Tuyển tập các báo cáo nghiên cứu về y học được đăng trên tạp chí y học quốc tế cung cấp cho các bạn kiến thức về ngành y đề tài: Amino acid size, charge, hydropathy indices and matrices for protein structure analysis | Theoretical Biology and Medical Modelling BioMed Central Research Open Access Amino acid size charge hydropathy indices and matrices for protein structure analysis JC Biro Address Homulus Foundation San Francisco CA USA Email JC Biro - Corresponding author Published 22 March 2006 Received 16 December 2005 Theoretical Biology and Medical Modelling2006 3 15 doi l742-4682-3-l5 Accepted 22 March 2006 This article is available from http content 3 l l5 2006Biro licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License http licenses by which permits unrestricted use distribution and reproduction in any medium provided the original work is properly cited. Abstract Background Prediction of protein folding and specific interactions from only the sequence ab initio is a major challenge in bioinformatics. It is believed that such prediction will prove possible if Anfinsen s thermodynamic principle is correct for all kinds of proteins and all the information necessary to form a concrete 3D structure is indeed present in the sequence. Results We indexed the 200 possible amino acid pairs for their compatibility regarding the three major physicochemical properties - size charge and hydrophobicity - and constructed Size Charge and Hydropathy Compatibility Indices and Matrices SCI SCM CCI CCM and HCI HCM . Each index characterized the expected strength of interaction compatibility of two amino acids by numbers from l not compatible to 20 highly compatible . We found statistically significant positive correlations between these indices and the propensity for amino acid co-locations in real protein structures a sample containing total 34630 co-locations in 80 different protein structures for HCI p n 400 in l0 subgroups for SCI p n 400 in l0 subgroups for CCI p n l75 . Size compatibility between residues well known to exist .
