title: Analysis of residue conformations in peptides in Cambridge structural database and protein-peptide structural complexes.
abstract: A comprehensive statistical analysis of the geometric parameters of peptide chains in a reduced dataset of protein-peptide complexes in Protein Data Bank (PDB) is presented. The angular variables describing the backbone conformations of amino acid residues in peptide chains shed insights into the conformational preferences of peptide residues interacting with protein partners. Nonparametric statistical approaches are employed to evaluate the interrelationships and associations in structural variables. Grouping of residues based on their structure into chemical classes reveals characteristic trends in parameter relationships. A comparison of canonical amino acid residues in free peptide structures in Cambridge structural database (CSD) with identical residues in PDB complexes, suggests that the information can be integrated from both the structural repositories enabling efficient and accurate modeling of biologically active peptides.
authors: National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India.
authors: Upadhyayula Surya
authors: US
authors: Raghavender
mesh_terms: D000577:Amides / Q000737:chemistry; D000596:Amino Acids / Q000032:analysis / Q000737:chemistry; D003627:Data Interpretation, Statistical; D030562:Databases, Protein; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry* / Q000378:metabolism; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D013455:Sulfur / Q000737:chemistry
chemical_list: D000577:Amides; D000596:Amino Acids; D010455:Peptides; D011506:Proteins; D013455:Sulfur
keywords: Cambridge structural database (CSD); conformation; kernel density estimates (KDE); peptides; protein data bank (PDB); protein-peptide complex