calculate interaction between aminoacids residues
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@fabien-crozet-444
Last seen 10.3 years ago
>From a particular PDB file I would like to calculate the interactions between residues. Two residues are considered interacting if any of their atoms (excluding hydrogen) are within a particular cutoff distance. The main goal is to compare 2 PDB files with little differences and then determines the number of interactions that are disrupted. I wonder if there are bioconductor package that can be adapted for these kinds of statiscal analysis... I don't know too much about the differents packages and if someone can give me a suggestion for it, i would appreciate a lot ! Thanks for help.
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A.J. Rossini ▴ 810
@aj-rossini-209
Last seen 10.3 years ago
As far as I'm aware, we don't yet have code to compute with proteins, though that is something that would be useful to do. best, -tony Fabien Crozet <fabien_crozet@yahoo.fr> writes: >>From a particular PDB file I would like to calculate > the interactions between residues. Two residues are > considered interacting if any of their atoms > (excluding hydrogen) are within a particular cutoff > distance. > The main goal is to compare 2 PDB files with little > differences and then determines the number of > interactions that are disrupted. > I wonder if there are bioconductor package that can be > adapted for these kinds of statiscal analysis... I > don't know too much about the differents packages and > if someone can give me a suggestion for it, i would > appreciate a lot ! > Thanks for help. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > -- rossini@u.washington.edu http://www.analytics.washington.edu/ Biomedical and Health Informatics University of Washington Biostatistics, SCHARP/HVTN Fred Hutchinson Cancer Research Center UW (Tu/Th/F): 206-616-7630 FAX=206-543-3461 | Voicemail is unreliable FHCRC (M/W): 206-667-7025 FAX=206-667-4812 | use Email CONFIDENTIALITY NOTICE: This e-mail message and any attachme...{{dropped}}
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Hi, > As far as I'm aware, we don't yet have code to compute with proteins, > though that is something that would be useful to do. but R has lots of facilities for matrix and vector calculation. As far as I understand, a protein in the sense of PDB is just an n x 3 matrix of coordinates, with the n the number of atoms. (Plus factors of length n with the atomic element, residue ID...). To do what Fabien has in mind, he would simply calculate the pairwise distances between all atoms in protein1 versus all atoms in protein2, and then look at the distance matrix. Best wishes Wolfgang ------------------------------------- Wolfgang Huber Division of Molecular Genome Analysis German Cancer Research Center Heidelberg, Germany Phone: +49 6221 424709 Fax: +49 6221 42524709 Http: www.dkfz.de/abt0840/whuber ------------------------------------- > Fabien Crozet <fabien_crozet@yahoo.fr> writes: > > >>From a particular PDB file I would like to calculate > > the interactions between residues. Two residues are > > considered interacting if any of their atoms > > (excluding hydrogen) are within a particular cutoff > > distance. > > The main goal is to compare 2 PDB files with little > > differences and then determines the number of > > interactions that are disrupted. > > I wonder if there are bioconductor package that can be > > adapted for these kinds of statiscal analysis... I > > don't know too much about the differents packages and > > if someone can give me a suggestion for it, i would > > appreciate a lot ! > > Thanks for help. > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > > > -- > rossini@u.washington.edu http://www.analytics.washington.edu/ > Biomedical and Health Informatics University of Washington > Biostatistics, SCHARP/HVTN Fred Hutchinson Cancer Research Center > UW (Tu/Th/F): 206-616-7630 FAX=206-543-3461 | Voicemail is unreliable > FHCRC (M/W): 206-667-7025 FAX=206-667-4812 | use Email > > CONFIDENTIALITY NOTICE: This e-mail message and any attachme...{{dropped}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >
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On Wed, 29 Oct 2003 w.huber@dkfz-heidelberg.de wrote: > To do what Fabien has in mind, > he would simply calculate the pairwise distances between all atoms in > protein1 versus all atoms in protein2, and then look at the distance > matrix. You need to take care of two more things as I can think of; 1. if the two proteins have long helix, the algorithm will focus on the helices and get low RMSD (Residue mean score distance). But other parts are aligned urgly, the alignment will not be good in a biologist's view. 2. there are some residues that are not alignable(they are two far apart). These residues should not be taken into account when calculating the final RMSD. Regards Junwen > > Best wishes > Wolfgang > > ------------------------------------- > Wolfgang Huber > Division of Molecular Genome Analysis > German Cancer Research Center > Heidelberg, Germany > Phone: +49 6221 424709 > Fax: +49 6221 42524709 > Http: www.dkfz.de/abt0840/whuber > ------------------------------------- > > > Fabien Crozet <fabien_crozet@yahoo.fr> writes: > > > > >>From a particular PDB file I would like to calculate > > > the interactions between residues. Two residues are > > > considered interacting if any of their atoms > > > (excluding