RSS 128 projects tagged "Bioinformatics"

Download Website Updated 15 Mar 2002 BioJava

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Pop 157.61
Vit 2.38

BioJava aims to provide a comprehensive set of Java components for the rapid development of applications in Bioinformatics. It contains interfaces for representing Sequences, Features, and other important bioinformatics concepts. It can also read and write sequence data in a variety of common formats and communicate with Ensembl databases and with DAS and BioCorba servers.

Download Website Updated 27 Sep 2009 Bioperl

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Pop 98.43
Vit 8.04

Bioperl is set of Perl Modules for bioinformatics. It contains objects for Sequences, features on Sequences, and other important bioinformatics attributes.

No download Website Updated 15 Aug 2001 Ensembl

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Pop 18.08
Vit 1.83

Ensembl is an open source project to create and automatically maintain annotations on DNA sequence.

Download Website Updated 22 Sep 2006 JChemPaint

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Pop 172.16
Vit 9.11

JChemPaint is a program for drawing 2D chemical structures like those found in most chemistry textbooks.

Download Website Updated 01 Oct 2006 Jmol

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Pop 199.53
Vit 8.19

Jmol is a Free, Open Source molecule viewer and editor. It is a collaboratively developed visualization and measurement tool for chemical scientists. Jmol is an active project, and there are new features being added to it on a daily basis. Users are encouraged to modify it to fit their needs and to contribute their changes to the project.

Download Website Updated 28 Oct 2011 NAMD

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Pop 58.58
Vit 9.35

NAMD is a parallel, object-oriented molecular dynamics program designed for high-performance simulation of large biomolecular systems.

Download Website Updated 14 Feb 2012 VMD

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Pop 129.81
Vit 13.41

VMD (Visual Molecular Dynamics) is designed for the visualization and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer. VMD uses OpenGL and OpenGL Programmable Shading Language for high performance rendering of large structures.

No download Website Updated 16 Mar 2006 CatDCD

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Pop 20.59
Vit 1.80

CatDCD functions much like the Unix "cat" command: it concatenates DCD files into a single DCD file. You can also use CatDCD to write only selected atoms to the final DCD file.

Download Website Updated 02 Mar 2001 FlipDCD

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Pop 15.49
Vit 1.00

FlipDCD is a small utility for reversing the endianism of binary DCD trajectory files from Charmm and NAMD. This can be useful when running simulations on one architecture and visualizing or analyzing the results on another. FixDCD is a tiny utility to modify the header of an X-PLOR DCD file to make it readable by programs expecting Charmm DCD files, at the expense of a Timestep size value in the header.

Download Website Updated 02 Mar 2001 MatDCD

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Pop 16.61
Vit 1.00

MatDCD is a Matlab package for reading/writing DCD-formatted molecular dynamics trajectory files. It supports Charmm and xplor-format DCD files, it can read both big- and little-endian storage formats, and it can specify which atom indices to load without having to load the entire file.

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