Steered molecular dynamics and mechanical functions of proteins.

By B. Isralewitz, Mu Gao, Klaus Schulten. Current Opinion in Structural Biology, 2001

928 citations recorded by the source corpus.

Subfields: Atomic and Molecular Physics, and Optics, Cell Biology

View Paper: https://www.semanticscholar.org/paper/15202288232aad81a6c59ffbd0c132278d6aa0ee

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In Atomic and Molecular Physics, and Optics

In Cell Biology

Citations in the corpus

Scalable molecular dynamics with NAMD (2005, methodology): “External forces have been applied using NAMD in a variety of ways to a diverse set of systems, yielding new information about the mechanics of proteins [54], for instance in [55,6,56,57,58,59,60,61,62,63,64,65,66,67] and other studies reviewed in [51].”
Nonequilibrium fluctuations in small systems: From physics to biology (2007, methodology): “Free-energy recovery techniques are also used in numerical simulations to evaluate free-energy differences [105, 106, 107, 108] and reconstruct free-energy profiles or potentials of mean-field force [109, 110].”
Graphene microsheets enter cells through spontaneous membrane penetration at edge asperities and corner sites (2013, methodology): “In type II simulations, the energy barrier associated with corner piercing is calculated by SMD simulations (38), in which a graphene corner is pulled across the bilayer by a virtual spring (see SI Text for more details).”
QM/MM Methods for Biological Systems (2006, background): “ADMP Atom-centred density-matrix propagation BFGS Broyden–Fletcher–Goldfarb–Shanno (Hessean update algorithm in minimizations) CASSCF Complete active space self-consistent field CCSD Coupled-cluster theory including single and double excitations COSMO Conductor-like screening model CP-MD Car–Parrine”
Discovery Through the Computational Microscope (2009, positive): “…processes have been accelerated by applying external forces in so-called steered molecular dynamics (SMD) simulations (Izrailev et al., 1999; Isralewitz et al., 2001b, 2001a; Grubmüller, 2005), bridging the timescale gap between experiment and simulation through a theoretical framework…”
Biomolecules under mechanical force (2010, methodology): “The method of steered MD (SMD) which combines the stretching condition with standard MD was initiated by Schulten and coworkers [105].”
Bridging Molecular Docking to Molecular Dynamics in Exploring Ligand-Protein Recognition Process: An Overview (2018, methodology): “…targeted molecular dynamics (TMD) are reported: in TMD a bias force is applied to conduct the system from an initial to a desired ﬁnal conﬁguration (Schlitter et al., 1993), leading to the individuation of a path that can be used as set of directions for an SMD simulation (Isralewitz et al., 2001).”