Difference between revisions of "Bioinformatics resource list"

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== Molecular docking resources ==
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* [http://www.chem.ox.ac.uk/curecancer.html CureCancer Screensaver Lifesaver] A large-scale distributed docking effort by Oxford University, NFCR and UnitedDevices, applying the LigandFit software, aimed to finding drugs for pancreatic cancer and leukemia.
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* [http://fightaidsathome.scripps.edu/ FIGHTAIDS@Home] A project by The Scripps Institute, applying the AutoDock drug-docking software towards discovery of new HIV therapies
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* [http://boinc.bakerlab.org/rosetta/ Rosetta@Home] A distributed computing project, aiming to improve the Rosetta software for protein prediction, design and docking
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* [http://nrc.bu.edu/cluster ClusPro] A docking program developed by the Camacho group at [[Boston University]]
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* [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]]
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* [http://www.scripps.edu/mb/olson/doc/autodock/ AutoDock] A docking program developed by the Olson group at [[The Scripps Research Institute]]
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* [http://dock.compbio.ucsf.edu/ DOCK] A docking program developed in the Kuntz and Shoichet groups at the [[University of California, San Francisco]]
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* [http://www.simbiosys.ca/ehits/ eHiTS] A docking program developed by [http://www.simbiosys.ca SimBioSys] in Toronto, [[Canada]]
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* [http://www.ccdc.cam.ac.uk/products/life_sciences/gold/ GOLD] A docking program produced by the CCDC in [[Cambridge]], [[UK]]
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* [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]]
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* [http://www.biosolveit.de/FlexX/ FlexX] A docking program developed by [http://www.biosolveit.de BioSolveIT] in [[Germany]]
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* [http://www.molegro.com/products.html Molegro Virtual Docker] A docking program developed by [http://www.molegro.com Molegro] in [[Denmark]]
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* [http://www.molsoft.com ICM] A docking program developed by Prof. Ruben Abagyan and Dr. Maxim Totrov at [http://www.molsoft.com Molsoft LLC]
  
 
== External links ==
 
== External links ==

Revision as of 06:05, 11 November 2006

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 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

Molecular docking resources

External links

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