Bioinformatics resource list - Revision history

Christoph: /* Graphics */

2008-05-20T06:08:52Z

‎Graphics

Christoph: /* Molecular docking resources */

2007-04-16T23:47:18Z

‎Molecular docking resources

Christoph: /* Molecular docking resources */

2006-11-11T06:07:23Z

‎Molecular docking resources

Christoph at 06:05, 11 November 2006

2006-11-11T06:05:47Z

Christoph at 21:39, 8 November 2006

2006-11-08T21:39:59Z

New page

This article will contain a list of useful ''resources'' for bioinformaticians (or computational biologists, or scientists in general). It will list software, libraries, web servers, general data, and any other resource I find useful.

Not all resources listed here are [[:Category:Open Source|open source]]. Since I am a firm believer in open source, I will eventually remove those resources listed below that are not open source in favour of those that are. This means they should be at least:
* GPL/LGPL;
* able to download from ''any'' machine (i.e. including non-academic);
* able to use for ''any'' purpose;
* zero registration required (not even an email address);
* absolutely '''''must''''' work on [[Linux]];
* the source files ''must'' be included (i.e. ''not'' just the binaries);
* preferably CLI-friendly (i.e. able to run entirely from the command-line); and
* preferably STDIN/STDOUT streams (i.e. input can be a pipe stream; in/out filenames are ''not'' arguments)

== Application/Bioinformatics ==

; 3ddock : A suite of automated docking tools. (''License: Cancer Research UK'')
; CHARMM : CHARMM - Molecular Dynamics Package. (''License: Harvard University'')
; amber : A package of molecular simulation programs. (''License: UCSF'')
; chimera : UCSF Chimera - A molecular viewer and analysis program. (''License: UCSF'')
; dms : DMS - Molecular Surface Program. (''License: UCSF'')
; dock : UCSF DOCK - A molecular docking program. (''License: UCSF'')
; gold : Protein-Ligand Docking. (''License: CCDC'')
; insightII : Ensemble Molecular Modeling Package. (''License: Accelrys'')
; libpdb : The library needed for PDB files read by the dms program. (''License: UCSF'')
; mfold : RNA and DNA secondary structure prediction. (''License: GPL'')
; pdb_h : The header needed for PDB files read by the dms program. (''License: UCSF'')
; sybyl : Ensemble Molecular Modeling Package. (''License: Tripos'')

== Application/Engingeering ==

; CCP4mg : The CCP4 Molecular Graphics Program. (''License: ccp4.ac.uk'')
; ImageJ : A Java Image Manipulation Tool. (''License: GPL'')
; alfresco : Comparative Genome Sequence Analysis Tool. (''License: GPL'')
; artemis : DNA sequence viewer and annotation tool. (''License: GPL'')
; autodock : A suite of automated docking tools. (''License: The Scripps Research Institute'')
; cn3d : Molecular Graphics Visualization Tool. (''License: GPL'')
; connolly : Molecular Surface Program. (''License: Indiana University'')
; delphi : DelPhi - A Finite Difference Poisson-Boltzman Solver. (''License: Columbia University''
; dotlet : A diagonal dot-plot tool. (''License: GPL'')
; dssp : Program to standardize secondary structure assignment. (''License: GPL'')
; genemine : Look/GeneMine. (''License: GPL'')
; jackal : JACKAL: A protein structure modeling package. (''License: GPL'')
; jalview : A Java Sequence Alignment Viewer. (''License: GPL'')
; mage : Molecular Graphics Visualization Tool. (''License: GPL'')
; mgltools : A suite of automated docking tools. (''License: Michael Sanner and TSRI'')
; moe : Molecular Operating Environment. (''License: Chemical Computing Group'')
; molauto : A program for producing good first-approximation MolScript input files. (''License: Avatar Software'')
; molscript : A program for displaying molecular 3D structures. (''License: Avatar Software AB'')
; msms : Computes, for a given probe radius, the reduced surface of a set of spheres. (''License: GPL'')
; namd : Not Another Molecular Dynamics. (''License: Univ of Illinois'')
; procheck : Programs to check the Stereochemical Quality of Protein Structures. (''License: EBI'')
; rasmol : Molecular Graphics Visualization Tool. (''License: GPL'')
; spdbv : Swiss-Prot DeepView. (''License: GPL'')
; stc : Structure-based thermodynamic analysis of the dissociation of protein phosphatase-1 catalytic subunit and microcystin-LR docked complexes. (''License: GPL'')
; vmd : Visualization and analysis tool of biological systems. (''License: Univ of Illinois'')
; x3dna : 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. (''License: GPL'')
; xpvm : A GUI interface for PVM, Parallel-Virtual Machine. (''License: GPL'')

