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Protocols

webPIPSA specifications

Information


Unique identifier OMICS_15050
Name webPIPSA
Alternative name Protein Interaction Property Similarity Analysis
Interface Web user interface
Restrictions to use None
Input data A set of protein coordinate files.
Input format PDB, PQR
Output data Electrostatic similarity matrices from an all-pairwise comparison of the proteins which can be subjected to clustering and visualized as epograms or heat maps.
Programming languages Java
License Other
Computer skills Basic
Version 1.6
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Stefan Richter

Publication for Protein Interaction Property Similarity Analysis

webPIPSA citations

 (12)
library_books

Electrostatic Variation of Haemagglutinin as a Hallmark of the Evolution of Avian Influenza Viruses

2018
Sci Rep
PMCID: 5792503
PMID: 29386534
DOI: 10.1038/s41598-018-20225-3

[…] efore, all models underwent refinement and quality analysis (see methods). Semi-quantitative ED evaluation and clustering of the spatial distributions of the electrostatic potentials were obtained by WebPIPSA (Protein Interaction Property Similarity Analysis). Heatmaps (Fig. ) showed that the ED among H9 representative viruses from ‘wild bird’ groups A+D+E and those from ‘poultry bird’ groups B+C […]

library_books

Evolution of an intricate J protein network driving protein disaggregation in eukaryotes

2017
eLife
PMCID: 5542770
PMID: 28504929
DOI: 10.7554/eLife.24560.020

[…] . All structures were superimposed with the alignment tool of the PyMOL software.The similarity of the calculated electrostatic potentials of the superimposed structures was computed using the PIPSA (Protein Interaction Property Similarity Analysis) software (). The resulting distance matrix was used for a Ward’s clustering. Only for Type A CTDs was an average-clustering used, but this yielded sim […]

library_books

Combination of X ray crystallography, SAXS and DEER to obtain the structure of the FnIII 3,4 domains of integrin α6β4

2015
PMCID: 4388270
PMID: 25849406
DOI: 10.1107/S1399004715002485

[…] & Steindel, 2012). Electrostatic properties were calculated with APBS (Baker et al., 2001) using the PARSE force field (Sitkoff et al., 1994), and the electrostatic potentials were compared with the webPIPSA server (Richter et al., 2008). Evolutionary conservation scores were calculated with ConSurf (Ashkenazy et al., 2010). Molecular figures were created using PyMOL (v.1.5.0.2; Schrödinger). […]

library_books

Electrostatic Similarities between Protein and Small Molecule Ligands Facilitate the Design of Protein Protein Interaction Inhibitors

2013
PLoS One
PMCID: 3794991
PMID: 24130741
DOI: 10.1371/journal.pone.0075762

[…] to perform comparison of electrostatic potentials resembles what has been done previously on proteins –. Analysis of Electrostatic Similarities of Proteins (AESOP) , the method of Dlugosz et al. and Protein Interaction Property Similarity Analysis (PIPSA) , also use APBS as their electrostatic computation engine. PIPSA can also use University of Houston Brownian Dynamics (UHBD). While EleKit re […]

call_split

Structural and Functional Analysis of the NLRP4 Pyrin Domain

2012
Biochemistry
PMCID: 3445046
PMID: 22928810
DOI: 10.1021/bi3007059
call_split See protocol

[…] ng up the asymmetric unit were evaluated using ProtorP. Structure visualization and analysis were performed in Pymol. Electrostatic surface potentials were calculated using APBS as part of the PIPSA (Protein Interaction Property Similarity Analysis) server to generate quantitative comparisons between PYD electrostatic surface potentials. […]

library_books

The Interaction Properties of the Human Rab GTPase Family – A Comparative Analysis Reveals Determinants of Molecular Binding Selectivity

2012
PLoS One
PMCID: 3327705
PMID: 22523562
DOI: 10.1371/journal.pone.0034870

[…] protein interactions, we carried out an extensive comparative analysis based on sequence, structure and molecular interaction fields. The analysis of molecular interaction fields (MIFs) by using the Protein Interaction Property Similarity Analysis (PIPSA) method , yields results that complement those from sequence analysis due to the consideration of the three-dimensional protein fold and the fa […]

Citations

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webPIPSA institution(s)
Molecular and Cellular Modeling Group, EML Research gGmbH, Heidelberg, Germany; BIOMS (Center for Modeling and Simulation in the Biosciences), University of Heidelberg, Heidelberg, Germany
webPIPSA funding source(s)
This work was supported by the BMBF Hepatosys programme (grant nos. 0313076 and 0313078C) and the Klaus Tschira Foundation.

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