TY - JOUR

T1 - webPIPSA

T2 - a web server for the comparison of protein interaction properties.

AU - Richter, Stefan

AU - Wenzel, Anne

AU - Stein, Matthias

AU - Gabdoulline, Razif R.

AU - Wade, Rebecca C.

N1 - Funding Information: This work was supported by the BMBF Hepatosys programme (grant nos. 0313076 and 0313078C) and the Klaus Tschira Foundation. We thank Nils Semmelrock and Bruno Besson for helping to implement early versions of this software. Funding to pay the Open Access publication charges for this article was provided by EML Research gGmbH.

PY - 2008/7/1

Y1 - 2008/7/1

N2 - Protein molecular interaction fields are key determinants of protein functionality. PIPSA (Protein Interaction Property Similarity Analysis) is a procedure to compare and analyze protein molecular interaction fields, such as the electrostatic potential. PIPSA may assist in protein functional assignment, classification of proteins, the comparison of binding properties and the estimation of enzyme kinetic parameters. webPIPSA is a web server that enables the use of PIPSA to compare and analyze protein electrostatic potentials. While PIPSA can be run with downloadable software (see http://projects.eml.org/mcm/software/pipsa), webPIPSA extends and simplifies a PIPSA run. This allows non-expert users to perform PIPSA for their protein datasets. With input protein coordinates, the superposition of protein structures, as well as the computation and analysis of electrostatic potentials, is automated. The results are provided as electrostatic similarity matrices from an all-pairwise comparison of the proteins which can be subjected to clustering and visualized as epograms (tree-like diagrams showing electrostatic potential differences) or heat maps. webPIPSA is freely available at: http://pipsa.eml.org.

AB - Protein molecular interaction fields are key determinants of protein functionality. PIPSA (Protein Interaction Property Similarity Analysis) is a procedure to compare and analyze protein molecular interaction fields, such as the electrostatic potential. PIPSA may assist in protein functional assignment, classification of proteins, the comparison of binding properties and the estimation of enzyme kinetic parameters. webPIPSA is a web server that enables the use of PIPSA to compare and analyze protein electrostatic potentials. While PIPSA can be run with downloadable software (see http://projects.eml.org/mcm/software/pipsa), webPIPSA extends and simplifies a PIPSA run. This allows non-expert users to perform PIPSA for their protein datasets. With input protein coordinates, the superposition of protein structures, as well as the computation and analysis of electrostatic potentials, is automated. The results are provided as electrostatic similarity matrices from an all-pairwise comparison of the proteins which can be subjected to clustering and visualized as epograms (tree-like diagrams showing electrostatic potential differences) or heat maps. webPIPSA is freely available at: http://pipsa.eml.org.

UR - http://www.scopus.com/inward/record.url?scp=48449097801&partnerID=8YFLogxK

U2 - 10.1093/nar/gkn181

DO - 10.1093/nar/gkn181

M3 - Journal article

C2 - 18420653

AN - SCOPUS:48449097801

VL - 36

SP - W276-280

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

IS - Web Server issue

ER -