== Applications/Bioinformatics ==

; DOMAINATRIX : EMBOSS:DOMAINATRIX Applications. (''License: GPL'')
; DOMALIGN : EMBOSS:DOMALIGN Applications. (''License: GPL'')
; DOMSEARCH : EMBOSS:DOMSEARCH Applications. (''License: GPL'')
; EMBOSS : The European Molecular Biology Open Software Suite. (''License: GPL/LGPL'')
; EMBOSS-Jemboss : Java based GUI for EMBOSS. (''License: GPL/LGPL'')
; EMBOSS-data : Extra data for EMBOSS. (''License: GPL/LGPL'')
; EMNU : EMBOSS:EMNU Applications. (''License: GPL'')
; ESIM4 : EMBOSS:ESIM4 Applications. (''License: GPL'')
; ESTScan : Program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. (''License: Copyright SIB, LICR and ISREC 1999'')
; HMMER : EMBOSS:HMMER Applications. (''License: GPL'')
; MEMENEW : EMBOSS:MEMENEW Applications. (''License: GPL'')
; MSE : EMBOSS:MEME Applications. (''License: GPL'')
; MYEMBOSS : EMBOSS:MYEMBOSS Applications. (''License: GPL'')
; PHYLIPNEW : EMBOSS:PHYLIP Applications. (''License: GPL'')
; SIGNATURE : EMBOSS:SIGNATURE Applications. (''License: GPL'')
; STRUCTURE : EMBOSS:STRUCTURE Applications. (''License: GPL'')
; TOPO : EMBOSS:TOPO Applications. (''License: GPL'')
; VIENNA : EMBOSS:VIENNA Applications. (''License: GPL'')
; blat : Basic Local Alignment Tool. (''License: LGPL'')
; gibbs : Gibbs motif sampler. (''License: Public Domain'')
; hbplus : A program for hydrogen bond calculation. (''License: biochem.ucl.ac.uk'')
; ligplot : A program for automatically plotting protein-ligand interactions. (''License: biochem.ucl.ac.uk'')
; paml : Phylogenetic analyses of DNA or protein sequences using maximum likelihood. (''License: free for academic use only'')
; phrap : phragment assembly program. (''License: Phil Green'')
; primer3 : Primer3 picks primers for PCR reactions. (''License: Copyright Whitehead Institute for Biomedical Research'')
; repeatmasker : RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. (''License: GPL'')
; seaview : Graphical multiple alignment editor. (''License: Freely available to all end users'')
; sim4 : Program to align cDNA and genomic DNA. (''License: GPL'')
; tree : Maximum likelihood analysis for nucleotide, amino acid and two-state data. (''License: GPL'')

== Applications/Engineering ==

; R : A statistical computation and graphics system. (''License: GNU'')
; matlab : Matlab 7, Release 14 Service Pack 2. (''License: 2005 Matlab'')
; modeller : Protein structure modeling by satisfaction of spatial restraints. (''License: Academic'')
; openbabel : A free, open-source version of the Babel chemistry file translation program. (''License: GPL'')

== Applications/Graphics ==

; gsview : PostScript and PDF previewer. (''License: Aladdin Free Public License, Ghostgum Software Pty Ltd'')

== Applications/Internet ==

; flash-plugin : Macromedia Flash Plug-In for Mozilla-Firefox. (''License: GPL'')
; j2re-plugin : Java 2 Plug-In for Mozilla-Firefox. (''License: GPL'')

== Applications/Mail ==

; pine : University of Washington Pine mail user agent. (''License: see file CPYRIGHT'')

== Applications/Math ==

; grace : Numerical Data Processing and Visualization Tool (grace). (''License: GPL'')

== Applications/Multimedia ==

; gd-progs : Utility programs that use libgd. (''License: BSD-style'')

