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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
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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.
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 Chemical Manager application can be of great help to Organic Chemistry Departments. University research groups will benefit from using this application, since it was optimized for their needs. Currently, Technion Chemistry department is benefiting from it.
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.
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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/
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.
PocketAnalyzerPCA combines a geometric algorithm for detecting pockets in proteins with Principal Component Analysis and clustering. This enables visualization and analysis of pocket conformational distributions of large sets of protein structures.
Methods and testing of methods for automatic analysis of in situ cyclic
voltammetry data.
This, at least initially, is the code from my masters thesis, which was
done as a contribution to a larger project called Aevum. Aevum is being
developed at t
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Metmask has moved to github http://github.com/hredestig/metmask
Metmask is a tool written in python for managing chemical identifiers for metabolomics experiments. It can incorporate identifiers from local textfiles, several online databases, query PubChem and record all found associations in a local sqlite database.
--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.
This software can be used to calculate thermochemical and kinetic quantities like, enthalpy, entropy, heat capacity and transition state theory rate constants from spectroscopic/quantum data.
Python program for fitting rate constants to primarily kinetic data as 1st or 2nd order kinetics or autocatalysis. It also allows specific noise cancelling, data smoothing by fourrier transform, box averaging and flowing mean. For Python 2.6 or earlier.
HOT is a package of Matlab and Octave compatible functions that manage thermodynamic data for a wide range of species. Functions calculate almost all the most common thermodynamic quantities of mixtures.
Python users may also want to look at PYroMat at https://chmarti1.github.io/PYroMat/index.html
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.
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++.
PyChemEq is an Open Source project which goal is to simulate chemical equilibrums. It provides classes (that are the project's "kernel" ) and a user interface using PyGtk and Glade. The whole project will be written in Python.
Goldify is a set of tools that allow automated addition of links into electronic documents. Its main purpose is to allow such addition of links into documents that wish to link to the IUPAC GoldBook (http://goldbook.iupac.org).
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