PIPSA (Protein Interaction Property Similarity Analysis)

References describing the method (to cite when applying PIPSA)

Blomberg N, Gabdoulline RR, Nilges M, and Wade RC.
Classification of protein sequences by homology modeling and quantitative analysis of electrostatic similarity.
Proteins: Str., Function and Genetics 1999, 37: 379-387. (Abstract)
First description of the PIPSA procedure.

Wade RC, Gabdoulline RR and De Rienzo F.
Protein Interaction Property Similarity Analysis.
Intl. J. Quant. Chem. 2001, 83: 122-127. (Abstract)
Detailed description of PIPSA.

Gabdoulline RR, Stein M, Wade RC.
qPIPSA: Relating enzymatic kinetic parameters and interaction fields
BMC Bioinformatics 2007, 8: 373. (Fulltext)
Description of how
PIPSA can be used for quantitative prediction purposes.

Richter S, Wenzel A, Stein M, Gabdoulline RR, Wade RC.
webPIPSA: a web server for the comparison of protein interaction properties
Nucleic Acid Research, Web Server early access, doi:10.1093/nar/gkn181 . (Fulltext)
Description of the PIPSA webserver

References describing applications

De Rienzo F, Gabdoulline RR, Menziani MC, Wade RC.
Blue copper proteins: a comparative analysis of their molecular interaction properties.
Protein Sci. 2000, 9: 1439-54. (Abstract)

De Rienzo F, Gabdoulline RR, Menziani MC, De Benedetti PG and Wade RC.
Electrostatic Analysis and Brownian Dynamics Simulation of the Association of Plastocyanin and Cytochrome F
Biophys. J. 2001, 81, 3090-3104. (Publication)

De Rienzo F, Grant GH, Menziani MC.
Theoretical descriptors for the quantitative rationalisation of plastocyanin mutant functional properties
J. Computer-Aided Molecular Design 2002, 16: 501-9. (Abstract)

Winn PJ, Religa TL, Battey JN, Banerjee A, Wade RC.
Determinants of functionality in the ubiquitin conjugating enzyme family.
Structure (Camb). 2004, 12: 1563-74. (Abstract)

Schleinkofer K. , Wiedemann U. , Otte l., Wang T., Krause G., Oschkinat H. and Wade R.C.
Comparative Structural and Energetic Analysis of WW Domain/Peptide Interactions.
J. Mol. Biol., 2004, 344, 865-881. (Abstract)

Flower DR and Attwood TK
Integrative bioinformatics for functional genome annotation: trawling for G protein-coupled receptors
Seminars in Cell &Developmental Biol. 2004, 15: 693. (Abstract)

Soares DC, Gerloff DL, Syme NR, Coulson AFW, Parkinson J and Barlow PN
Large-scale modelling as a route to multiple surface comparisons of the CCP module family
Protein Eng. Design Selection 2005, 18: 379-388 (Fulltext)

Wade RC
Calculation and Application of Molecular Interaction Fields.
In "Molecular Interaction Fields. Applications in Drug Discovery and ADME Prediction", Ed. Cruciani, G., Wiley-VCH, Weinheim. (ISBN 3-527-31087-8)
(2005) Ch. 2, pp27-42. (Publisher link)

Zhang L, Morikis D

Immunophysical Properties and Prediction of Activities for Vaccinia Virus Complement Control Protein and Smallpox Inhibitor of Complement Enzymes Using Molecular Dynamics and Electrostatics
Biophys. J 2006 90: 3106-19. (Fulltext)

Winn PJ, Zahran M, Battey JND, Zhou Y, Wade RC, Banerjee A
Structural and electrostatic properties of ubiquitination and related pathways
Frontiers in Bioscience (2007) 12, 3419-3430.  (Abstract) (Figures)
Check also: Ubiquitin and Ubiquitin-like Protein Web Resource .

Stein M, Gabdoulline RR, Wade RC
Bridging from molecular simulations to biochemical networks
Curr. Op. Struct. Biol. 2007, 2: 166-172 (Abstract)

Henrich S, Richter S, Wade RC
On the use of PIPSA to guide target-selective drug design
ChemMedChem (2008) i3, 413-417. (Abstract)

José M Eirín-López, Rodrigo González-Romero, Deanna Dryhurst, Toyotaka Ishibashi and Juan Ausió
The evolutionary differentiation of two histone H2A.Z variants in chordates (H2A.Z-1 and H2A.Z-2) is mediated by a stepwise mutation process that affects three amino acid residues
BMC Evolutionary Biology 2009, 9:31 doi:10.1186/1471-2148-9-31 (Link).

Giorgio Cozza, Andrea Bortolato, and Stefano Moro
How Druggable Is Protein Kinase CK2?
Medicinal Research Reviews, Vol. 30, No. 3, 419--462, 2010 (Abstract)

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