Improved application of the oscillating method for the isoelectric point determination of protein: Potential connection with protein data banks

• Published in: Computers in biology and medicine Vol. 38; no. 1; pp. 23 - 30
• Main Authors: Maldonado, Andrés, Vara, Francisco, Sillero, Antonio
• Format: Journal Article
• Language: English
• Published: United States Elsevier Ltd 01.01.2008; Elsevier Limited
• Subjects: Acid–base residues; Amino Acids - chemistry; Computational Biology - methods; Databases, Protein; Electric charge; Hydrogen-Ion Concentration; Internal Medicine; Internet; Isoelectric Point; Other; PI theoretical determination; PICAL; Proteins; Proteins - chemistry; Software; Static Electricity; User-Computer Interface; Visual basic; Proteins; PI theoretical determination; Electric charge; PH; Acid–base residues; PICAL; Visual basic
• ISSN: 0010-4825; 1879-0534
• DOI: 10.1016/j.compbiomed.2007.06.004

Abstract The oscillating method (OM) for the theoretical determination of the pI values, one by one, of proteins and other macromolecules has been previously published [Sillero and Maldonado, Comput. Biol. Med 36 (2006) 157–166]. An improved application of the method, here named as improved oscillating method (IOM), allows the pI determination of group of proteins. This characteristic may be useful to explore the pI value and electric charge of family of enzymes. As an example the pI values of 1630 enzymes collected in a Swiss-Prot data bank (www.expasy.org), as belonging to the enzymes ligases (EC 6. 2. 1. *) is presented. The method also permits the determination of the pI value of any group of proteins stored in data banks provided that they can be supplied to the program in a FASTA format. Free access to IOM can be reached at http://www.bq.uam.es/otros/pical3.zip.