-Boltzmann electrostatics calculations ( http://www.poissonboltzmann.org/ )
pdbcat : Manipulate and process PDB files using commonly available tools such as Perl, awk, etc ( http://www.ks.uiuc.edu/Development/MDTools/pdbcat/ )
pdbcns : Convert atom names for common amino acids and nucleic acid bases from PDB format to CNS or back ( http://www.mybiosoftware.com/3d-molecular-model/314/ )
pdbmat : Calculate Tirion's model from pdb structures ( http://ecole.modelisation.free.fr/modes.html )
phaser : A program for phasing macromolecular crystal structures ( http://www-structmed.cimr.cam.ac.uk/phaser )
platon : Versatile, SHELX-97 compatible, multipurpose crystallographic tool ( http://www.cryst.chem.uu.nl/platon/ )
pointless : Scores crystallographic Laue and space groups ( ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/pointless.html )
povscript+ : Modified molscript that uses POV-Ray, does thermal ellipsoids, and more ( https://sites.google.com/site/timfenn/povscript )
prekin : Prepares molecular kinemages (input files for Mage and KiNG) from PDB-format coordinate files ( http://kinemage.biochem.duke.edu/software/prekin.php )
probe : Evaluates atomic packing within or between molecules ( http://kinemage.biochem.duke.edu/software/probe.php )
procheck : Checks the stereochemical quality of a protein structure ( http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html )
prodecomp : Decomposition-based analysis of NMR projections ( http://www.lundberg.gu.se/nmr/software.php?program=PRODECOMP )
propka : Prediction of the pKa values of ionizable groups in proteins and protein-ligand complexes ( http://propka.ki.ku.dk/ )
psi : Suite of ab initio quantum chemistry programs to compute various molecular properties ( http://www.psicode.org/ )
pymol : A Python-extensible molecular graphics system ( http://www.pymol.org/ )
pymol-apbs-plugin : APBS plugin for pymol ( http://sourceforge.net/projects/pymolapbsplugin/ )
pymol-plugins-bni-tools : Gives Pymol additional functionalities and presets to the PyMOL GUI ( http://bni-tools.sourceforge.net/ )
pymol-plugins-caver : Calculation of pathways from buried cavities to outside solvent in protein structures ( http://loschmidt.chemi.muni.cz/caver/" elog "from ${HOMEPAGE}. This requires registration. )
pymol-plugins-dssp : DSSP Plugin for PyMOL ( http://www.biotec.tu-dresden.de/~hongboz/dssp_pymol/dssp_pymol.html )
pymol-plugins-dynamics : Molecular dynamics in Pymol ( https://github.com/tomaszmakarewicz/Dynamics )
pymol-plugins-emovie : eMovie is a plug-in tool for the molecular visualization program PyMOL ( http://www.weizmann.ac.il/ISPC/eMovie.html )
pymol-plugins-msms : GUI for MSMS and displaying its results in PyMOL ( http://www.biotec.tu-dresden.de/~hongboz/msms_pymol/msms_pymol.html )
pymol-plugins-promol : Fast and accurate regognition of active sites ( http://www.rit.edu/cos/ezviz/ProMOL_dl.html )
pymol-plugins-psico : Pymol ScrIpt COllection ( https://github.com/speleo3/pymol-psico/ )
rasmol : Molecular Graphics Visualisation Tool ( http://www.openrasmol.org/ )
raster3d : Generation high quality raster images of proteins or other molecules ( http://www.bmsc.washington.edu/raster3d/raster3d.html )
reduce : Adds hydrogens to a Protein Data Bank (PDB) molecule structure file ( http://kinemage.biochem.duke.edu/software/reduce.php )
refmac : Macromolecular crystallographic refinement program ( http://www.ysbl.york.ac.uk/~garib/refmac" ${HOMEPAGE}/data/refmac_stable/refmac_${PV}.tar.g )
relax : Molecular dynamics by NMR data analysis ( http://www.nmr-relax.com/ )
scala : Scale together multiple observations of reflections ( http://www.ccp4.ac.uk/dist/html/scala.html )
sfcheck : Program for assessing the agreement between the atomic model and X-ray data or EM map ( http://www.ysbl.york.ac.uk/~alexei/sfcheck.html )
shelx : Programs for crystal structure determination from single-crystal diffraction data ( http://shelx.uni-ac.gwdg.de/SHELX/" elog "Go to ${HOMEPAGE} )
solve-resolve-bin : Automated crystallographic structure solution for MIR, SAD, and MAD ( http://www.solve.lanl.gov/index.html )
sparky : Graphical NMR assignment and integration program for proteins, nucleic acids, and other polymers ( http://www.cgl.ucsf.edu/home/sparky/ )
suitename : The ROC RNA Ontology Consortium consensus RNA backbone nomenclature and conformer-list development ( http://kinemage.biochem.duke.edu/software/suitename.php )
theseus : Maximum likelihood superpositioning and analysis of macromolecular structures ( http://www.theseus3d.org/ )
threeV : 3V: Voss Volume Voxelator ( http://geometry.molmovdb.org/3v/ )
tinker : Molecular modeling package that includes force fields, such as AMBER and CHARMM ( http://dasher.wustl.edu/tinker/ )
tm-align : Quick and Accurate Structural Alignment ( http://zhanglab.ccmb.med.umich.edu/TM-align/ )
viewmol : Open-source graphical front end for computational chemistry programs ( http://viewmol.sourceforge.net/ )
vmd : Visual Molecular Dynamics ( http://www.ks.uiuc.edu/Research/vmd/ )
votca-csg : Votca coarse-graining engine ( http://www.votca.org )
votca-csgapps : Extra applications for votca-csg ( http://www.votca.org )
wxmacmolplt : Chemical 3D graphics program with GAMESS input builder ( http://www.scl.ameslab.gov/MacMolPlt/ )
xds-bin : X-ray Detector Software for processing single-crystal monochromatic diffraction data ( http://xds.mpimf-heidelberg.mpg.de/ )
xdsgui : GUI for XDS that is supposed to help both novice and experienced users ( http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/XdsGUI )
xdsi : A crude interface for running the XDS ( http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Xdsi )
xdsstat-bin : Prints various statistics (that are not available from XDS itself) ( http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/XDSSTAT )
xia2 : An automated data reduction system for crystallography ( http://www.ccp4.ac.uk/xia/ )
xyza2pipe : Cross conversion environment of NMR spectra ( http://fermi.pharm.hokudai.ac.jp/olivia/api/index.php/Xyza2pipe_src )
Add an ebuild in portage :
The ebuild is now in the portage tree.
You can also use layman : emerge layman then layman -a funtoo
For Paludis use this rsync : rsync://gentoo.zugaina.org/funtoo-portage
If you have a problem : ycarus(-at-)zugaina.org