Search Results for "command line"

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.

'isotope' is a small command-line utility to calculate the isotope pattern for a given chemical formula. It allows to run calculations interactively, in batch mode, via the command line, or (using a webserver) via a web interface.

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.

A perl molecular toolkit designed to assist in general molecular modelling activities. Silico provides file format conversion, molecular manipulation and analysis and a simple way to write wrapper scripts around other preexisting software packages.

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.

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.

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...

PSI is an open-source program for computing molecular properties using high-accuracy, ab initio, quantum mechanical models.

mobcalPARSER is a command line based PERL frontend/interface for MOBCAL with limited wrapper functionality. "MOBCAL - A Program to Calculate Mobilities" is available from Professor Martin F. Jarrold's webpage http://www.indiana.edu/~nano/software.html.

A command-line biochemical network compiler for systems biology.

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".

Wio-gpc is a command line driven perl application designed for polymers molecular weight calculations based on chromatographic data. Results of GPC, SEC or GFC analysis can be converted to Mn, Mw and molecular weight distributions (MWD).

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.

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

mySQL db app that stores chemical structures, calc. descriptors and property values. It has a descriptor calculator and a method that filters descriptors correlated with property values. Easy to plug-in your descriptor calc. Ideal for QSAR specialists!

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.

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.