Open Source Perl Chemistry Software

The Sashimi project hosts the Trans-Proteomic Pipeline (TPP), a mature suite of tools for mass-spec (MS, MS/MS) based proteomics: statistical validation, quantitation, visualization, and converters from raw MS data to the open mzML/mzXML formats.

IFEFFIT is a library and set of interactive programs for the analysis of x-ray absorption fine-structure (XAFS) data. IFEFFIT combines state-of-the-art analysis algorithms with graphical display of XAFS data, and general data manipulation. It can be

free2bind a suite of general purpose bioinformatics tools for computing the minimum free energy (the most stable) binding between two separate RNA molecules.

MeltDNA Tool For Prediction of DNA Duplex Hybridization & Melting Thermodynamics (delta G°, delta H° and delta S° ,Tm,Ta Prediction)

The Blue Obelisk Data Repository lists many important chemoinformatics data such as element and isotope properties, atomic radii, etc. including references to original literature. Developers can use this repository to make their software interoperable.

The program does nmr product operator calculations for one, two, three and four spins. Receiver phase cycling is possible in conjunction with pulse phase cycling to simulate coherence pathway selection. An extensive manual and help files are included. Currently running under Linux and Windows.

This project contains a custom version of the GROMACS molecular dynamics software package that helps users to choose parameters for the PME electrostatics model which produce a known error in the PME approximation for minimal computational cost.

AutoMap takes a series of poses obtained from molecular docking and applies the site, epitope and conformational mapping techniques to the poses to select likely ligand binding modes.

ALC (Automated Layer Construction) is a computer program that highly simplifies the building of reduced modular models of signaling systems, according to the layer-based approach.

CHIMP aims to provide a complete suite of tools for the investigation and modeling of chemical systems. It currently is able to parse chemical reaction mechanisms and run kinetic Monte Carlo simulations on the reacting system.

The Functional Annotation and Correlation Tool allows the meta-analysis of data from high-throughput experiments (typically microarrays) by annotating (clones, genes, GeneOntology, location, etc.) and correlating data sets to identify important patterns.

Gaussian Output Tools is a package of simple scripts to extract data from Gaussian output files.

GVIB is a user friendly package for vibrational analysis. Given a molecular geometry, it will calculate vibrational frequencies and intensities using anharmonic internuclear potential.

LabJ-ng is a laboratory notebook for organic chemists. It has a client-server architecture with a web browsers interface. Data is stored on MySQL database. Chemical reactions are drawned in java applet window. See projct website for example.

NX is a program for nonadiabatic molecular dynamics in the electronic excited states. It is based on the surface hooping approach.

Diversity assessments and comparisons of large compound databases require calculating similarities of millions of compounds in an affordable time. ParaSim addresses this challenge by parallelizing the calculations according to the number of computing cores available on a single machine. It is optimized for the throughput of very large numbers of query structures against very large numbers of reference structures. As as special feature, ParaSim allows to store and and to access frequently queried datasets as persistant objects in memory for short response times. ParaSim calculates chemical similarities based on binary structural fingerprints. It does not compute fingerprints by itself but relies on third party software to do so. Basically, all types of structural fingerprints which can be stored in an array of bits (a bitset) can be used by ParaSim. See the Wiki (https://sourceforge.net/p/parasim/wiki/Documentation/) for detailed documentation. FEEDBACK HIGHLY APPRECIATED!

PerlMol is a collection of Perl modules for chemoinformatics and computational chemistry with the philosophy that "simple things should be simple". It should be possible to write one-liners that use this toolkit to do meaningful "molecular munging".

Plotamber is a Perl script for an easy and automated plotting of properties derived from molecular dynamics or minimization calculations done with Amber, NAMD or Charmm.

ProgPorts is an administrative and easy user interface to hundreds of proteomics, molecular dynamics, and protein crystallography programs. It is a hybrid of the prog/setup system, developed at Johns Hopkins University, and GNU-Darwin ports system.

SDF or Structures Data File is a file format developed by MDL to handle a list of molecular structures with associated properties. The SDF toolkit provides small tools to read and parse SDFs, filter, and add/remove properties.

wacrgEIS is software developed for the West Australian Corrosion Research Group (wacrg) for analysis of Electrochemical Impedance Spectroscopy (EIS) data.

A command-line biochemical network compiler for systems biology.

hr ("High Resolution") is a small command-line utility to calculate possible elemental compositions for a given mass. It allows to run calculations interactively, in batch mode, via the command line, or (using a webserver) via a web interface.

htcontrol is a software to control high-temperature single crystal XRD experiments on a STOE IPDS II or 2T diffractometer platform. A Manson SDP2210 power unit is needed as well as the ICP DAS I7019 data acquisition interface (amount of investment approx. 600 EUR). htcontrol is written in Perl and runs on a cygwin platform to be installed on the WinXP/10 host. Data collections are performed with Stoe's WinXpose (>=1.7.3) via the non-interactive XML interface. For details see: J. Appl. Crystallogr. 42(1), 140-142, DOI:10.1107/S0021889808035607