OpenScience / Software / Chemistry



NAB

Posted on February 23, 2001 by Dan Gezelter

The NAB molecular manipulation language – a computer language (specified through lex and yacc) that allows nucleic acid structures to be described in a hierarchical fashion, using a language similar to C or awk, but designed especially for the manipulatio … Continue reading →

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EMBOSS

Posted on February 23, 2001 by Dan Gezelter

EMBOSS is “The European Molecular Biology Open Software Suite”. EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety … Continue reading →

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Ghemical

Posted on February 23, 2001 by Dan Gezelter

Ghemical is a computational chemistry software package released under the GNU GPL. Ghemical can do all-atoms molecular mechanics (there is an experimental Tripos 5.2-like force field for organic molecules), and reduced protein models. Find Ghemical at: http://www.bioinformatics.org/ghemical/ghemical/index.html

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Posted in Molecular Dynamics, Molecule Viewers and Editors | Leave a comment

MMTK

Posted on February 23, 2001 by Dan Gezelter

The Molecular Modelling Toolkit (MMTK) is a Python-based Open Source program library for molecular simulation applications. Find MMTK at: http://dirac.cnrs-orleans.fr/MMTK/

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GPeriodic

Posted on February 23, 2001 by Dan Gezelter

a periodic table application. Find GPeriodic at: http://www.frantz.fi/software/gperiodic.php

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qmol

Posted on February 23, 2001 by Dan Gezelter

qmol is a simple molecular weight calculator. You can enter a formula, (e.g. CH3(CH2)2OH) and get its molecular weight (60.0959 g/mol) and its elemental composition (C3H8O: C 59.96; H 13.42; O 26.62 %). Find qmol at: https://sourceforge.net/p/qmol/wiki/Home/

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Kemistry

Posted on February 23, 2001 by Dan Gezelter

KDE-inspired molecular weight calculator Find Kemistry at: http://kemistry.sourceforge.net/

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DomainFinder

Posted on February 23, 2001 by Dan Gezelter

a free interactive program for the determination and characterization of dynamical domains in proteins. Find DomainFinder at: http://dirac.cnrs-orleans.fr/DomainFinder/

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LabJ

Posted on February 23, 2001 by Dan Gezelter

LabJ (a.k.a Electronic Laboratory Notebook, ELN, Laboratory Journal) assists in planning chemical reactions and stores chemical information. Open Source, but it requires ISIS Desktop package from MSI. Find LabJ at: http://www.karolgrela.eu/labj/

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OSET

Posted on February 23, 2001 by Dan Gezelter

Organic Synthesis Exploration Tool is a program for the retrosynthetic analysis of target molecules. It is free software distributed under the GNU General Public License. Find OSET at: http://ivan.tubert.org/caos/

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Posted in Synthesis | 5 Comments