Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations

By Ignasi Buch, Toni Giorgino, G. de Fabritiis. Proceedings of the National Academy of Sciences of the United States of America, 2011

617 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology, Radiology, Nuclear Medicine and Imaging

View Paper: https://www.semanticscholar.org/paper/86ba02a990c3506505ecc10ebee71e105e8c4085

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In Materials Chemistry

In Molecular Biology

In Radiology, Nuclear Medicine and Imaging

Citations in the corpus

The future of molecular dynamics simulations in drug discovery (2011, background): “Benzamidine bound spontaneously to trypsin in MD simulations, achieving a good match to the crystal-structure–deﬁned pose and revealing the binding pathway [40].”
Structural mechanism of a drug-binding process involving a large conformational change of the protein target (2023, neutral): “interacted with Abl kinase at the following five labeled regions: (1) the ATP-binding”
Identification of slow molecular order parameters for Markov model construction. (2013, background): “Rare conformational transitions can be explicitly traced by either single-molecule experiments [70, 88, 17, 44] or by high-throughput molecular dynamics simulations, either realized with few long trajectories [84, 48] or with many shorter trajectories [92, 11, 67, 13, 77, 12].”
Unsupervised Learning Methods for Molecular Simulation Data (2021, background): “28,29 In some cases, featurizations involving assignment to secondary structure elements, 30 solvent-acces-sible surface area, 31 or hand-picked features may be most appropriate.”
Molecular dynamics simulation for all (2018, neutral): “, 2014; Figure 4)? What are the factors controlling ligand binding and dissociation kinetics (Buch et al., 2011; Dror et al., 2011b; González et al., 2011; Wacker et al., 2017b)? What is the structural basis for water and ion transport across a membrane (Liang et al.”
Multiensemble Markov models of molecular thermodynamics and kinetics (2016, methodology): “33 as follows: [34] Eqs.”
Markov state models of biomolecular conformational dynamics (2014, background): “The viability of using MSMs to study small molecule ligand binding in atomistic detail was established in an initial study of the binding kinetics of the trypsin inhibitor benzamidine was described by an MSM constructed from a collection of short trajectories, revealing the existence of long-lived b”