autodock_vina
- Ebuilds: 1, Stable: 1.2.7, Testing: 1.2.7 Description:
AutoDock Vina is a new open-source program for drug discovery, molecular
docking and virtual screening, offering multi-core capability, high
performance and enhanced accuracy and ease of use. [1]
AutoDock Vina has been designed and implemented by Dr. Oleg Trott
in the Molecular Graphics Lab at The Scripps Research Institute.
If you used AutoDock Vina in your work, please cite:
O. Trott, A. J. Olson, AutoDock Vina: improving the speed and accuracy
of docking with a new scoring function, efficient optimization and
multithreading
Journal of Computational Chemistry 31 (2010) 455-461
Homepage:http://vina.scripps.edu/ License: Apache-2.0
bodr
- Ebuilds: 1, Testing: 10 Description:
Blue Obelisk Data Repository (BODR) is a shared data repository. It lists
many important chemoinformatics data such as elemental properties, atomic
radii, etc. including references to original literature. Software developers
can use this repository on online webpages or in chemistry software for
free.
Homepage:https://sourceforge.net/projects/bodr License: MIT
cara-bin
- Ebuilds: 1, Testing: 1.8.4-r2 Description: Analysis of NMR spectra and Computer Aided Resonance Assignment
Homepage:http://www.nmr.ch License: CARA
chimera
- Ebuilds: 2, Testing: 1.19 Description: Next generation molecular visualization program from RBVI
Homepage:https://www.cgl.ucsf.edu/chimera/ License: chimera
clashlist
- Ebuilds: 1, Stable: 3.17-r1, Testing: 3.17-r1 Description:
Clashlist is a simple UNIX script which uses the awk facility along with
the programs Probe and Cluster to build lists of van der Waals clashes
from an input PDB-format molecular data file (with H atoms). These lists
are organized such that collections of interacting residues are grouped
together, sorted by the worst clash. For the purposes of this analysis,
a clash is defined as a van der Waals overlap >= 0.4 A.
Homepage:http://kinemage.biochem.duke.edu/software/index.php License: richardson
cluster
- Ebuilds: 2, Stable: 1.3.081231-r2, Testing: 1.3.081231-r2 Description:
Cluster is a simple UNIX C++ program to build lists of collections
of interacting items from records containing interacting pairs
and larger fragments.
It reads in lines consisting of two or more names and output
connected clusters of names. Each line of output is
prefixed with a cluster number, the size of the cluster
and an optional name string.
Homepage:http://kinemage.biochem.duke.edu/software/index.php License: richardson
easychem
- Ebuilds: 1, Stable: 0.6-r2, Testing: 0.6-r2 Description:
EasyChem is a program designed to draw chemical molecules, written under
Linux using Gtk+ 2.4. It is implemented with a strong focus on producing
press quality molecules. Easychem can be a little more difficult to learn to
use, but when mastered it can be very fast and powerful. It can draw
ornaments easily, and exports to EPS with LaTeX fonts among other things.
Homepage:http://easychem.sourceforge.net/ License: GPL-2
elem
- Ebuilds: 1, Stable: 1.0.3-r3, Testing: 1.0.3-r3 Description: periodic table of the elements
Homepage:http://elem.sourceforge.net/ License: GPL-2
erkale
- Ebuilds: 1, Testing: 0_p20220106 Description:
ERKALE is a quantum chemistry program used to solve the electronic
structure of atoms, molecules and molecular clusters. It was developed at
the University of Helsinki, and is currently developed at Aalto University.
The main use of ERKALE is the computation of x-ray properties, such as
ground-state electron momentum densities and Compton profiles, and core
(x-ray absorption and x-ray Raman scattering) and valence electron
excitation spectra of atoms and molecules.
Homepage:https://github.com/susilehtola/erkale License: GPL-2
gelemental
- Ebuilds: 1, Stable: 2.0.2, Testing: 2.0.2 Description: Periodic table viewer with detailed information on the chemical elements
Homepage:https://github.com/ginggs/gelemental/ License: GPL-3 MIT
gnome-chemistry-utils
- Ebuilds: 1, Testing: 0.14.17_p6-r4 Description: Programs and library containing GTK widgets and C++ classes related to chemistry
Homepage:https://gchemutils.nongnu.org/ License: GPL-3
gperiodic
- Ebuilds: 1, Stable: 3.0.3-r1, Testing: 3.0.3-r1 Description:
GPeriodic is a program for looking up various data about elements from the
periodic table, based on the GTK2 toolkit. It also features a command line
interface.
