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The basis sets included with ECCE have -- as far as I can tell -- not been updated for many years. In addition, many of the newer basis sets that come with nwchem aren't included, such as the def2- series. nwbas2ecce is a python script that aims to automate as much as possible of the conversion process of a nwchem basis set file into the files necessary for ECCE to included it in the basis set tool. The process isn't completely automatic, but I also believe that it shouldn't be to...

is a interactive molecular visualisation program designed especially designed for coarse-grained simulation of non-spherical particles. Ellipsoids (Gay-Berne), disks, and custom shaped uniaxial particle (e.g. pear-shaped particles) can be represented.

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.

UPDATE: The latest version of NNScore1 can be found here: http://git.durrantlab.com/jdurrant/nnscore1 The latest version of NNScore2 can be found here: http://git.durrantlab.com/jdurrant/nnscore2 ================ NNScore is a scoring function for characterizing the potency of receptor-ligand complexes. It is based on neural networks, computational models that simulate the microscopic organization of the brain.

DArmstadt MAgnetic Resonance Instrument Software

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.

xyz2eps.py is an command line utility written in Python programing language which prints the geometry from xyz-file directly to the eps-file format. Originally it was designed to study the problems related to grain boundaries in graphene.

PyBact is an open source software written in Python for Bacterial Identification. The software generates simulated data matrix which accurately represents the probabilistic positive/negative results of the tested biochemical test.

A GUI program to create the plasmid database forms for BGME lab. This program presents user with a data entry form for entering plasmid information and automatically converts DNA sequence to protein, aligns it, and creates text output file.

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.

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.

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.

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.

This is a set of scripts that helps with processing of NMR pH titration data. These scripts allow for fitting (using R) and plotting of data of multiple residues. The program needs to be made more user friendly.

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/

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.

pyitc is designed for processing and analysing isothermal titration calorimetry experimental data (Microcal instruments).

CellPublisher is a free, open source program to improve the navigation of biological pathways. It converts CellDesigner diagrams into fully-featured maps that live inside a browser. The navigation is based on the Google maps API.

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.

CoCOOT is an extended collaboration system of COOT(Crystallographic Object Oriendted Toolit). It operates an add-on of original Coot. It enables to collaboration through internet.

Use SASSIE to generate and manipulate large numbers of molecular structures and then calculate the SAXS, SANS, and neutron reflectivity profiles from atomistic structures. Use for intrinsically disordered proteins. We need alpha-testers and developers.

This Project moved to https://sourceforge.net/projects/synbiowave/ because the name GeneWave is a registered trademark... Please do not use this project anymore.

Pythia is a thermodynamically based PCR primer design program.

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.

cnsFace is a GUI for the Crystallography and NMR System.