The basic concepts of molecular modeling.
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.
Saxena
Akansha
A
Biomedical Engineering, Washington University, St Louis, Missouri, USA.
Wong
Diana
D
Biomedical Engineering, Washington University, St Louis, Missouri, USA.
Diraviyam
Karthikeyan
K
Biomedical Engineering and Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.
Sept
David
D
Biomedical Engineering and Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.
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