Homepage:https://sourceforge.net/projects/gperiodic/ License: GPL-2
mdtraj
- Ebuilds: 1, Testing: 1.10.3 Description: Read, write and analyze MD trajectories with only a few lines of Python code
Homepage:https://mdtraj.org License: LGPL-2.1+
mics
- Ebuilds: 1, Testing: 1.00.2011.327.12.00-r1 Description: Prediction of Protein Structural Motifs from NMR Chemical Shifts
Homepage:https://spin.niddk.nih.gov/bax/software/MICS/ License: all-rights-reserved
molsketch
- Ebuilds: 2, Testing: 0.8.4 Description:
Molsketch is a 2D molecular editing tool. Its goal is to help you draw
molecules quick and easily. Of course you're creation can be exported
afterwards in high quality in a number of vector and bitmap formats.
Homepage:https://molsketch.sourceforge.io/ https://github.com/hvennekate/Molsketch/ License: GPL-2
mpqc
- Ebuilds: 1, Testing: 2.3.1-r4 Description: The Massively Parallel Quantum Chemistry Program
Homepage:http://www.mpqc.org/ License: GPL-2
openbabel
- Ebuilds: 3
Description:
Open Babel is a chemical toolbox designed to speak the many languages of
chemical data. It's an open, collaborative project allowing anyone to
search, convert, analyze, or store data from molecular modeling, chemistry,
solid-state materials, biochemistry, or related areas.
Homepage:https://openbabel.org/ https://github.com/openbabel/openbabel/
panav
- Ebuilds: 1, Testing: 0.20130730 Description:
It has been estimated that more than 20% of the proteins in the BMRB are
improperly referenced and that about 1% of all chemical shift assignments are
mis-assigned. These statistics also reflect the likelihood that any newly
assigned protein will have shift assignment or shift referencing errors. The
relatively high frequency of these errors continues to be a concern for the
biomolecular NMR community. While several programs do exist to detect and/or
correct chemical shift mis-referencing or chemical shift mis-assignments, most
can only do one, or the other. The one program (SHIFTCOR) that is capable of
handling both chemical shift mis-referencing and mis-assignments, requires the
3D structure coordinates of the target protein. Given that chemical shift
mis-assignments and chemical shift re-referencing issues should ideally be
addressed prior to 3D structure determination, there is a clear need to develop
a structure-independent approach. Here, we present a new structure-independent
protocol, which is based on using residue-specific and secondary
structure-specific chemical shift distributions calculated over
small (3–6 residue) fragments to identify mis-assigned resonances. The method
is also able to identify and re-reference mis-referenced chemical shift
assignments. Comparisons against existing re-referencing or mis-assignment
detection programs show that the method is as good or superior to existing
approaches.
Homepage:https://link.springer.com/article/10.1007%2Fs10858-010-9407-y/fulltext.html License: all-rights-reserved
pdbcat
- Ebuilds: 1, Testing: 1.3-r1 Description:
The Brookhaven Protein Data Bank stores atomic coordinate information
for protein structures in a column based format. This is designed to
be read easily read by FORTRAN programs. Indeed, if you get the
format description (from anonymous ftp to ftp.pdb.bnl.gov, the file
/pub/format.desc.ps) they show the single input line needed to read
each record type.
However, I am a C/C++ programmer in the Unix environment. It is a
easier for me to deal with field based input than column based ones.
If the fields are white space delimited I can easily use awk and perl
to manipulate the coordinate information. So I needed some way to
convert the ATOM and HETATM records of PDB files from the standard
column based format to a field based one and back again. It needed
to denote missing fields if they exist.
That converter is `pdbcat'.
Homepage:https://www.ks.uiuc.edu/Development/MDTools/pdbcat/ License: free-noncomm
pdbmat
- Ebuilds: 1, Testing: 3.89-r1 Description:
A fortran program in which Tirion's model (also called the Elastic Network
Model) is implemented. Within the frame of this model, atoms (particles)
less than cutoff (angstroms) away from each others are linked by springs of
same strength. Alternatively, a list of interacting atoms can be given to the
program.
