RSS 6 projects tagged "Bioinformatics"

No download Website Updated 02 Nov 2004 Cactus

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Pop 153.49
Vit 3.46

Cactus is a general, modular, parallel environment for solving systems of partial differential equations. The code has been developed over many years by a large international collaboration of numerical relativity and computational science research groups and can be used to provide a portable platform for solving any system of partial differential equations.

Download Website Updated 03 Jan 2006 Staden Package

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Pop 35.20
Vit 1.90

The Staden Package is a set of interactive tools for DNA sequence assembly and editing, as well as DNA and protein sequence analysis, the best known of which is "gap4".

Download Website Updated 25 May 2006 Pattern Classification Program

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Pop 78.61
Vit 2.68

PCP (Pattern Classification Program) is a machine learning program for supervised classification of patterns. It runs in interactive and batch modes, and implements the following machine learning algorithms and methods: k-means clustering, Fisher's linear discriminant, dimension reduction using Singular Value Decomposition, Principal Component Analysis, feature subset selection, Bayes error estimation, parametric classifiers (linear and quadratic), pseudo-inverse linear discriminant, k-Nearest Neighbor method, neural networks, Support Vector Machine algorithm (SVM), model selection for SVM, cross-validation, and bagging (committee) classification.

Download Website Updated 07 Jun 2007 octopus TDDFT

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Pop 49.72
Vit 1.53

octopus is a program aimed at the ab initio virtual experimentation on a hopefully ever increasing range of systems types. Electrons are describe quantum-mechanically within the Density-Functional Theory (DFT), in its time-dependent form (TDDFT) when doing simulations in time. Nuclei are described classically as point particles. Electron-nucleus interaction is described within the Pseudopotential approximation.

No download Website Updated 24 Feb 2007 APBS

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Pop 23.75
Vit 51.13

APBS is a software package for the numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. Continuum electrostatics plays an important role in several areas of biomolecular simulation, including simulation of diffusional processes to determine ligand-protein and protein-protein binding kinetics, implicit solvent molecular dynamics of biomolecules, solvation and binding energy calculations to determine ligand-protein and protein-protein equilibrium binding constants and aid in rational drug design, and biomolecular titration studies.

No download Website Updated 24 Feb 2007 PDB2PQR

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Pop 13.27
Vit 51.13

PDB2PQR is a Python software package that automates many of the common tasks of preparing structures for continuum electrostatics calculations, providing a platform-independent utility for converting protein files in PDB format to PQR format. These tasks include adding a limited number of missing heavy atoms to biomolecular structures, determining side-chain pKas, placing missing hydrogens, optimizing the protein for favorable hydrogen bonding, assigning charge and radius parameters from a variety of force fields.

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Open Camera

A camera app for Android.

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Project Spotlight

Canumb

Software that converts data into something meaningful and interpretable.