title: Current state-of-the-art molecular dynamics methods and applications.
abstract: Molecular dynamics simulations are used to describe the patterns, strength, and properties of protein behavior, drug-receptor interactions, the solvation of molecules, the conformational changes that a protein or molecule may undergo under various conditions, and other events that require the systematic evaluation of molecular properties in dynamic molecular systems. Only few years ago proteins were considered to be rigid body structures with very limited conformational flexibility. However, it is now clear that proteins are highly dynamic structures, the internal organization of which is the key to their 3D spatial arrangement and hence biological function. The study of protein dynamics in the lab is a very complicated, expensive, and time-consuming process. Therefore, a lot of effort and hope lies with the computers and the in silico study of protein structure and molecular dynamics. Herein, an effort has been made to describe the ever-evolving field of molecular dynamics, the different algorithms, and force fields that are being used as well as to provide some insight on what the near future holds for this auspicious field of computational structural biology.
authors.affiliation: Bioinformatics & Medical Informatics Team, Biomedical Research Foundation, Academy of Athens, Athens, Greece.
authors.forename: Dimitrios
authors.initials: D
authors.lastname: Vlachakis
authors.affiliation: Bioinformatics & Medical Informatics Team, Biomedical Research Foundation, Academy of Athens, Athens, Greece; Laboratory of Biomedical Microbiology and Immunology, University of Veterinary Medicine and Pharmacy, Kosice, Slovakia.
authors.forename: Elena
authors.initials: E
authors.lastname: Bencurova
authors.affiliation: Bioinformatics & Medical Informatics Team, Biomedical Research Foundation, Academy of Athens, Athens, Greece.
authors.forename: Nikitas
authors.initials: N
authors.lastname: Papangelopoulos
authors.affiliation: Bioinformatics & Medical Informatics Team, Biomedical Research Foundation, Academy of Athens, Athens, Greece. Electronic address: skossida@bioacademy.gr.
authors.forename: Sophia
authors.initials: S
authors.lastname: Kossida
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D056004:Molecular Dynamics Simulation; D012984:Software
keywords: Drug–receptor interactions; Molecular dynamics algorithms; Molecular dynamics force fields; Molecular dynamics simulations; Protein behavior; Protein conformational changes; Solvation of molecules