Improvements to the APBS biomolecular solvation software suite (Q38610791)

4 September 2017

title

Improvements to the APBS biomolecular solvation software suite (English)

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4 September 2017

24

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4 September 2017

23

J Andrew McCammon

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4 September 2017

Elizabeth Jurrus

1

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4 September 2017

Dave Engel

2

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4 September 2017

Keith Star

3

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4 September 2017

Kyle Monson

4

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4 September 2017

Juan Brandi

5

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4 September 2017

Lisa E Felberg

6

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4 September 2017

David H Brookes

7

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4 September 2017

Leighton Wilson

8

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4 September 2017

Jiahui Chen

9

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4 September 2017

Karina Liles

10

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4 September 2017

Minju Chun

11

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4 September 2017

Peter Li

12

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4 September 2017

David W Gohara

13

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4 September 2017

Todd Dolinsky

14

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4 September 2017

Robert Konecny

15

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4 September 2017

David R Koes

16

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4 September 2017

Jens Erik Nielsen

17

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4 September 2017

Teresa Head-Gordon

18

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4 September 2017

Weihua Geng

19

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4 September 2017

Robert Krasny

20

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4 September 2017

Guo-Wei Wei

21

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4 September 2017

Michael J Holst

22

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4 September 2017

publication date

24 August 2017

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4 September 2017

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PB-AM: An open-source, fully analytical linear poisson-boltzmann solver

4 September 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

Energy Minimization of Discrete Protein Titration State Models Using Graph Theory

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

Optimized Radii for Poisson-Boltzmann Calculations with the AMBER Force Field

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

An Analytical Electrostatic Model for Salt Screened Interactions between Multiple Proteins

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKa Values.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

Electrostatic-Consistent Coarse-Grained Potentials for Molecular Simulations of Proteins

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

Calculating the Bimolecular Rate of Protein-Protein Association with Interacting Crowders

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

SDA 7: A modular and parallel implementation of the simulation of diffusional association software

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

MemProtMD: Automated Insertion of Membrane Protein Structures into Explicit Lipid Membranes.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

3Dmol.js: molecular visualization with WebGL.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

The effect of protein corona composition on the interaction of carbon nanotubes with human blood platelets

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

Understanding nucleic acid-ion interactions

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

Origin of parameter degeneracy and molecular shape relationships in geometric-flow calculations of solvation free energies

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

Structural basis for modulation of a G-protein-coupled receptor by allosteric drugs.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

DOT2: Macromolecular docking with improved biophysical models.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

A general and robust ray-casting-based algorithm for triangulating surfaces at the nanoscale.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

ISA-TAB-Nano: a specification for sharing nanomaterial research data in spreadsheet-based format

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

Biomolecular electrostatics and solvation: a computational perspective

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

Parameterization of a geometric flow implicit solvation model

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

Variational approach for nonpolar solvation analysis

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

iAPBS: a programming interface to Adaptive Poisson-Boltzmann Solver (APBS).

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

Atomic detail brownian dynamics simulations of concentrated protein solutions with a mean field treatment of hydrodynamic interactions

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

DelPhi: a comprehensive suite for DelPhi software and associated resources

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

Biomolecules in the computer: Jmol to the rescue

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

Web servers and services for electrostatics calculations with APBS and PDB2PQR

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

ePMV Embeds Molecular Modeling into Professional Animation Software Environments

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

Differential geometry based solvation model II: Lagrangian formulation

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

Browndye: A Software Package for Brownian Dynamics

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

Differential geometry based solvation model I: Eulerian formulation

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

A New and Efficient Poisson-Boltzmann Solver for Interaction of Multiple Proteins

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

CHARMM: the biomolecular simulation program

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

webPIPSA: a web server for the comparison of protein interaction properties

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

Continuum molecular electrostatics, salt effects, and counterion binding--a review of the Poisson-Boltzmann theory and its modifications

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

Highly accurate biomolecular electrostatics in continuum dielectric environments

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

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

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

Polarizable atomic multipole solutes in a Poisson-Boltzmann continuum

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

Finite element analysis of the time-dependent Smoluchowski equation for acetylcholinesterase reaction rate calculations

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

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

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

Modeling electrostatic effects in proteins

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

Optimized atomic radii for protein continuum electrostatics solvation forces

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

31 August 2018

Implicit solvent models

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

How well does Poisson-Boltzmann implicit solvent agree with explicit solvent? A quantitative analysis

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

Development, validation, and application of adapted PEOE charges to estimate pKa values of functional groups in protein-ligand complexes

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

Very fast empirical prediction and rationalization of protein pKa values

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

Scalable molecular dynamics with NAMD

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

The Amber biomolecular simulation programs

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

PDBML: the representation of archival macromolecular structure data in XML.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

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

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

UCSF Chimera--a visualization system for exploratory research and analysis

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

Finite element simulations of acetylcholine diffusion in neuromuscular junctions

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

Electrostatics of nanosystems: application to microtubules and the ribosome

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

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

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

Generalized born models of macromolecular solvation effects

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

VMD: visual molecular dynamics

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

The interpretation of protein structures: Estimation of static accessibility

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

Electrostatic interactions in macromolecules: theory and applications

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

Electrostatic effects in proteins

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5734301

GMRES: A Generalized Minimal Residual Algorithm for Solving Nonsymmetric Linear Systems

31 August 2018

1 reference

Crossref

https://api.crossref.org/works/10.1002/PRO.3280

Molecular simulations of diffusion and association in multimacromolecular systems

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/28836357

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Impact of protein modification on the protein corona on nanoparticles and nanoparticle-cell interactions

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/28836357

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1002/PRO.3280

1 reference

4 September 2017

1 reference

0 references

1 reference