hydrogen) are within a particular cutoff > > > distance. > > > The main goal is to compare 2 PDB files with little > > > differences and then determines the number of > > > interactions that are disrupted. > > > I wonder if there are bioconductor package that can be > > > adapted for these kinds of statiscal analysis... I > > > don't know too much about the differents packages and > > > if someone can give me a suggestion for it, i would > > > appreciate a lot ! > > > Thanks for help. > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor@stat.math.ethz.ch > > > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > > > > > > -- > > rossini@u.washington.edu http://www.analytics.washington.edu/ > > Biomedical and Health Informatics University of Washington > > Biostatistics, SCHARP/HVTN Fred Hutchinson Cancer Research Center > > UW (Tu/Th/F): 206-616-7630 FAX=206-543-3461 | Voicemail is unreliable > > FHCRC (M/W): 206-667-7025 FAX=206-667-4812 | use Email > > > > CONFIDENTIALITY NOTICE: This e-mail message and any attachme...{{dropped}} > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >
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Junwen wang ▴ 30
@junwen-wang-439
Last seen 10.3 years ago
You may use some software that can superimpose two PDB files, such as MAMMOTH, VEST or DALI. The programs will provide the coordinates and you can then calculate their distances. But most of the programs only superimpose a-carbon of the residue. Good luck! On Wed, 29 Oct 2003, [iso-8859-1] Fabien Crozet wrote: > >From a particular PDB file I would like to calculate > the interactions between residues. Two residues are > considered interacting if any of their atoms > (excluding hydrogen) are within a particular cutoff > distance. > The main goal is to compare 2 PDB files with little > differences and then determines the number of > interactions that are disrupted. > I wonder if there are bioconductor package that can be > adapted for these kinds of statiscal analysis... I > don't know too much about the differents packages and > if someone can give me a suggestion for it, i would > appreciate a lot ! > Thanks for help. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >
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In addition to those programs mentioned by Fabien, I think that Willie Taylor's program SAP should calculate the RMSD (root mean square deviation) between all pairs. Also SwissPDB viewer is very nice for visualising distance between two or multiple protein sequences. In SwissPDB viewer the amino acids in a protein structure can be coloured by distance to another protein. This visualisation can be very useful if you are generating protein models (and for presentations). Aedin -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of Junwen wang Sent: 29 October 2003 13:28 To: Fabien Crozet Cc: bioconductor@stat.math.ethz.ch Subject: Re: [BioC] calculate interaction between aminoacids residues You may use some software that can superimpose two PDB files, such as MAMMOTH, VEST or DALI. The programs will provide the coordinates and you can then calculate their distances. But most of the programs only superimpose a-carbon of the residue. Good luck! On Wed, 29 Oct 2003, [iso-8859-1] Fabien Crozet wrote: > >From a particular PDB file I would like to calculate > the interactions between residues. Two residues are considered > interacting if any of their atoms (excluding hydrogen) are within a > particular cutoff distance. > The main goal is to compare 2 PDB files with little > differences and then determines the number of > interactions that are disrupted. > I wonder if there are bioconductor package that can be > adapted for these kinds of statiscal analysis... I > don't know too much about the differents packages and > if someone can give me a suggestion for it, i would > appreciate a lot ! > Thanks for help. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
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A.J. Rossini ▴ 810
@aj-rossini-209
Last seen 10.3 years ago
w.huber@dkfz-heidelberg.de writes: > Hi, > >> As far as I'm aware, we don't yet have code to compute with proteins, >> though that is something that would be useful to do. > > but R has lots of facilities for matrix and vector calculation. As far as > I understand, a protein in the sense of PDB is just an n x 3 matrix of > coordinates, with the n the number of atoms. (Plus factors of length n > with the atomic element, residue ID...). To do what Fabien has in mind, > he would simply calculate the pairwise distances between all atoms in > protein1 versus all atoms in protein2, and then look at the distance > matrix. I definitely agree, but I'm thinking about the difference between computing with proteins and computing statistics -- we could do much of what we are doing now with R without Bioconductor, but it's far less intuitive and provides less of a macro view of the world and less of a straightforward view of the operations that one wants to do on the data. best, -tony -- rossini@u.washington.edu http://www.analytics.washington.edu/ Biomedical and Health Informatics University of Washington Biostatistics, SCHARP/HVTN Fred Hutchinson Cancer Research Center UW (Tu/Th/F): 206-616-7630 FAX=206-543-3461 | Voicemail is unreliable FHCRC (M/W): 206-667-7025 FAX=206-667-4812 | use Email CONFIDENTIALITY NOTICE: This e-mail message and any attachme...{{dropped}}
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