autodock-vina : Program for drug discovery, molecular docking and virtual screening ( http://vina.scripps.edu/ )
cclib : Library for parsing and interpreting the results of computational chemistry packages ( http://cclib.sourceforge.net/ )
ccp1gui : A free, extensible Graphical User Interface (GUI) for community chemistry programs ( http://www.cse.scitech.ac.uk/ccg/software/ccp1gui/ )
ccp4mg : This is a sample skeleton ebuild file ( http://www.ysbl.york.ac.uk/~ccp4mg/ )
dssp : The protein secondary structure standard ( http://swift.cmbi.ru.nl/gv/dssp/" elog "Go to ${HOMEPAGE} and return the license agreement. )
dsv : Discovery Studio Visualizer ( http://www.accelrys.com/products/downloads/ds_visualizer/" einfo "Go to ${HOMEPAGE} )
epmr : Crystallographic molecular replacement by evolutionary search ( http://www.epmr.info/" elog "The user manual is available at ${HOMEPAGE} )
espresso : opEn-Source Package for Research in Electronic Structure, Simulation, and Optimization ( http://www.pwscf.org/ )
gridzilla : A GUI-based application designed to create grid screens for protein crystal optimization ( http://www.code-itch.com/gridzilla/Gridzilla.html )
imosflm : A new GUI for the Mosflm crystallographic data processing tool ( http://www.mrc-lmb.cam.ac.uk/harry/imosflm" SRC_URI="${HOMEPAGE}/ver${MY_PV}/downloads/${P}.zip )
kincontour : Read value/coordinate lists to produce contour maps in kinemage format ( http://kinemage.biochem.duke.edu/software/kincon.php )
king : An interactive system for 3D graphics (primarily molecular) ( http://kinemage.biochem.duke.edu/software/king.php )
mage : Mage is a 3D vector display program which shows 'kinemage' graphics ( http://kinemage.biochem.duke.edu/software/mage.php )
mole-bin : A toolkit for automated location channels, tunnels and pores in molecular structures ( http://mole.chemi.muni.cz/ )
mopac2007-bin : Powerful, fast semi-empirical package ( http://openmopac.net/ )
mopro-bin : Crystallographic structure or charge density refinement ( http://www.lcm3b.uhp-nancy.fr/lcm3b/Logiciels-labo/MoPro.htm )
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/${MY_P}.tgz )
mustang : MUltiple STructural AligNment AlGorithm. ( http://www.cs.mu.oz.au/~arun/mustang/" SRC_URI="${HOMEPAGE}${SRC_P}.tgz )
namd : A powerful and highly parallelized molecular dynamics code ( http://www.ks.uiuc.edu/Research/namd/ )
open3dqsar : Pharmacophore exploration by high-throughput chemometric analysis of molecular interaction fields (MIFs) ( http://www.open3dqsar.org/" elog "Register at ${HOMEPAGE}, then download ${SRC_URI} and place it in ${DISTDIR}. )
pmb : Automated structure refinement tools for CNS ( http://xray.utmb.edu/PMB/ )
prekin : Prepares molecular kinemages (input files for Mage and KiNG) from PDB-format coordinate files ( http://kinemage.biochem.duke.edu/software/prekin.php )
profit : Designed to be the ultimate protein least squares fitting program ( http://www.bioinf.org.uk/software/profit/" elog "Download ${ORIG_URI} from ${HOMEPAGE} )
pyitc : Software for processing isothermal titration calorimetry (ITC) data ( http://pyitc.sourceforge.net/ )
pymss : Multiple superposition of proteins, using a genetic algorithm for optimization ( http://reillygroup.cheme.iastate.edu/pymss/ )
pyrx : GUI for Virtual Screening with AutoDock ( http://pyrx.sf.net )
qutemol : High quality molecular visualization system that exploits GPU capabilites through OpenGL shaders ( http://qutemol.sourceforge.net/ )
rasmol : Free program that displays molecular structure. ( http://www.rasmol.org/ )
rdkit : www.rdkit.org/ ( A software suite for cheminformatics, computational chemistry, and predictive modeling )
reduce : Adds hydrogens to a Protein Data Bank (PDB) molecule structure file ( http://kinemage.biochem.duke.edu/software/reduce.php )
shakerr : Macromolecular crystal structure precision calculator ( http://shakerr.sourceforge.net/ )
solve-resolve-bin : Automated crystallographic structure solution for MIR, SAD, and MAD ( http://www.solve.lanl.gov/index.html )
theseus : Maximum likelihood superpositioning and analysis of macromolecular structures ( http://www.theseus3d.org/" SRC_URI="${HOMEPAGE}src/theseus_${PV}.tar.gz )
usf-rave-bin : The tools package from USF for macromolecular crystallography ( http://alpha2.bmc.uu.se/usf/rave.html )
usf-voidoo-bin : The tools package from USF for macromolecular crystallography ( http://alpha2.bmc.uu.se/usf/voidoo.html )
vasco : Calculates and visualizes annotated protein surfaces ( genome.tugraz.at/VASCo/ )
zodiac : Software for molecular modelling - computer-aided drug design ( http://www.zeden.org/ )
Add an ebuild in portage :
The ebuild is now in the portage tree.
You can also use layman : emerge layman then layman -a dberkholz
For Paludis use this rsync : rsync://gentoo.zugaina.org/dberkholz-portage
If you have a problem : ycarus(-at-)zugaina.org