Protein Folding source code
Hi all, I'm looking for an OpenSource protein folding program under Linux, so I could take a look at the source code and figure out how it works... Please, don't point me to the Folding@Home Project as they don't distribute the source code for any of their versions... ;) Any thoughts? TIA, Martin
Martin Mielke wrote:
I'm looking for an OpenSource protein folding program under Linux, so I could take a look at the source code and figure out how it works...
I'd suggest that a better way into the problem is to study the research papers. The code's not likely to be particularly enlightening and even if you got to understand exactly how one group did it, that wouldn't tell you anything about how other groups do it, or which aspects of the programs are seen as cool and which as kludges. There's a list of research groups here http://www.fccc.edu/research/labs/roder/folding_groups.html that will give you a starting point to find either literature or code. Cheers, Dave -- Dave Howorth MRC Centre for Protein Engineering Cambridge, UK
Dave Howorth wrote:
Martin Mielke wrote:
I'm looking for an OpenSource protein folding program under Linux, so I could take a look at the source code and figure out how it works...
I'd suggest that a better way into the problem is to study the research papers. The code's not likely to be particularly enlightening and even if you got to understand exactly how one group did it, that wouldn't tell you anything about how other groups do it, or which aspects of the programs are seen as cool and which as kludges.
There's a list of research groups here http://www.fccc.edu/research/labs/roder/folding_groups.html that will give you a starting point to find either literature or code.
Cheers, Dave
Hi, let me clear things up... I look for an OpenSource tool not *only* to take a look at the code and learn. As Dave stated, there are better (and clever) ways to do it. The main reason to use OpenSource is mainly cost-related and to have a 100% GPL'ed software installed. That GROMACS looks very nice (thanks Luca!) and I'll give it a try. Althought I'm not pretty sure whether this performs the same actions as http://www.stanford.edu/group/pandegroup/folding/ -- BTW, that's what I meant with "protein folding". Martin
That GROMACS looks very nice (thanks Luca!) and I'll give it a try. Althought I'm not pretty sure whether this performs the same actions as http://www.stanford.edu/group/pandegroup/folding/ -- BTW, that's what I meant with "protein folding".
Folding@home uses the Gromacs core. Snip from log file: [04:03:05] + Processing work unit [04:03:05] Core required: FahCore_78.exe [04:03:05] Core found. [04:03:05] Working on Unit 09 [May 5 04:03:05] [04:03:05] + Working ... [04:03:05] [04:03:05] *------------------------------* [04:03:05] Folding@home Gromacs Core [04:03:05] Version 1.62 (April 2, 2004) [04:03:05] [04:03:05] Preparing to commence simulation [04:03:05] - Assembly optimizations manually forced on. [04:03:05] - Not checking prior termination. [04:03:05] - Expanded 197783 -> 955477 (decompressed 483.0 percent) [04:03:05] - Starting from initial work packet [04:03:05] [04:03:05] Project: 1042 (Run 5, Clone 66, Gen 2) [04:03:05] [04:03:05] Assembly optimizations on if available. [04:03:05] Entering M.D. [04:03:11] Protein: p1042_nat96_273 [04:03:11] [04:03:11] Writing local files [04:03:11] Extra SSE boost OK. [04:03:11] Writing local files [04:03:11] Completed 0 out of 2500000 steps (0%) [04:13:26] Writing local files [04:13:26] Completed 25000 out of 2500000 steps (1%)
Hi again, replying to myself? no :P I just want to add something on this subject: can this software (GROMACS or whatever) be used to calculate/simulate proteine torsion/flexibility? Thanx, Martin
On Wednesday 05 May 2004 16:49, Martin Mielke wrote:
Hi again,
replying to myself? no :P I just want to add something on this subject: can this software (GROMACS or whatever) be used to calculate/simulate proteine torsion/flexibility?
GROMACS is a very powerful tool, but it does not do everything auomatically: very often in order to compute some parameters you have to use the options flag for each command and/or modify the index files (the files that contain parts of the system defined through atomic poition and topologies). For example, Phi/Psi angles are not computed automatically for each residue, but I have managed to compute them for a single residue setting up the index file correctly and defining planes, dihedral and vectors accordingly So, very often with GROMACS you have to work a lot in a tuning fashion in order to compute quantities you are interested in. Please browse GMX mailing list at the URL http://www.gromacs.org/search/index.php and maybe you will find something about your query: this mailing list is very active, and you wil find almost every answers to your questions. cheers LM
Martin, just a few remarks about GROMACS usage: 1. GROMACS is based on FFT software (Fourier Transformation), so you have to install it before installing GROMACS 2. GROMACS output files are pdb/gro files for structures and xvg for raw data. pdb files are readable by Rasmol, VMD and other common molecular graphics tools, bu gro files are only processed and displayed by VMD, so I sugges to download it. xvg files are naturally read by xmgr, but I don't know if it is mantained yet or not: a good alternative is xmgr. SUSE 9.0 provides xmgr, but you can also download it from the web (Weizman Institute is the software provider and mantainer, if I remember well). 3. In the GROMACS section dedicated to developers, you can find also some unofficial tools for GROMACS: browse the section for your purpose. LM
On Thursday 06 May 2004 11:54, Luca Mollica wrote:
a few remarks about GROMACS
~ i did a bit of 'folding at home' . . . i was frightened off, because it seems, one has to grant the folding program the authority to download executables to ones 'puter, without warning . . . is this true ? thanks ____________ sent on Linux ____________
Hi all,
I'm looking for an OpenSource protein folding program under Linux, so I could take a look at the source code and figure out how it works...
Martin, what do you mean exactly with the term protein folding program?? If you are looking for a Molecular Dynamics software, my advice would be GROMACS, that's distributed under GPL, so the source code is accesible: www.gromacs.org Recently some relevant studies on petides folding have been published using GROMACS/GROMOS force fieds and softwares ......for instance, check a couple of papers of Wilfred van Gunsteren's group about folding of small peptides(they have been published recently, or at least, they are going to be published ASAP)
Please, don't point me to the Folding@Home Project as they don't distribute the source code for any of their versions... ;)
...and in order to get reliable version you sould wait for a long time, using for example a single processor machine...... :-( Moreover, advice provided by Dave Howorth is the best one, maybe: the technical literature is the best way to understand the principles upon wich these softwares and codes are based. "Proteins" may be good starting point, and also "Journal of Computational Chemistry" can also be a good source of infos. Cheers LM
Martin Mielke wrote:
Hi all,
I'm looking for an OpenSource protein folding program under Linux, so I could take a look at the source code and figure out how it works...
Please, don't point me to the Folding@Home Project as they don't distribute the source code for any of their versions... ;)
Any thoughts?
TIA, Martin
participants (5)
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Dave Howorth
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jim barnes
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Luca Mollica
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Martin Mielke
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pinto