Re: [Apbs-users] electrostatic surfaces

[Nathan B. <ba...@bi...>]

Yes -- we've actually been working in this area, although the software 
is not ready for general consumption.  Here are some other references:

Blomberg N, Gabdoulline RR, Nilges M, Wade RC.  Classification of 
protein sequences by homology modeling and quantitative analysis of 
electrostatic similarity.  Proteins-Structure Function and Genetics.  37 
(3), 379-87, 1999. 
http://www3.interscience.wiley.com/cgi-bin/fulltext/68502071/HTMLSTART


Ferrè F, Ausiello G, Zanzoni A, Helmer-Citterich M.  Surface: A database 
of protein surface regions for functional annotation.  Nucleic Acids 
Research.  32 D240-D4, 2004. 
http://nar.oupjournals.org/cgi/content/full/32/suppl_1/D240


Gabdoulline RR, Wade RC.  Analytically defined surfaces to analyze 
molecular interaction properties.  Journal of Molecular Graphics.  14 
(6), 341-53, 1996.  http://dx.doi.org/10.1016/S0263-7855(97)00008-8


Gabdoulline RR, Wade RC, Walther D.  Molsurfer: Two-dimensional maps for 
navigating three-dimensional structures of proteins.  Trends in 
Biochemical Sciences.  24 (7), 285-7, 1999. 
http://dx.doi.org/10.1016/S0968-0004(99)01412-7


Kinoshita K, Nakamura H.  Protein informatics towards function 
identification.  Current Opinion in Structural Biology.  13 (3), 
396-400, 2003.  http://dx.doi.org/10.1016/S0959-440X(03)00074-5


Kinoshita K, Nakamura H.  Ef-site and pdbjviewer: Database and viewer 
for protein functional sites.  Bioinformatics.  20 (8), 1329-30, 2004. 
http://dx.doi.org/10.1093/bioinformatics/bth073


Livesay DR, Jambeck P, Rojnuckarin A, Subramaniam S.  Conservation of 
electrostatic properties within enzyme families and superfamilies. 
Biochemistry.  42 (12), 3464-73, 2003.  http://dx.doi.org/10.1021/bi026918f


McCoy AJ, Chandana Epa V, Colman PM.  Electrostatic complementarity at 
protein/protein interfaces.  Journal of Molecular Biology.  268 (2), 
570-84, 1997. 
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9159491


Ray N, Cavin X, Paul J-C, Maigret B.  Intersurf: Dynamic interface 
between proteins.  Journal of Molecular Graphics and Modelling.  23 (4), 
347-54, 2005.  http://dx.doi.org/10.1016/j.jmgm.2004.11.004


Sheinerman FB, Norel R, Honig B.  Electrostatic aspects of 
protein-protein interactions.  Current Opinion in Structural Biology. 
10 (2), 153-9, 2000.  http://dx.doi.org/10.1016/S0959-440X(00)00065-8


Ullmann GM, Hauswald M, Jensen A, Knapp E-W.  Structural alignment of 
ferredoxin and flavodoxin based on electrostatic potentials: 
Implications for their interactions with photosystem i and 
ferredoxin-nadp reductase.  Proteins.  38 (3), 301-9, 2000. 
http://www3.interscience.wiley.com/cgi-bin/fulltext/70003975/HTMLSTART


Wade RC, Gabdoulline RR, De Rienzo F.  Protein interaction property 
similarity analysis.  International Journal of Quantum Chemistry.  83 
(3-4), 122-7, 2001. 
http://www3.interscience.wiley.com/cgi-bin/abstract/80002581/ABSTRACT




On 9/9/2005 2:58 PM, Narcis Fernandez-Fuentes wrote:
> Anybody knows how to quantitatively compare 2 electrostatic potential
> maps?
> 
> Thanks
> 
> Narcis
> 
> _______________________________________________
> apbs-users mailing list
> apb...@ch...
> http://cholla.wustl.edu/mailman/listinfo/apbs-users

-- 
Assistant Professor, Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology, Washington University in St. Louis
Web: http://cholla.wustl.edu/