TY - JOUR
T1 - Discovery Through the Computational Microscope
AU - Lee, Eric H.
AU - Hsin, Jen
AU - Sotomayor, Marcos
AU - Comellas, Gemma
AU - Schulten, Klaus
N1 - Funding Information:
We gratefully acknowledge Peter Freddolino for helpful discussions on performance optimizations for simulations. The molecular images in this paper were created with the molecular graphics program VMD ( Humphrey et al., 1996 ) and MD simulations were performed using NAMD. E.L. was supported in part by the Hazel I. Craig Fellowship. G.C. was supported by the Caja Madrid Graduate Fellowship. M.S. is a Howard Hughes Medical Institute fellow of the Helen Hay Whitney Foundation at the laboratories of D.P. Corey and R. Gaudet. This work was supported by funds of the National Institutes of Health (grants 1 R01 GM073655 and P41 RR05969). The authors also acknowledge computer time provided by the National Science Foundation through the Large Resource Allocations Committee grant MCA93S028.
PY - 2009/10/14
Y1 - 2009/10/14
N2 - 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.".
AB - 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.".
KW - PROTEINS
UR - http://www.scopus.com/inward/record.url?scp=70349779536&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=70349779536&partnerID=8YFLogxK
U2 - 10.1016/j.str.2009.09.001
DO - 10.1016/j.str.2009.09.001
M3 - Review article
C2 - 19836330
AN - SCOPUS:70349779536
VL - 17
SP - 1295
EP - 1306
JO - Structure with Folding & design
JF - Structure with Folding & design
SN - 0969-2126
IS - 10
ER -