Using PconsC4 and PconsFold2 to Predict Protein Structure. Issue 1 (7th May 2019)

• Record Type: Journal Article
• Authors: Bassot, Claudio; Menendez Hurtado, David; Elofsson, Arne
• Editors: Baxevanis, Andreas D.; Petsko, Gregory A.; Stein, Lincoln D.; Stormo, Gary D.
• Is Part Of: Current protocols in bioinformatics. Volume 66:Issue 1(2019)
• Page Start: n/a
• Page End: n/a
• Publication Date: 2019-05-07
• Subjects: contact prediction -- PconsC4 -- PconsFold2 -- protein structure prediction -- template‐free modeling; Bioinformatics -- Laboratory manuals; Nucleotide sequence -- Laboratory manuals; Amino acid sequence -- Laboratory manuals; Base Sequence; Amino Acid Sequence; Computational Biology -- methods; Databases, Genetic; Proteins -- analysis; Sequence Analysis -- methods; Sequence Homology; Amino acid sequence; Bioinformatics; Nucleotide sequence; Laboratory Manuals; Laboratory manuals; 570.285
• DOI: 10.1002/cpbi.75
• Languages: English
• ISSNs: 1934-3396

Abstract

Abstract: In spite of the fact that there has been a significant increase in the number of solved protein structures, structural information is missing for many proteins. Although structural information is codified in the amino acid sequence, computational prediction using only this information is still an unsolved problem. However, one successful method to model a protein's structure starting from the primary sequence is to use contact prediction derived from multiple sequence alignment (MSA). Here we use our contact predictor PconsC4 to generate a list of probable contacts between residues in the primary sequences. These contacts are then used together with the secondary structure prediction as constraints for the CONFOLD folding method. In this way, a 3D protein model can be built starting directly from the primary sequence. © 2019 by John Wiley & Sons, Inc.