(Q34185206)

31 July 2017

title

Finite element solution of the steady-state Smoluchowski equation for rate constant calculations (English)

1 reference

31 July 2017

2

Yongjie Zhang

1 reference

31 July 2017

5

J Andrew McCammon

1 reference

31 July 2017

Yuhua Song

1

1 reference

31 July 2017

Tongye Shen

series ordinal

3

1 reference

31 July 2017

Chandrajit L Bajaj

series ordinal

4

1 reference

31 July 2017

Nathan A Baker

series ordinal

6

1 reference

31 July 2017

language of work or name

English

0 references

publication date

1 April 2004

1 reference

31 July 2017

1 reference

31 July 2017

volume

86

1 reference

31 July 2017

issue

4

1 reference

31 July 2017

page(s)

2017-2029

1 reference

Robust Biased Brownian Dynamics for Rate Constant Calculation

31 July 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304055

Finite element simulations of acetylcholine diffusion in neuromuscular junctions

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304055

A Monte Carlo model reveals independent signaling at central glutamatergic synapses

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304055

Monte carlo simulations of enzyme reactions in two dimensions: fractal kinetics and spatial segregation.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304055

Modeling diverse range of potassium channels with Brownian dynamics.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304055

Biased Brownian dynamics for rate constant calculation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304055

Electrostatic aspects of protein-protein interactions.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304055

Dynamic modulation of cerebral cortex synaptic function by nitric oxide.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304055

A lattice relaxation algorithm for three-dimensional Poisson-Nernst-Planck theory with application to ion transport through the gramicidin A channel.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304055

Analysis of synaptic transmission in the neuromuscular junction using a continuum finite element model

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304055

Conformation gating as a mechanism for enzyme specificity

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304055

Multiple time step diffusive Langevin dynamics for proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304055

Enhancement of protein-protein association rate by interaction potential: accuracy of prediction based on local Boltzmann factor

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304055

Electrostatic influence on the kinetics of ligand binding to acetylcholinesterase. Distinctions between active center ligands and fasciculin

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304055

Simulation of the diffusional association of barnase and barstar.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304055

Acetylcholinesterase: role of the enzyme's charge distribution in steering charged ligands toward the active site

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304055

Theory and simulation of the time-dependent rate coefficients of diffusion-influenced reactions

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304055

Wiring and volume transmission in the central nervous system: the concept of closed and open synapses

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304055

Orientational steering in enzyme-substrate association: ionic strength dependence of hydrodynamic torque effects

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304055

Acetylcholinesterase inhibition by fasciculin: crystal structure of the complex

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304055

Gating of the active site of triose phosphate isomerase: Brownian dynamics simulations of flexible peptide loops in the enzyme

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304055

Brownian dynamics study of the influences of electrostatic interaction and diffusion on protein-protein association kinetics

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304055

Molecular modeling methods. Basic techniques and challenging problems

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304055

Acetylcholinesterase: diffusional encounter rate constants for dumbbell models of ligand

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304055

Electrostatic and hydrodynamic orientational steering effects in enzyme-substrate association

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304055

The Smoluchowski-Poisson-Boltzmann description of ion diffusion at charged interfaces

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304055

Fractional diffusion-limited component of reactions catalyzed by acetylcholinesterase

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304055

Computer-aided molecular design

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304055

Brownian dynamics simulation of protein association.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304055

Brownian dynamics of cytochrome c and cytochrome c peroxidase association

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304055

Kinetics of protein-protein association explained by Brownian dynamics computer simulation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304055

Lateral diffusion and aggregation. A Monte Carlo study

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304055

Constructing irregular surfaces to enclose macromolecular complexes for mesoscale modeling using the discrete surface charge optimization (DISCO) algorithm

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304055

Dielectric boundary force and its crucial role in gramicidin.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304055

Improved 3D continuum calculations of ion flux through membrane channels.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304055

Crossover in diffusion equation: anomalous and normal behaviors.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304055

Influence of epithelial lining fluid lipids on NO(2)-induced membrane oxidation and nitration

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304055

Ion permeation and selectivity of OmpF porin: a theoretical study based on molecular dynamics, Brownian dynamics, and continuum electrodiffusion theory.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304055

Boundary element modeling of biomolecular transport.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304055

Self-consistent generalized Langevin equation for colloid dynamics.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304055

Derivation of Poisson and Nernst-Planck equations in a bath and channel from a molecular model.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304055

Rapid binding of a cationic active site inhibitor to wild type and mutant mouse acetylcholinesterase: Brownian dynamics simulation including diffusion in the active site gorge

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304055

Acetylcholinesterase: electrostatic steering increases the rate of ligand binding.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304055

Effective charge on acetylcholinesterase active sites determined from the ionic strength dependence of association rate constants with cationic ligands.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304055

Protein-protein association: investigation of factors influencing association rates by Brownian dynamics simulations

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304055

Monte Carlo simulations of ion selectivity in a biological Na channel: Charge–space competition

28 October 2018

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2804%2974263-0

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2804%2974263-0

A Monte Carlo simulation study of the influence of internal motions on the molecular conformation deduced from two-dimensional NMR experiments

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2804%2974263-0

Internal motions of antibody molecules

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2804%2974263-0

Localization of calcium signals by a mobile calcium buffer in frog saccular hair cells

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2804%2974263-0

Diffusion-controlled reactions with mobile traps

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2804%2974263-0

Simulation of enzyme–substrate encounter with gated active sites

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2804%2974263-0

On the calculation of diffusive reaction rates using Brownian dynamics simulations

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2804%2974263-0

Correlation between rate of enzyme-substrate diffusional encounter and average Boltzmann factor around active site

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2804%2974263-0

10.1016/S0006-3495(04)74263-0

7 January 2021

Identifiers

DOI

1 reference

31 July 2017

1 reference

31 July 2017

1 reference