(Q48247516)

English

SEEKR: Simulation Enabled Estimation of Kinetic Rates, A Computational Tool to Estimate Molecular Kinetics and Its Application to Trypsin-Benzamidine Binding.

scientific article published on 13 February 2017

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scholarly article

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Europe PubMed Central

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28191969%20AND%20SRC:MED&resulttype=core&format=json

2 April 2020

SEEKR: Simulation Enabled Estimation of Kinetic Rates, A Computational Tool to Estimate Molecular Kinetics and Its Application to Trypsin-Benzamidine Binding (English)

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28191969%20AND%20SRC:MED&resulttype=core&format=json

2 April 2020

1

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2 April 2020

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28191969%20AND%20SRC:MED&resulttype=core&format=json

2 April 2020

author name string

Benjamin R Jagger

2

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2 April 2020

Alexandra L Heyneman

3

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2 April 2020

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3 March 2017

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2 April 2020

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10

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Journal of Physical Chemistry B

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2 April 2020

121

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2 April 2020

15

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2 April 2020

3597-3606

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28191969%20AND%20SRC:MED&resulttype=core&format=json

2 April 2020

Perspective: On the importance of hydrodynamic interactions in the subcellular dynamics of macromolecules

1 reference

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Two Relations to Estimate Membrane Permeability Using Milestoning

1 reference

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ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB.

1 reference

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Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning

1 reference

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Bridging scales through multiscale modeling: a case study on protein kinase A

1 reference

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Protein conformational plasticity and complex ligand-binding kinetics explored by atomistic simulations and Markov models

1 reference

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Molecular determinants of drug-receptor binding kinetics

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Long-timescale molecular dynamics simulations elucidate the dynamics and kinetics of exposure of the hydrophobic patch in troponin C

1 reference

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Oncogenic mutations counteract intrinsic disorder in the EGFR kinase and promote receptor dimerization

1 reference

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Calculating kinetics and pathways of protein-ligand association

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Markov state model reveals folding and functional dynamics in ultra-long MD trajectories

1 reference

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The moderately efficient enzyme: evolutionary and physicochemical trends shaping enzyme parameters

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Revisiting and computing reaction coordinates with Directional Milestoning

1 reference

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Browndye: A Software Package for Brownian Dynamics

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Everything you wanted to know about Markov State Models but were afraid to ask

1 reference

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Finding transition pathways using the string method with swarms of trajectories

1 reference

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PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations

1 reference

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MolProbity: all-atom contacts and structure validation for proteins and nucleic acids

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Automatic atom type and bond type perception in molecular mechanical calculations

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Scalable molecular dynamics with NAMD

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Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew

1 reference

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1 reference

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MD simulation of protein-ligand interaction: formation and dissociation of an insulin-phenol complex

1 reference

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Adaptive Multilevel Splitting Method for Molecular Dynamics Calculation of Benzamidine-Trypsin Dissociation Time

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Full kinetics of CO entry, internal diffusion, and exit in myoglobin from transition-path theory simulations

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Foundations of biomolecular modeling

1 reference

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1 reference

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1 reference

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12 December 2020

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10.1021/ACS.JPCB.6B09388

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2 April 2020

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Europe PubMed Central

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2 April 2020

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Europe PubMed Central

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