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acpype
almost
all atom molecular simulation toolkit
ambertools
apbs
Software for evaluating the electrostatic properties of nanoscale biomolecular systems
aqua
aria
Software for automated NOE assignment and NMR structure calculation.
arp-warp-bin
ARP/wARP is a software for improvement and interpretation of crystallographic electron density maps
autodock
A suite of automated docking tools
autodock-vina
autodock_vina
AutoDock Vina is a new program for drug discovery and molecular docking
avogadro
Advanced molecular editor that uses Qt4 and OpenGL
avogadro2
azara
A suite of programmes to process and view NMR data
babel
balbes
Automated molecular replacement (MR) pipeline
ball
bist
Bist, the chemical drawing tool
bkchem
A chemical drawing program
bodr
The Blue Obelisk Data Repository listing element and isotope properties.
burrow-owl
Visualize multidimensional nuclear magnetic resonance (NMR) spectra
camshift
cara-bin
An application for the analysis of NMR spectra and Computer Aided Resonance Assignment
cclib
Library for parsing and interpreting the results of computational chemistry packages
ccp1gui
A free, extensible Graphical User Interface (GUI) for community chemistry programs
ccp4
Protein X-ray crystallography toolkit -- meta package
ccp4-apps
Protein X-ray crystallography toolkit
ccp4i
Protein X-ray crystallography toolkit -- graphical interface
ccp4mg
ccpn
The Collaborative Computing Project for NMR
chemBuild
chemical-mime-data
A collection of data files to add support for chemical MIME types.
chemtool
A GTK program for drawing organic molecules
chimera-bin
chooch
a program that will automatically determine values of the anomalous scattering factors
clashlist
cluster
cns
Crystallography and NMR System
cnsface
concoord
coot
Crystallographic Object-Oriented Toolkit for model building, completion and validation
cs-rosetta
curvefit
cyana
Combined assignment and dynamics algorithm for NMR applications
direx
Low Resolution Structure Refinement
dl_poly
drawxtl
This software can be used to produce crystal structure drawings from structural data
dssp
The protein secondary structure standard
dssp2pdb
convert dssp to pdb
dsv
Discovery Studio Visualizer
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
epmr
Crystallographic molecular replacement by evolutionary search
erkale
freeon
gabedit
GUI for computational chemistry packages
gamess
A powerful quantum chemistry package
gamessq
Simple job manager for GAMESS-US
gelemental
a periodic table viewer that provides detailed information on the chemical elements.
ghemical
Chemical quantum mechanics and molecular mechanics
gnome-chemistry-utils
gopenmol
gOpenMol is a tool for the visualization and analysis of molecular structures
gperiodic
Periodic table application for Linux
gridzilla
A GUI-based application designed to create grid screens for protein crystal optimization
gromacs
The ultimate molecular dynamics simulation package
GromacsWrapper
gsim
Programm for visualisation and processing of experimental and simulated NMR spectra
gtk-gamess
GTK-GAMESS is a graphical frontend for GAMESS
hollow
hoomd
hydronmr
icm
MolSoft LCC ICM Pro
icm-browser
MolSoft LCC ICM Browser
imosflm
A new GUI for the Mosflm crystallographic data processing tool
jana2000
the crystallographic computing system
jligand
a Java interface which allows links descriptions to be created
jmol
Jmol is a java molecular viever for 3-D chemical structures.
jmol-applet
jspecview
kincontour
Read value/coordinate lists to produce contour maps in kinemage format
king
An interactive system for 3D graphics (primarily molecular)
ksdssp
ksdssp is an open source implementation of dssp
ligplot+
mage
Mage is a 3D vector display program which shows 'kinemage' graphics
makecif
mars
massxpert
A software suite to predict/analyze mass spectrometric data on (bio)polymers.
mdanalysis
mddnmr
Program for processing of non-uniformly sampled (NUS) multidimensional NMR spectra
mdsctk
mead
Macroscopic Electrostatics with Atomic Detail
mgltools
Software to visualization and analysis of molecular structures
mgltools-autodocktools
mgltools plugin -- autodocktools
mgltools-bhtree
mgltools plugin -- bhtree
mgltools-cadd
mgltools-cmolkit
mgltools plugin -- cMolKit
mgltools-dejavu
mgltools plugin -- dejavu
mgltools-geomutils
mgltools plugin -- geomutils
mgltools-gle
mgltools plugin -- gle
mgltools-mglutil
mgltools plugin -- mglutil
mgltools-molkit
mgltools plugin -- MolKit
mgltools-networkeditor
mgltools plugin -- NetworkEditor
mgltools-opengltk
mgltools plugin -- opengltk
mgltools-pmv
mgltools plugin -- pmv
mgltools-pyautodock
mgltools plugin -- PyAutoDock
mgltools-pybabel
mgltools plugin -- PyBabel
mgltools-pyglf
mgltools plugin -- pyglf
mgltools-qslimlib
mgltools plugin -- qslimlib
mgltools-scenario2
mgltools-sff
mgltools plugin -- sff
mgltools-support
mgltools plugin -- support
mgltools-symserv
mgltools plugin -- symserv
mgltools-utpackages
mgltools plugin -- UTpackages
mgltools-viewer-framework
mgltools plugin -- Viewer-Framework
mgltools-vision
mgltools plugin -- vision
mgltools-visionlib
mgltools plugin -- visionlib
mgltools-volume
mgltools plugin -- volume
mgltools-webservices
mgltools plugin -- webservices
mics
mm-align
modelfree
modeller
MODELLER is used for homology or comparative modeling of protein three-dimensional structures
molden
Display molecular density from GAMESS-UK, GAMESS-US, GAUSSIAN and Mopac/Ampac.
