Open Source Python Molecular Science Software - Page 3

A simple tool to design DNA primers for mutagenesis in BGME lab (JHU). Allows users to select or enter background sequence and add current and new mutations. During the design process, users are presented with various updating checks to guide them.

ProtPOS is a self-contained, lightweight, and easy-to-use software package for predicting the preferred orientation of protein on a given surface upon initial adsorption. It searches quickly for the low energy protein poses in all translational and rotational degrees of freedom of the protein with respect to the surface using particle swarm optimization. Each successful run returns the lowest energy orientation of the protein on the surface in PDB format, which is readily used for MD simulations. ProtPOS is implemented in Python, making use of the PyMOL library for generating protein conformations and calling GROMACS externally to calculate protein-surface interaction energies. https://cbbio.online/software/protpos/

Software to identify cavities and crevices in proteins. The goal is to be able to take a protein structure, and to differentiate between five different types of environments for each residue: buried, surface, interfacial, cavity, or crevice.

The Protein Geometry Database hosts the development code for a flexible database for searching protein geometry, as well as a library for accessing this data for protein modeling & refinement programs.

Sign up to our mailing list at http://www.protospacer.com/contact.html. Protospacer allows researchers to build, analyze, and share their own database of CRISPR target-sites. This enables the development of custom libraries and helps to transfer the CRISPR technology to new organisms. Each Protospacer database is a simple catalogue of all possible Cas9 target-sites within a given FASTA sequence, i.e. all NGG/NAG sites. Protospacer then allows the user to sub-select targets from the database by gene ID, by exon/intron/UTR location, by sequence similarity, or by genomic co-ordinate. From here, users are able to evaluate potential off targeting, to export results in FASTA format or tabulated (e.g. for Microsoft Excel), and to connect to the Integrative Genomics Viewer (IGVref) and view target-sites in the context of genomic annotations, amino acid translations, and HT-Seq data (for off-target validation). We provide online video tutorials and a toy database from our main website.

PyCancerDB is a source code distribution providing a Web-based interface for browsing and updating the Cancer Proteomics Database, together with scripts for maintaining the database.

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/

PySpline is a graphical, cross-platform program for processing X-ray absorption spectroscopy (XAS) and Extended X-ray absorption fine structure (EXAFS) data. It allows processing parameters to be adjusted and observe the effect on R-space data.

Quantum Chemistry Import Tool is a django application that parses the output file of quantum chemistry software as NWChem, Octopus, Gaussian, etc. The result can be saved in relational database.

SMMP (Simple Molecular Mechanics for Proteins) is a program library for protein simulations with an emphasis on advanced Monte Carlo algorithms. It includes various force fields to calculate the energy of a protein and protein-protein interactions.

The Structural Proteomics Application Development Environment is a Python tool kit for developing and deploying bioinformatics applications. Handles graphics, analysis, and modeling of protein sequence and structure. Source and Win installers available. SPADE source code can be cloned from http://www.github.com/deaconjs/SPADE.

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

:awsum: You lost the game.

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

SynBioLib -- your toolkit for synthetic biology applications. SynBioLib aims to establish a platform on which the Synthetic Biology community can develop and share code that is common to many tasks and programs.

A bioinformatics tool for the annotation and tag-counting of next-gen Illumina Solexa datasets. TASE works with CASAVA 1.0 builds, providing annotation, tag counts and visualization in a rapid manner.

The CCP1GUI project aims to develop a free, extensible Graphical User Interface to various computational chemistry codes developed by the worldwide academic community, with an emphasis on ab initio Quantum Chemistry codes.

Very simple python script which saves you the pains of counting the amino acids/DNA bases in fasta files from the Uniprot and NCBI RefSeq Database (1, 2). Lets say you want the amino acid sequence of range 128-387 from a 1000 amino acid protein - this script will help you to avoid counting mistakes by just showing you the specified sequence in amino acids and coding DNA base pairs (ideal for amplification primer design) of a specified Uniprot ID. - Requires BioPython (3) and Bioservices Package (4) (1) The UniProt Consortium UniProt: a hub for protein information Nucleic Acids Res. 43: D204-D212 (2015). (2) RefSeq: an update on mammalian reference sequences. Nucleic Acids Res. 2014 Jan 1;42(1):D756-63. (3) Cock PJ et al. Bioinformatics (2009) (4) Cokelaer et al, Bioinformatics (2013)

Wattos is a collection of mostly Java programs for Structural Biology and NMR Spectroscopy. It's programs analyze, annotate, parse, archive, and disseminate experimental NMR data deposited by authors world wide into the PDB and BMRB.

WebBabel is a python web application using OpenBabel to convert files from one format to another. It runs under Windows, Mac or Linux on your desktop, workstation or laptop. It uses the Jmol (or Marvin) viewer to show the structures being converted.

Collection of utilities based on two basics classes: Matematica and VarData. Matematica) performs math operations on vectors and matrices for smoothing, interpolation, convolution, image processing... VarData) manipulate a structure of points connected by links. Addraw) openGL engine. ElPoly) analyze mechanical properties of polymer and membrane like structures. Addyn) perform molecular dynamics and Monte Carlo simulations and has a solver for 4th oder PDE. Avvis) perform all the operation of Matematica on different sets of data visualized on a Qt graphical interface. DrImage) image manipulation on the Matematica filters. The program is intended to use as less as possible external libs (optional: openGL, gsl, fftw, cgal, png, tiff, boost, MPI, Qt...).

Cca-forum unifies the Common Component Architecture tools and tutorial. It includes the CCA specifications, the Ccaffeine framework for HPC, and related tools. These support multilanguage scientific and parallel computing.

cnsFace is a GUI for the Crystallography and NMR System.

A laboratory information management system (LIMS) geared towards academic research groups in the life sciences. Written in Python and using the Django framework, you run this software on your own server.

Esra is a 100% pure java library for the interactive analysis of molecular mechanics data. Mangles your data in your favorite scripting language.