title: The basic concepts of molecular modeling.
abstract: Molecular modeling techniques have made significant advances in recent years and are becoming essential components of many chemical, physical and biological studies. Here we present three widely used techniques used in the simulation of biomolecular systems: structural and homology modeling, molecular dynamics and molecular docking. For each of these topics we present a brief discussion of the underlying scientific basis of the technique, some simple examples of how the method is commonly applied, and some discussion of the limitations and caveats of which the user should be aware. References for further reading as well as an extensive list of software resources are provided.
authors.affiliation: Biomedical Engineering, Washington University, St Louis, Missouri, USA.
authors.forename: Akansha
authors.initials: A
authors.lastname: Saxena
authors.affiliation: Biomedical Engineering, Washington University, St Louis, Missouri, USA.
authors.forename: Diana
authors.initials: D
authors.lastname: Wong
authors.affiliation: Biomedical Engineering and Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.
authors.forename: Karthikeyan
authors.initials: K
authors.lastname: Diraviyam
authors.affiliation: Biomedical Engineering and Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.
authors.forename: David
authors.initials: D
authors.lastname: Sept
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D016208:Databases, Factual; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D015394:Molecular Structure; D025341:Principal Component Analysis; D011487:Protein Conformation; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein; D012984:Software