AutoMap is a tool for structural biology and drug design.
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.
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.
A combination of useful tools for High School classes, including math classes ranging from prealgebra to calculus, and science classes ranging from IPS to AP Physics.
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.
The HyperGlossary Project enables real-time annotations of web sites for the purpose of explaining jargon-heavy pages with pop-up definitions and other resources, such as powerpoints and videos.
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
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.
MeltDNA Tool For Prediction of DNA Duplex Hybridization & Melting Thermodynamics (delta G°, delta H° and delta S° ,Tm,Ta Prediction)
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.
Parallelized calculation of molecular similarities
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!
Peptide is a project to develop an integrated software tool for Mass Spectroscopy analysis of peptides.
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.
Little script for quantum-chemical software
Ugly Perl script for processing bunches of output files from quantum-chemical software (mainly Gaussian 09).
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.
Management and Analysis Laboratory analysis
Labotaririos Control System of Hematology, blood chemistry, electrolytes, pH and Gases. Developed with Perl and MySQL symfony Order is generated análisi and prints a bar code, the sample is the parser processes the sample data capture drivers analyzers from R232 or Ethernet port and sends the data in a MySQL database then screen can montrar in symfony
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.
free2bind a suite of general purpose bioinformatics tools for computing the minimum free energy (the most stable) binding between two separate RNA molecules.
A freely available clone of the excellent molecular modelling program "O" from Alwyn Jones.
A Tk frontend to MD trajectories analysis program carma
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.