Discovery Through the Computational Microscope

By Eric H. Lee, Jen Hsin, M. Sotomayor, Gemma Comellas, Klaus Schulten. Structure, 2009

323 citations recorded by the source corpus.

Summary All-atom molecular dynamics simulations have become increasingly popular as a tool to investigate protein function and dynamics. However, researchers are concerned about the short time scales covered by simulations, the apparent impossibility to model large and integral biomolecular systems, and the actual predictive power of the molecular dynamics methodology. Here we review simulations that were in the past both hotly disputed and considered key successes, namely of proteins with mainly mechanical functions (titin, fibrinogen, ankyrin, and cadherin). The simulation work covered shows how state-of-the-art modeling alleviates some of the prior concerns, and how unrefuted discoveries are made through the “computational microscope".

Subfields: Atomic and Molecular Physics, and Optics, Molecular Biology, Pulmonary and Respiratory Medicine

View Paper: https://www.semanticscholar.org/paper/c930a781cc632144d02ce9cd1f61f128ab7fdefd

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In Atomic and Molecular Physics, and Optics

In Molecular Biology

Citations in the corpus

Integrating protein structural dynamics and evolutionary analysis with Bio3D (2014, background): “In addition to multiple structure comparisons, computational methods including molecular dynamics (MD) and normal mode analysis (NMA) have emerged as popular approaches for characterizing protein dynamics and flexibility [7-9].”
The power of coarse graining in biomolecular simulations (2013, methodology): “9 Provided that one respects the limitations of the CG model at hand, CG modeling has five powerful advantages, namely: (1) enabling efficient simulations of huge system sizes, with simulation volumes up to WIREs Comput Mol Sci 2014, 4:225–248.”
Stochastic mechano-chemical kinetics of molecular motors: A multidisciplinary enterprise from a physicist’s perspective (2012, background): “But, conceptually dividing these processes into shorter sub-processes, it has been possible to study the sub-processes independently by carrying out MD simulations of the corresponding atomistic models [384, 385].”