High pKa variability of cysteine residues in structural databases and the effect of H-bond contributions
TURKISH JOURNAL OF BIOCHEMISTRY-TURK BIYOKIMYA DERGISI, vol.39, no.4, pp.435-739, 2014 (SCI-Expanded, Scopus, TRDizin)
- Publication Type: Article / Article
- Volume: 39 Issue: 4
- Publication Date: 2014
- Doi Number: 10.5505/tjb.2014.55823
- Journal Name: TURKISH JOURNAL OF BIOCHEMISTRY-TURK BIYOKIMYA DERGISI
- Journal Indexes: Science Citation Index Expanded (SCI-EXPANDED), Scopus, TR DİZİN (ULAKBİM)
- Page Numbers: pp.435-739
- Keywords: Cysteine, redox biology, bioinformatics, biochemistry, PK(A) VALUES, PREDICTION, RATIONALIZATION, SPECIFICITY, MOLECULES
- Akdeniz University Affiliated: Yes
Abstract
Objective: Our first objective was to extensively compare two most common empirical protein pKa predictors, propka1.0 (ppka1) and propka3.0 (ppka3); we have specifically compared them as tools for high-throughput analyses of structural datasets with a particular focus on the amino acid Cysteine (Cys); afterwards, our goal was to assess their performances with known instances of reactive Cys residues.