Thread: [Apbs-users] Is it possible to determine pKas for RNA?
Biomolecular electrostatics software
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From: William S. <wg...@ch...> - 2007-05-29 06:23:09
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I tried pdb2pqr/propka but it appears to prefer enzymes that are made of amino acids. Is there a way to do this for RNA? Thanks. Bill William G. Scott contact info: http://chemistry.ucsc.edu/~wgscott |
From: Nathan B. <sob...@gm...> - 2007-05-29 20:51:51
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Hi Bill -- Currently, PDB2PQR/PROPKA only supports proteins. I'll Cc Jan to check if he has any plans for nucleic acid support. We're working on Poisson-based pKa tool with Jens Nielsen that should be adaptable to nucleic acid pKas but that's definitely a ways off in the pipeline. Thanks, Nathan On May 29, 2007, at 1:22 AM, William Scott wrote: > I tried pdb2pqr/propka but it appears to prefer enzymes that are made > of amino acids. > > Is there a way to do this for RNA? > > Thanks. > > Bill > > > William G. Scott > > contact info: http://chemistry.ucsc.edu/~wgscott > > > > > > ---------------------------------------------------------------------- > --- > This SF.net email is sponsored by DB2 Express > Download DB2 Express C - the FREE version of DB2 express and take > control of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > _______________________________________________ > apbs-users mailing list > apb...@li... > https://lists.sourceforge.net/lists/listinfo/apbs-users -- Associate Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ |
From: Jan H. J. <jhj...@ke...> - 2007-05-30 07:50:37
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we do indeed have plans for nucleic acid support in PROPKA, but this is also a ways off for us. Alexov and Honig have recently published (JMB 2007) such a method based on Marilyn Gunner MCCE program. Perhaps that's the best approach for now. Best regards, Jan At 3:51 PM -0500 5/29/07, Nathan Baker wrote: >Hi Bill -- > >Currently, PDB2PQR/PROPKA only supports proteins. I'll Cc Jan to >check if he has any plans for nucleic acid support. > >We're working on Poisson-based pKa tool with Jens Nielsen that >should be adaptable to nucleic acid pKas but that's definitely a >ways off in the pipeline. > >Thanks, > >Nathan > >On May 29, 2007, at 1:22 AM, William Scott wrote: > >>I tried pdb2pqr/propka but it appears to prefer enzymes that are made >>of amino acids. >> >>Is there a way to do this for RNA? >> >>Thanks. >> >>Bill >> >> >>William G. Scott >> >>contact info: http://chemistry.ucsc.edu/~wgscott >> >> >> >> >> >>------------------------------------------------------------------------- >>This SF.net email is sponsored by DB2 Express >>Download DB2 Express C - the FREE version of DB2 express and take >>control of your XML. No limits. Just data. Click to get it now. >>http://sourceforge.net/powerbar/db2/ >>_______________________________________________ >>apbs-users mailing list >>apb...@li... >>https://lists.sourceforge.net/lists/listinfo/apbs-users > >-- >Associate Professor, Dept. of Biochemistry and Molecular Biophysics >Center for Computational Biology, Washington University in St. Louis >Web: http://cholla.wustl.edu/ -- =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Jan H. Jensen Associate Research Professor Department of Chemistry jhj...@ke... University of Copenhagen Phone: +45 35 32 02 39 Universitetsparken 5 FAX: +45 35 32 02 14 2100 Copenhagen Denmark http://propka.ki.ku.dk/~jhjensen =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- |