Open Source Python Bio-Informatics Software for Linux

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.

The software package 'relax' is designed for the study of molecular dynamics through the analysis of experimental NMR data. Organic molecules, proteins, RNA, DNA, sugars, and other biomolecules are all supported. It supports exponential curve fitting for the calculation of the R1 and R2 relaxation rates, calculation of the NOE, reduced spectral density mapping, the Lipari and Szabo model-free analysis, study of domain motions via the N-state model and frame order dynamics theories using anisotropic NMR parameters such as RDCs and PCSs, the investigation of stereochemistry in dynamic ensembles, and the analysis of relaxation dispersion data.

ABE is a small, fast and convenient program for visualizing and modeling experimental bioassay data. The data can be modeled using either polynomials or a more specific four-parameter model based upon the standard, sigmoidal dose-response curve.

This project is A Mitochondrial OxydoReduction Simulation System. It consists of two linked projects: a program for displaying and analysing large biomolecular systems (Floral) and a multi-agent simulator for biomolecular oxydoreduction systems (AMORSS).

This software has moved to http://www.poissonboltzmann.org/.

We here present a novel computer algorithm, called AutoClickChem, capable of performing many click-chemistry reactions in silico. In silico modeling of click-chemistry products may prove useful in rational drug design and drug optimization.

The Collaborative Computational Project for NMR (CCPN) provides tools and knowledge to maximise the impact of the biological NMR studies. The CCPN software facilitates data analysis and software integration. The project actively promotes the exchange of knowledge and provides training and best practices for the NMR community. CCPN also has a leading role in the development of a NMR data-sharing standard and coordination of NMR instrumentation proposals for RCUK and BIS. The 28 partners of CCPN jointly cover all aspects of biomolecular NMR and together they promote excellence in science in their respective fields.

[NOTICE!] FingerID since version 1.4 will be hosted on github: https://github.com/icdishb/fingerid A metabolite identification software using tandem mass spectrometry and kernel methods. The related paper can be found at http://bioinformatics.oxfordjournals.org/content/early/2012/07/18/bioinformatics.bts437.abstract. Now it supports unix/linux like system.

Frowns is a chemoinformatics system written almost entirely in python.

LATEST VERSION NOW LOCATED AT http://git.durrantlab.com/jdurrant/lipidwrapper As ever larger and more complex biological systems are modeled in silico, approximating physiological lipid bilayers with simple planar models becomes increasingly unrealistic. When building large-scale models of whole subcellular environments, models of lipid membranes with carefully considered, biologically relevant curvature are essential. LipidWrapper, written by Jacob Durrant in the lab of Rommie E. Amaro, is capable of creating curved membrane models with geometries derived from various possible sources, both experimental and theoretical. We are hopeful that this utility will be a useful tool for the computational-biology community.

Command-line, PubChem PUG client, written in Python; developed for Linux

Client to the PubChem Tool (PCT), The Power User Gateway (PUG). Written in Python and developed for use with Linux.

Python module for manipulation of Crystallographic Information Framework (CIF) files

A univariate and multivariate analysis UI. This project is no longer under development. Please use as you wish.

PyMOL Plugins aims to provide many plugins for the PyMOL software. You can find further informations about PyMOL on this website: http://www.pymol.org/

PySCeS is the Python Simulator of Cellular Systems. For a network of coupled reactions it does a stoichiometric matrix analysis, calculates the time course and steady state, and does a complete control analysis.

Stochastic simulator for signaling pathways occuring in biological cells. Handles reaction-diffusion processes in 3D tetrahedral meshes. Please check our new repository: https://github.com/CNS-OIST/STEPS

A tool to calculate atoms exposition to a probe in a three dimensional molecule structure.

A repository of Python extension scripts for use with the Sparky (http://www.cgl.ucsf.edu/home/sparky) NMR assignment package. No packaged releases yet, but there are scripts in the Sourceforge CVS@ http://sparkyscripts.cvs.sourceforge.net/sparkyscripts

UPDATE: LATEST VERSION AT http://git.durrantlab.com//jdurrant/wisp Allostery can occur by way of subtle cooperation among protein residues (e.g., amino acids) even in the absence of large conformational shifts. Dynamical network analysis has been used to model this cooperation, helping to computationally explain how binding to an allosteric site can impact the behavior of a primary site often many angstroms away. Traditionally, computational efforts have focused on the most optimal path of correlated motions leading from the allosteric to the primary active site. We present a program called Weighted Implementation of Suboptimal Paths (WISP) capable of rapidly identifying additional suboptimal pathways that may also play important roles in the transmission of allosteric signals. Aside from providing signal redundancy, suboptimal paths traverse residues that, if disrupted through pharmacological or mutational means, could modulate the allosteric regulation of important drug targets.

Sharing lists of molecular structures with associated chemical properties is a common task in computer-aided drug design and medicinal chemistry. WebChem Viewer is a simple, free, open-source program that generates HTML-formatted output that can be viewed in any modern web browser, on any operating system (including mobile), without requiring the installation of additional software. The output can also be easily incorporated into existing web pages. WebChem Viewer is released under the FreeBSD license. It was created by Jacob Durrant, a post-doc in the lab of Rommie E. Amaro.

--UPDATE-- New Version is now integrated in the official PyMOL plugin repository! --UPDATE-- The BNI (Beyond Normal Interaction)- Tools is a plug in for the PyMOL molecular visualization system which adds additional functionalities and presets to the PyMOL GUI and also adds useful extended commands.

defunct

geostd is an open-source set of restraints for molecules involved in macromolecular structure refinement. The restraints reduce the number of variables making the solution of protein structures a more tractable process.

Tandem mass spectral peptide identification and validation software, similar to X!Tandem, OMSSA, MyriMatch. Suitable for single hosts through large clusters. Written in Python for simplicity, with performance-critical sections in C++.