Patch Finder Plus (PFplus): a web server for extracting and displaying positive electrostatic patches on protein surfaces.
Positively charged electrostatic patches on protein surfaces are usually indicative of nucleic acid binding interfaces. Interestingly, many proteins which are not involved in nucleic acid binding possess large positive patches on their surface as well. In some cases, the positive patches on the protein are related to other functional properties of the protein family. PatchFinderPlus (PFplus) http://pfp.technion.ac.il is a web-based tool for extracting and displaying continuous electrostatic positive patches on protein surfaces. The input required for PFplus is either a four letter PDB code or a protein coordinate file in PDB format, provided by the user. PFplus computes the continuum electrostatics potential and extracts the largest positive patch for each protein chain in the PDB file. The server provides an output file in PDB format including a list of the patch residues. In addition, the largest positive patch is displayed on the server by a graphical viewer (Jmol), using a simple color coding.
Shazman
Shula
S
Department of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel.
Celniker
Gershon
G
Haber
Omer
O
Glaser
Fabian
F
Mandel-Gutfreund
Yael
Y
D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D006863:Hydrogen-Ion Concentration; D020407:Internet; D008958:Models, Molecular; D008968:Molecular Conformation; D010940:Plant Proteins / Q000737:chemistry; D011381:Programming Languages; D011506:Proteins / Q000737:chemistry*; D012984:Software; D055672:Static Electricity; D013499:Surface Properties; D014584:User-Computer Interface; D014764:Viral Proteins / Q000737:chemistry
D010940:Plant Proteins; D011506:Proteins; D014764:Viral Proteins