== Applications/Science ==

; gromacs : Molecular dynamics package (non-parallel version). (''License: GPL'')
; gromacs-devel : Header files and static libraries for GROMACS. (''License: GPL'')

== Applications/System ==

; gnupg : A GNU utility for secure communication and data storage. (''License: GPL'')

== Bioinformatics/SequenceAnalysis ==

; footprinter : A program that performs phylogenetic footprinting. (''License: 1999-2002 Mathieu Blanchette and Martin Tompa'')

== Development/Debuggers ==

; xxgdb : An X Window System graphical interface for the GNU gdb debugger. (''License: MIT'')

== Development/Languages ==

; icm-browser : The ICM (Internal Coordinate Mechanics) software project. (''License: Molsoft L.L.C'')
; icmbrowser-desktop : Menu Item for ICM-Browser. (''License: Molsoft L.L.C'')
; intel-ifort8 : Intel(R) Fortran Compiler for 32-bit applications, Version 8. (''License: Intel(R) Copyright 2003'')
; molsoft : ICM-Browser Support. (''License: UMDNJ 2004'')

== Development/Libraries ==

; EMBOSS-devel : Header files and static libraries for EMBOSS. (''License: GPL/LGPL'')
; NCBI-devel : The development libraries and header files for ncbi. (''License: GPL'')
; fftw-devel : headers, libraries, and docs for FFTW fast fourier transform library. (''License: GPL'')
; fftw3-devel : Headers, libraries and docs for the FFTW library. (''License: GPL'')
; gd-devel : The development libraries and header files for gd. (''License: BSD-style'')
; perl-RNA : Vienna RNA package Perl module. (''License: Free for non-commercial use'')

== Development/Tools ==

; blt : A Tk toolkit extension. (''License: MIT'')
; jdk : Java(TM) 2 Platform Standard Edition Development Kit. (''License: Sun Microsystems Binary Code License (BCL)'')
; jdk-path : Java 2 SDK Path Modifier. (''License: GPL'')

== Graphics ==

; Raster3D : Raster3D photorealistic molecular graphics package. (''License: Source freely available, redistribution restricted'')

== Libraries ==

; fftw : fast fourier transform library. (''License: GPL'')
; netcdf : Libraries to use the Unidata network Common Data Form (netCDF). (''License: distributable'')
; pdflib : Portable C library for dynamically generating PDF files. (''License: Aladdin Free Public License'')
; pdflib-devel : Header file for pdflib. (''License: Aladdin Free Public License'')

== Scientific/Cluster ==

; NCBI : NCBI Toolkit. (''License: GPL'')

== Scientific/Engineering ==

; NCBI-C++ : NCBI C++ Toolkit. (''License: GPL'')
; clustalx : ClustalX. (''License: GPL'')

== System Environment/Libraries ==

; fftw3 : Fast Fourier Transform library. (''License: GPL'')
; gd : A graphics library for quick creation of PNG or JPEG images. (''License: BSD-style'')
; glut : GL Utility Toolkit (GLUT). (''License: Freely Redistributable'')

== Miscellaneous ==

* blt-scripts
* cups
* cups-common
* fonts-ttf-latex
* gcc-gfortran
* libgfortran0
* lyx
* rdate
* tetex-afm
* unrar (?)
* xdrawchem
* xxdiff

== External links ==
* [[wikipedia:Open Bioinformatics Foundation]]
* [[wikipedia:Protein structure prediction software]]
* [[wikipedia:Sequence alignment software]]
* [[wikipedia:Phylogenetics software]]
* [[wikipedia:List of GNU packages]]
* [[wikipedia:List of raster to vector conversion software]]

[[Category:Bioinformatics]]

@@ Line 201: / Line 201: @@
 * [http://boinc.bakerlab.org/rosetta/ Rosetta@Home] A distributed computing project, aiming to improve the Rosetta software for protein prediction, design and docking
 * [http://nrc.bu.edu/cluster ClusPro] A docking program developed by the Camacho group at Boston University
-* [http://structure.pitt.edu/servers/smoothdock/ SmoothDock] A docking prediction program and Online server by Prof. Carlos J. Camacho and P. Christoph Champ at University of Pittsburgh
+* [http://structure.pitt.edu/servers/smoothdock/ SmoothDock] A docking prediction program and Online server by Prof. Carlos J. Camacho and [[P. Christoph Champ|Christoph Champ]] at University of Pittsburgh
 * [http://www.scripps.edu/mb/olson/doc/autodock/ AutoDock] A docking program developed by the Olson group at The Scripps Research Institute
 * [http://dock.compbio.ucsf.edu/ DOCK] A docking program developed in the Kuntz and Shoichet groups at the University of California, San Francisco