Requirements: a file with the coordinates of the system, in PDB (Protein Data
Bank) or "x y z mass" format.
Output: the hessian (the mass-weighted second derivatives of energy matrix),
in the "i j non-zero-ij-matrix-element" format.
Diagstd, a fortran program with a standard diagonalization routine, can next
be used in order to obtain the corresponding normal modes of the system. If
the system is large, the RTB approximation can prove usefull (see below).
Homepage:http://ecole.modelisation.free.fr/modes.html License: CeCILL-2
propka
- Ebuilds: 1, Testing: 3.5.1 Description: pKa-value prediction of ionizable groups in protein and protein-ligand complexes
Homepage:https://github.com/jensengroup/propka License: LGPL-2.1
psi
- Ebuilds: 1, Stable: 3.4.0-r3, Testing: 3.4.0-r3 Description: Suite for ab initio quantum chemistry computing various molecular properties
Homepage:http://www.psicode.org/ License: GPL-2
sage-jmol-bin
- Ebuilds: 1, Testing: 14.29.52 Description: Jmol is a java molecular viever for 3-D chemical structures.
Homepage:https://jmol.sourceforge.net/ License: LGPL-2.1
suitename
- Ebuilds: 1, Testing: 0.3.070628 Description:
Suitename is a new C program that supports the ROC RNA Ontology Consortium
consensus RNA backbone nomenclature and conformer-list development (see our RNA
backbone rotamer section.
From dihedral-angle input for a specific RNA structure (usually from Dangle),
Suitename categorizes the RNA backbone geometry of each suite (the
sugar-to-sugar version of a residue) either as an outlier ("!!") or as belonging
to one of the 53 defined conformer bins. The output is either a
one-line-per-suite report, or a linear conformer string (as shown below the
image here) in one of several variant formats. Suitename is built into
MolProbity, producing entries in the multi-criterion chart for an RNA model and
also a suitestring file. The Suitename code is made available here for bulk or
individual command-line use.
Homepage:http://kinemage.biochem.duke.edu/software/suitename.php License: richardson
tinker
- Ebuilds: 1, Testing: 8.2.1-r1 Description: Molecular modeling package that includes force fields, such as AMBER and CHARMM
Homepage:https://dasher.wustl.edu/tinker/ License: Tinker
tm-align
- Ebuilds: 1, Stable: 20150914-r1, Testing: 20150914-r1 Description:
TM-align is a computer algorithm for protein structure alignment using dynamic
programming and TM-score rotation matrix. An optimal alignment between two
proteins, as well as the TM-score, will be reported for each comparison. The
value of TM-score lies in (0,1]. In general, a comparison of TM-score smaller
0.2 indicates that there is no similarity between two structures; a TM-score
greater 0.5 means the structures share the same fold.
What is the difference between TM-score and TM-align? The TM-score program
is to compare two models based on their given and known residue equivalency.
It is usually NOT applied to compare two proteins of different sequences. The
TM-align is a structural alignment program for comparing two proteins whose
sequences can be different. The TM-align will first find the best equivalent
residues of two proteins based on the structure similarity and then output a
TM-score. The TM-score values in both programs have the same definition.
Homepage:https://zhanggroup.org/TM-align/ License: tm-align
vesta (ambiguous, available in 2 overlays)
- Ebuilds: 4, Testing: 3.5.8 Description: Visualization for Electronic and STructural Analysis
Homepage:https://jp-minerals.org/vesta License: VESTA
wxmacmolplt
- Ebuilds: 1, Testing: 7.7.2-r1 Description:
wxMacMolPlt is a program for plotting 3D molecular structures and normal modes (vibrations), various orbitals and electron density maps. It reads a variety of file formats including any GAMESS input, log or IRC file directly to create animations. It has a simple GAMESS input (.inp) builder and a primitive molecule builder.
Homepage:http://brettbode.github.io/wxmacmolplt/ License: GPL-2
xds-bin
- Ebuilds: 1, Testing: 20240831 Description: Software for processing single-crystal X-ray monochromatic diffraction data
Homepage:https://xds.mr.mpg.de License: free-noncomm