MIBPB: a software package for electrostatic analysis (Q41260030)

28 September 2017

MIBPB: a software package for electrostatic analysis (English)

1 reference

28 September 2017

0 references

1 reference

Duan Chen

1

1 reference

28 September 2017

Zhan Chen

2

1 reference

28 September 2017

Changjun Chen

3

1 reference

28 September 2017

Weihua Geng

4

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28 September 2017

Guo-Wei Wei

5

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28 September 2017

15 September 2010

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Journal of Computational Chemistry

28 September 2017

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28 September 2017

32

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28 September 2017

756-770

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28 September 2017

4

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Generalized Born model with a simple, robust molecular volume correction

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3005000

Matched interface and boundary (MIB) for the implementation of boundary conditions in high-order central finite differences

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3005000

Computational methods for optical molecular imaging

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3005000

PBEQ-Solver for online visualization of electrostatic potential of biomolecules

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3005000

Implicit modeling of nonpolar solvation for simulating protein folding and conformational transitions.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3005000

Explicit ion, implicit water solvation for molecular dynamics of nucleic acids and highly charged molecules

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3005000

Continuum simulations of acetylcholine diffusion with reaction-determined boundaries in neuromuscular junction models

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3005000

Poisson-Boltzmann calculations of nonspecific salt effects on protein-protein binding free energies

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3005000

1 October 2017

Implicit solvent models

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3005000

Improving implicit solvent simulations: a Poisson-centric view

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3005000

Continuum diffusion reaction rate calculations of wild-type and mutant mouse acetylcholinesterase: adaptive finite element analysis

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3005000

Recent advances in the development and application of implicit solvent models in biomolecule simulations

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3005000

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3005000

GRASP2: visualization, surface properties, and electrostatics of macromolecular structures and sequences

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3005000

Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energy

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3005000

Comparison of calculation and experiment implicates significant electrostatic contributions to the binding stability of barnase and barstar

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3005000

Salt-dependent monomer-dimer equilibrium of bovine beta-lactoglobulin at pH 3

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3005000

Electrostatics of nanosystems: application to microtubules and the ribosome

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3005000

Macromolecular electrostatics: continuum models and their growing pains

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3005000

Generalized born models of macromolecular solvation effects

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3005000

Brownian dynamics simulation of protein-protein diffusional encounter

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3005000

Reduced surface: an efficient way to compute molecular surfaces

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3005000

Classical electrostatics in biology and chemistry

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3005000

The interpretation of protein structures: Estimation of static accessibility

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3005000

Electrostatic interactions in macromolecules: theory and applications

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3005000

Areas, volumes, packing and protein structure

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3005000

Computer simulations of actin polymerization can explain the barbed-pointed end asymmetry

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3005000

A new method for computing the macromolecular electric potential.

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3005000

Polarizable continuum model with the fragment molecular orbital-based time-dependent density functional theory

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3005000

Treatment of charge singularities in implicit solvent models.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3005000

Treatment of geometric singularities in implicit solvent models.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3005000

Highly accurate biomolecular electrostatics in continuum dielectric environments.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3005000

Calculation of pKas in RNA: on the structural origins and functional roles of protonated nucleotides.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3005000

Optimized atomic radii for protein continuum electrostatics solvation forces.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3005000

A state-specific polarizable continuum model time dependent density functional theory method for excited state calculations in solution.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3005000

Quantum mechanical continuum solvation models.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3005000

Implicit solvation based on generalized Born theory in different dielectric environments.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3005000

Hybrid boundary element and finite difference method for solving the nonlinear Poisson-Boltzmann equation.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3005000

Accelerated Poisson-Boltzmann calculations for static and dynamic systems

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3005000

Optimizing the hydrogen-bond network in Poisson-Boltzmann equation-based pK(a) calculations.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3005000

Classification of protein sequences by homology modeling and quantitative analysis of electrostatic similarity.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3005000

Protein-protein interactions in colicin E9 DNase-immunity protein complexes. 1. Diffusion-controlled association and femtomolar binding for the cognate complex.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3005000

Family of G protein alpha chains: amphipathic analysis and predicted structure of functional domains

19 August 2018

1 reference

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

21 January 2018

1 reference

Analytical molecular surface calculation

21 January 2018

1 reference

Poisson–Boltzmann Methods for Biomolecular Electrostatics

21 January 2018

1 reference

Protein molecular dynamics with electrostatic force entirely determined by a single Poisson-Boltzmann calculation

21 January 2018

1 reference

Limitations of atom-centered dielectric functions in implicit solvent models

21 January 2018

1 reference

Focusing of electric fields in the active site of Cu-Zn superoxide dismutase: effects of ionic strength and amino-acid modification

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3005000

Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian Dynamics program

4 November 2018

1 reference

Computational studies of the early intermediates of the bacteriorhodopsin photocycle

21 January 2018

1 reference

12 December 2020

Comparative study of generalized born models: Born radii and peptide folding

1 reference

12 December 2020

Calculation of the electric potential in the active site cleft due to alpha-helix dipoles

1 reference

12 December 2020

Conservation of electrostatic properties within enzyme families and superfamilies

1 reference

12 December 2020

Identifiers

DOI

10.1002/JCC.21646

1 reference

28 September 2017

journals/jcc/ChenCCGW11

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

28 September 2017

1 reference