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Prot-SSP: a tool for amino acid pairing pattern analysis in secondary structures
Miguel de Sousa * 1 , Cristian Robert Munteanu 2 , Alexandre Lopes Magalhães 1
1  UCIBIO/REQUIMTE/University of Porto, R. Campo Alegre 687, 4169-007 Porto, Portugal
2  RNASA-IMEDIR group, Computer Science Faculty, University of A Coruna, Campus de Elviña S/N, 15071, A Coruña, Spain (Department of Information and Communication Technologies)

10.3390/MOL2NET-1-F010
Abstract:

It is known that individual amino acids can have a decisive role in the stabilization of a protein structure. Moreover, it is likely that specific amino acid combinations also fulfil structural and stabilizing roles in protein structure. We present Prot-SSP, an analytical Python tool designed to gather and parse sequence and structural data from sets of PDB files and determine amino acid residue pairing propensities and correlations in alpha helices and beta strands, in various secondary structure contexts. This versatile and user-friendly bioinformatic tool has proven useful for the analysis of a selected set of protein structures as shown in an illustrative example.

Keywords: secondary structure; amino acid pair, alpha helix, beta strand; software
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