Категория sci-chemistry
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
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
azara
A suite of programmes to process and view NMR data
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
ccpn
The Collaborative Computing Project for NMR
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
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
dssp
The protein secondary structure standard
easychem
Chemical structure drawing program - focused on presentation
eden
A crystallographic real-space electron-density refinement & 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
gelemental
Periodic table viewer with detailed information on the chemical elements
ghemical
Chemical quantum mechanics and molecular mechanics
gperiodic
Periodic table application for Linux
gromacs
The ultimate molecular dynamics simulation package
GromacsWrapper
Python framework for Gromacs
hollow
Production of surface images of proteins
jmol
Java molecular viever for 3-D chemical structures
ksdssp
ksdssp is an open source implementation of dssp
mars
Robust automatic backbone assignment of proteins
mdanalysis
A python library to analyze and manipulate molecular dynamics trajectories
mdtraj
Read, write and analyze MD trajectories with only a few lines of Python code
mm-align
Protein Complex Structural Alignment
modeller
Homology or comparative modeling of protein three-dimensional structures
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
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
nmrdepaker
Program to perform NMR spectra 'De-Pake-ing' and moment calculation
nmrglue
A module for working with NMR data in Python
numbat
new user-friendly method built for automatic dX-tensor determination
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)
ParmEd
Parameter/topology editor and molecular simulator
pdb-tools
Tools for manipulating and calculations on wwPDB macromolecule structure files
pdb2pqr
Automated pipeline for performing Poisson-Boltzmann electrostatics calculations
pdbcat
Manipulate and process PDB files using tools such as Perl, awk, etc
pdbcns
Convert atom names for amino acids/nucleic acid bases between PDB and CNS format
pdbmat
Calculate Tirion's model from pdb structures
povscript+
Modified molscript that uses POV-Ray, does thermal ellipsoids, and more
prekin
Prepares molecular kinemages 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
prody
Protein Dynamics Analysis
propka
pKa-value prediction of ionizable groups in protein and protein-ligand complexes
psi
Suite for ab initio quantum chemistry computing various molecular properties
pymol
A Python-extensible molecular graphics system
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-dynamics
Molecular dynamics in Pymol
pymol-plugins-emovie
PyMOL plugin for convinient movie creation
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
relax
Molecular dynamics by NMR data analysis
shelx
Crystal structure determination from single-crystal diffraction data
sparky
Graphical NMR assignment and integration program for large polymers
suitename
The ROC RNA Ontology 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
votca-ctp
Votca charge transport module
votca-xtp
Votca excitation and charge properties module
wxmacmolplt
Chemical 3D graphics program with GAMESS input builder
xds-bin
Software for processing single-crystal X-ray monochromatic diffraction data
xdsstat-bin
Prints various statistics (that are not available from XDS itself)
xyza2pipe
Cross conversion environment of NMR spectra