Molecular Science
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molR The "molR" is a set of R functions for working with and manipulating (bio)molecular data.
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molDX a flash software for molecule demostration
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PocketDepth : binding site prediction PocketDepth helps determine binding grooves for protein molecules. Applicable in Bioinformatics and Drug discovery. Literature - http://www.ncbi.nlm.nih.gov/pubmed/17949996 Author's thesis - http://openwetware.org/wiki/Kalidas_Y
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PEAT Protein Engineering Analysis Tool (PEAT) is a suite of programs for the capture, analysis and prediction of biophysical characteristics of proteins
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TARIS TARIS (Tree Analysis and Representation of Isopotential Surfaces) is a software package designed for molecular similarity purposes in the field of Computational Chemistry. Users are allowed to compare molecules through their MEP loading .cube files.
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SPADE 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.
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LigandAlign This software is developed by Kalidas (http://openwetware.org/wiki/Kalidas_Y) as part of his Ph.D. thesis. The method enables alignment of ligand molecules considered molecular graphs. It is useful in the domain of drug discovery and bioinformatics.
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Java n-body simulator An attempt to make a n-body simulator with java
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Tools for SAXS Simulation A family of programs for building coarse-grained models (eg. of macromolecules), manipulating them (geometrical transformations and more) and calculating their X-ray scattering patterns (1D and 2D too). Uses PVM for parallelization.
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lady The project devoted to develop LADY software. LADY is a abbreviation formed from LAttice DYnamics toolkit. The software is the semi-emperical program which aids to simulate the dynamical property of crystals within a selected potential function.
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mobcalPARSER A cross-platform interface for the *.mfj file format.
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QMGA QMGA is a Qt-based molecular graphics application for visualizing large ensembles of ellipsoids, spherocylinders or spheres. It is conceived for coarse-grained mesoscopic molecular simulation, but can be used for any kind of convex body systems.
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HOPPscore - Protein Structure Quality HOPPscore is a simple application for evaluating the structural quality of theoretical or experimental protein structures. Protein are evaluated by comparing structure fragments to a reference dictionary of fragments from high resolution structures.
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Spheritool Develop a basic understanding of the behavior of polar spherical coordinates through selected examples. Provide sample files for diverse mathematics engines
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Best Reciprocal Hit from BLAST alignment Windows command line utility calculating protein orthologs using best reciprocal hit from BLAST alignment output
5 weekly downloads -
bb aaa
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specmark SpecMark (spectral Markov) is a method for calculating the joint probability distribution over species in a regulatory network.
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OpenCFU An application to count bacterial colonies and other circular objects
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ERmod Approximate solvation free energy calculator
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arrayplex ArrayPlex integrates various forms of microarray data from diverse annotation and primary data sources. It provides a programmatic framework (API set) for collaborative development and deploys as easy to maintain client-server architecture.
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sibRNAfold The sibRNAfold program is a modification of the Vienna RNAfold program for RNA secondary structure prediction through energy minimization.
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ProSpectND ProSpectND is a software package for signal processing of multidimensional NMR spectra.
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Mazridge Mazridge is a free rigid body dynamics engine written in C/C++ for use as a library.
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librysq librysq is C/C++ implementation of the Rys quadrature for computing arbitrary electron repulsion integrals on CPU and CUDA GPUs. A FORTRAN interface is provided for compatibility with the existing chemistry packages.
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BAIT Software to help analyse Strand-Seq data
2 weekly downloads
