title: Conformational flexibility in designing peptides for immunology: the molecular dynamics approach.
abstract: Computational modeling techniques and computer simulations have become a routine in biological sciences and have gained great attention from researchers. Molecular dynamics simulation is a valuable tool towards an understanding of the complex structure of biological systems, especially in the study of the flexibility of the biological molecules such as peptides or proteins. Peptides play a very important role in human physiology and control many of the processes involved in the immune system response. Designing new and optimal peptide vaccines is one of the hottest challenges of the 21(st) century science and it brings together researchers from different fields. Molecular dynamics simulations have proven to be a helpful tool assisting laboratory work, saving financial sources and opening possibilities for exploring properties of the molecular systems that are hardly accessible by conventional experimental methods. Present review is dedicated to the recent contributions in applications of molecular dynamics simulations in peptide design for immunological purposes, such as B or T cell epitopes.
authors.affiliation: Department of Economics, University of Ioannina, Ioannina, Greece. astavrak@cc.uoi.gr
authors.forename: Athanassios
authors.initials: A
authors.lastname: Stavrakoudis
mesh_terms: D000818:Animals; D000936:Antigen-Antibody Complex / Q000737:chemistry / Q000276:immunology; D003198:Computer Simulation; D017076:Computer-Aided Design; D015195:Drug Design; D006801:Humans; D008958:Models, Molecular; D018716:Molecular Mimicry; D010455:Peptides / Q000737:chemistry* / Q000276:immunology; D011487:Protein Conformation; D055550:Protein Stability; D011948:Receptors, Antigen, T-Cell / Q000737:chemistry / Q000276:immunology; D013329:Structure-Activity Relationship; D013601:T-Lymphocytes / Q000276:immunology; D013816:Thermodynamics; D014612:Vaccines / Q000737:chemistry* / Q000276:immunology
chemical_list: D000936:Antigen-Antibody Complex; D010455:Peptides; D011948:Receptors, Antigen, T-Cell; D014612:Vaccines