moldy
Program for performing molecular dynamics simulations.
mole-bin
A toolkit for automated location channels, tunnels and pores in molecular structures
molequeue
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
mongochem
mopac2007-bin
Powerful, fast semi-empirical package
mopac7
Autotooled, updated version of a powerful, fast semi-empirical package
mopro-bin
Crystallographic structure or charge density refinement
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
mtz2hkl
Intended to facilitate the transition from refmac5 refinement to shelxh or shelxl refinement
mtz2sca
Converts CCP4 mtz-files containing anomalous data to Scalepack format
mustang
MUltiple STructural AligNment AlGorithm.
namd
A powerful and highly parallelized molecular dynamics code
nMOLDYN
nmrglue
nmrpipe
Spectral visualisation, analysis and Fourier processing
nmrview
Visualisation and analysis of processed NMR data
numbat
nwchem
oasis
A direct-method program for SAD/SIR phasing
objcryst-fox
open3dqsar
openbabel
interconverts file formats used in molecular modeling
openbabel-java
openbabel-perl
Perl bindings for OpenBabel
openbabel-python
Python bindings for OpenBabel (including Pybel)
openbabel-ruby
Ruby bindings for OpenBabel
ortep3
Thermal ellipsoid plot program for crystal structure illustrations
p3d
panav
parassign
pdb-extract
Tools for extracting mmCIF data from structure determination applications
pdb-tools
pdb2pqr
pdb2pqr is an automated pipeline for performing Poisson-Boltzmann electrostatics calculations
pdbcat
pdbcns
pdbmat
pesto
phaser
Phasing macromolecular crystal structures with maximum likelihood methods
phenix-bin
pjnmr
platon
Versatile, SHELX-97 compatible, multipurpose crystallographic tool
pmb
Automated structure refinement tools for CNS
pointless
Scores crystallographic Laue and space groups
polygon
shows qualitatively if some models parameters are over- or under-refined
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
profit
Designed to be the ultimate protein least squares fitting program
propka
psi
pyitc
PyMca
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
pymol-plugins-dssp
pymol-plugins-dynamics
pymol-plugins-emovie
eMovie is a plug-in tool for the molecular visualization program PyMOL
pymol-plugins-ezviz
assistance tool for the difficult to understand user interface of PyMOL
pymol-plugins-msms
pymol-plugins-promol
Fast and accurate regognition of active sites
pymol-plugins-psico
pymss
Multiple superposition of proteins, using a genetic algorithm for optimization
pyquante
pyrx
GUI for Virtual Screening with AutoDock
qutemol
High quality molecular visualization system that exploits GPU capabilites through OpenGL shaders
rasmol
Free program that displays molecular structure.
raster3d
a set of tools for generating high quality raster images of proteins or other molecules
rdkit
reduce
Adds hydrogens to a Protein Data Bank (PDB) molecule structure file
refmac
Macromolecular crystallographic refinement program
relax
rosetta
Prediction and design of protein structures, folding mechanisms, and protein-protein interactions
rosetta-tools
Additional scripts for rosetta
scala
scale together multiple observations of reflections
scicraft
sfcheck
Program for assessing the agreement between the atomic model and X-ray data or EM map
shakerr
shelx
Programs for crystal structure determination from single-crystal diffraction data
shiftx
With this form you can predict 1H, 13C and 15N chemical shifts for your favorite protein
shiftx2
simpson
smmp
Simple Molecular Mechanics for Proteins
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
specView
ssp
suitename
surf
talosn
theseus
Maximum likelihood superpositioning and analysis of macromolecular structures
threeV
tinker
TINKER is a molecular modeling package that includes force fields for handing large molecules and large systems, such as AMBER and CHARMM. A Java based visualization front end is included.
tisean
tm-align
trajng
unio
usf-rave-bin
The tools package from USF for macromolecular crystallography
usf-tools
usf-voidoo-bin
The tools package from USF for macromolecular crystallography
vasco
viewmol
Open-source graphical front end for computational chemistry programs
vmd
Visual Molecular Dynamics
votca-csg
Votca coarse-graining engine
votca-csgapps
webmo
Web-based interface to computational chemistry packages
wxmacmolplt
Chemical 3D graphics program with GAMESS input builder
xcrysden
xds-bin
X-ray Detector Software for processing single-crystal monochromatic diffraction data.
xdsgui
xdsi
xdsstat-bin
prints various statistics (that are not available from XDS itself)
xia2
An automated data reduction system for crystallography
xyza2pipe