H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations (Q36088442)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22570416%20AND%20SRC:MED&resulttype=core&format=json

31 January 2020

title

H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations (English)

1 reference

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31 January 2020

0 references

1

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31 January 2020

author name string

Boris Aguilar

series ordinal

2

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31 January 2020

Alexey V Onufriev

series ordinal

3

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language of work or name

English

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publication date

8 May 2012

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31 January 2020

published in

Nucleic Acids Research

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31 January 2020

volume

40

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31 January 2020

issue

Web Server issue

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31 January 2020

page(s)

W537-41

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Creative Commons Attribution-NonCommercial 3.0 Unported

31 January 2020

copyright license

start time

5 October 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Open Babel: An open chemical toolbox

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394296

Biomolecularmodeling and simulation: a field coming of age.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394296

Charges in the hydrophobic interior of proteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394296

Molecular determinants of the pKa values of Asp and Glu residues in staphylococcal nuclease

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394296

A fast and accurate computational approach to protein ionization

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394296

A buried lysine that titrates with a normal pKa: Role of conformational flexibility at the protein-water interface as a determinant of pKavalues

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394296

Molecular simulations of protein dynamics: new windows on mechanisms in biology

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394296

Chemically accurate protein structures: validation of protein NMR structures by comparison of measured and predicted pKa values.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394296

Molecular dynamics simulations of the complete satellite tobacco mosaic virus

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394296

The Amber biomolecular simulation programs

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394296

H++: a server for estimating pKas and adding missing hydrogens to macromolecules

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394296

Molecular dynamics and protein function

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394296

Combining conformational flexibility and continuum electrostatics for calculating pK(a)s in proteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394296

Molecular dynamics simulations of biomolecules

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394296

pKa calculations suggest storage of an excess proton in a hydrogen-bonded water network in bacteriorhodopsin

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394296

What are the dielectric "constants" of proteins and how to validate electrostatic models?

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394296

Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394296

A Novel View of pH Titration in Biomolecules†

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394296

2 October 2017

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394296

Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394296

Prediction of pH-dependent properties of proteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394296

pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394296

MCCE2: improving protein pKa calculations with extensive side chain rotamer sampling

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394296

A summary of the measured pK values of the ionizable groups in folded proteins

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394296

Sensitivity of molecular dynamics simulations to the choice of the X-ray structure used to model an enzymatic reaction

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394296

Titration of aspartate-85 in bacteriorhodopsin: what it says about chromophore isomerization and proton release

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394296

Protonation of interacting residues in a protein by a Monte Carlo method: application to lysozyme and the photosynthetic reaction center of Rhodobacter sphaeroides

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394296

Electrostatic forces in two lysozymes: calculations and measurements of histidine pKa values

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394296

Electrostatic calculations of the pKa values of ionizable groups in bacteriorhodopsin

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394296

Analysis of basic clustering algorithms for numerical estimation of statistical averages in biomolecules

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394296

A simple clustering algorithm can be accurate enough for use in calculations of pKs in macromolecules

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394296

Constant pH molecular dynamics in generalized Born implicit solvent

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394296

Proton Affinity Changes Driving Unidirectional Proton Transport in the Bacteriorhodopsin Photocycle

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394296

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

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394296

Electrostatic models for computing protonation and redox equilibria in proteins.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394296

Intrinsic pKas of ionizable residues in proteins: an explicit solvent calculation for lysozyme

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394296

Interpretation of protein titration curves. Application to lysozyme

21 October 2018

1 reference

12 December 2020

On the calculation of pKas in proteins

1 reference

12 December 2020

Constant-pH molecular dynamics using continuous titration coordinates

1 reference

12 December 2020

pH dependence of light-induced proton release by bacteriorhodopsin

1 reference

12 December 2020

Identifiers

DOI

10.1093/NAR/GKS375

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22570416%20AND%20SRC:MED&resulttype=core&format=json

journals/nar/AnandakrishnanAO12

31 January 2020

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22570416%20AND%20SRC:MED&resulttype=core&format=json

31 January 2020

PubMed publication ID

22570416

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22570416%20AND%20SRC:MED&resulttype=core&format=json