@@ Line 200: / Line 200: @@
 * [http://fightaidsathome.scripps.edu/ FIGHTAIDS@Home] A project by The Scripps Institute, applying the AutoDock drug-docking software towards discovery of new HIV therapies
 * [http://boinc.bakerlab.org/rosetta/ Rosetta@Home] A distributed computing project, aiming to improve the Rosetta software for protein prediction, design and docking
-* [http://nrc.bu.edu/cluster ClusPro] A docking program developed by the Camacho group at [[Boston University]]
+* [http://nrc.bu.edu/cluster ClusPro] A docking program developed by the Camacho group at Boston University
-* [http://structure.pitt.edu/servers/smoothdock/ SmoothDock] A docking prediction program and Online server by Carlos J. Camacho and P. Christoph Champ at [[University of Pittsburgh]]
+* [http://structure.pitt.edu/servers/smoothdock/ SmoothDock] A docking prediction program and Online server by Prof. Carlos J. Camacho and P. Christoph Champ at University of Pittsburgh
-* [http://www.scripps.edu/mb/olson/doc/autodock/ AutoDock] A docking program developed by the Olson group at [[The Scripps Research Institute]]
+* [http://www.scripps.edu/mb/olson/doc/autodock/ AutoDock] A docking program developed by the Olson group at The Scripps Research Institute
-* [http://dock.compbio.ucsf.edu/ DOCK] A docking program developed in the Kuntz and Shoichet groups at the [[University of California, San Francisco]]
+* [http://dock.compbio.ucsf.edu/ DOCK] A docking program developed in the Kuntz and Shoichet groups at the University of California, San Francisco
-* [http://www.simbiosys.ca/ehits/ eHiTS] A docking program developed by [http://www.simbiosys.ca SimBioSys] in Toronto, [[Canada]]
+* [http://www.simbiosys.ca/ehits/ eHiTS] A docking program developed by [http://www.simbiosys.ca SimBioSys] in Toronto, Canada
-* [http://www.ccdc.cam.ac.uk/products/life_sciences/gold/ GOLD] A docking program produced by the CCDC in [[Cambridge]], [[UK]]
+* [http://www.ccdc.cam.ac.uk/products/life_sciences/gold/ GOLD] A docking program produced by the CCDC in Cambridge, UK
-* [http://www.schrodinger.com/ProductDescription.php?mID=6&sID=6 Glide] A docking program developed and commercialized by [http://www.schrodinger.com Schrödinger] in the [[US]]
+* [http://www.schrodinger.com/ProductDescription.php?mID=6&sID=6 Glide] A docking program developed and commercialized by [http://www.schrodinger.com Schrödinger] in the US
-* [http://www.biosolveit.de/FlexX/ FlexX] A docking program developed by [http://www.biosolveit.de BioSolveIT] in [[Germany]]
+* [http://www.biosolveit.de/FlexX/ FlexX] A docking program developed by [http://www.biosolveit.de BioSolveIT] in Germany
-* [http://www.molegro.com/products.html Molegro Virtual Docker] A docking program developed by [http://www.molegro.com Molegro] in [[Denmark]]
+* [http://www.molegro.com/products.html Molegro Virtual Docker] A docking program developed by [http://www.molegro.com Molegro] in Denmark
 * [http://www.molsoft.com ICM] A docking program developed by Prof. Ruben Abagyan and Dr. Maxim Totrov at [http://www.molsoft.com Molsoft LLC]

@@ Line 157: / Line 157: @@
 == Graphics ==
-; Raster3D : Raster3D photorealistic molecular graphics package. (''License: Source freely available, redistribution restricted'')
+; [[Raster3D]] : Raster3D photorealistic molecular graphics package. (''License: Source freely available, redistribution restricted'')
 == Libraries ==

@@ Line 195: / Line 195: @@
 * xdrawchem
 * xxdiff
 == External links ==