PPD v1.0--an integrated, web-accessible database of experimentally determined protein pKa values (Q25257782)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16381845%20AND%20SRC:MED&resulttype=core&format=json

14 January 2020

title

PPD v1.0--an integrated, web-accessible database of experimentally determined protein pKa values (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16381845%20AND%20SRC:MED&resulttype=core&format=json

14 January 2020

0 references

Christopher P. Toseland

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16381845%20AND%20SRC:MED&resulttype=core&format=json

14 January 2020

author name string

Helen McSparron

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16381845%20AND%20SRC:MED&resulttype=core&format=json

14 January 2020

Matthew N Davies

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16381845%20AND%20SRC:MED&resulttype=core&format=json

14 January 2020

Darren R Flower

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16381845%20AND%20SRC:MED&resulttype=core&format=json

14 January 2020

language of work or name

English

0 references

publication date

1 January 2006

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16381845%20AND%20SRC:MED&resulttype=core&format=json

14 January 2020

published in

Nucleic Acids Research

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16381845%20AND%20SRC:MED&resulttype=core&format=json

14 January 2020

volume

34

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16381845%20AND%20SRC:MED&resulttype=core&format=json

14 January 2020

issue

Database issue

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16381845%20AND%20SRC:MED&resulttype=core&format=json

14 January 2020

page(s)

D199-203

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16381845%20AND%20SRC:MED&resulttype=core&format=json

NMPdb: Database of Nuclear Matrix Proteins

14 January 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1347398

siRNAdb: a database of siRNA sequences

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1347398

7 April 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=1347398

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1347398

The role of Tyr41 and His155 in the functional properties of superoxide dismutase from the archaeon Sulfolobus solfataricus

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1347398

The ionization of a buried glutamic acid is thermodynamically linked to the stability of Leishmania mexicana triose phosphate isomerase

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1347398

The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1347398

Mechanistic roles of Thr134, Tyr160, and Lys 164 in the reaction catalyzed by dTDP-glucose 4,6-dehydratase

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1347398

Classical electrostatics in biology and chemistry

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1347398

Calculating pKa values in enzyme active sites

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1347398

On the evaluation and optimization of protein X-ray structures for pKa calculations

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1347398

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1347398

Empirical relationships between protein structure and carboxyl pKa values in proteins.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1347398

Electrostatic contributions to protein-protein interactions: fast energetic filters for docking and their physical basis

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1347398

The pKa of His-24 in the folding transition state of apomyoglobin

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1347398

Prediction of pH-dependent properties of proteins

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1347398

Energetics of enzyme catalysis

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1347398

Electrostatic calculations of the pKa values of ionizable groups in bacteriorhodopsin

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1347398

Analysis of the pH-dependent folding and stability of histidine point mutants allows characterization of the denatured state and transition state for protein folding

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1347398

Improved pKa calculations through flexibility based sampling of a water-dominated interaction scheme.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1347398

Variability in the pKa of histidine side-chains correlates with burial within proteins

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1347398

Continuum electrostatic analysis of irregular ionization and proton allocation in proteins

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1347398

Ionization properties of titratable groups in ribonuclease T1. II. Electrostatic analysis

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1347398

Ionization properties of titratable groups in ribonuclease T1. I. pKa values in the native state determined by two-dimensional heteronuclear NMR spectroscopy

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1347398

The determinants of pKas in proteins

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1347398

Calculations of enzymatic reactions: calculations of pKa, proton transfer reactions, and general acid catalysis reactions in enzymes.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1347398

Insensitivity of perturbed carboxyl pK(a) values in the ovomucoid third domain to charge replacement at a neighboring residue

28 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/16381845

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/GKJ035

2 references

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16381845%20AND%20SRC:MED&resulttype=core&format=json

journals/nar/ToselandMDF06

14 January 2020

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

2 references

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16381845%20AND%20SRC:MED&resulttype=core&format=json

14 January 2020

PubMed publication ID

16381845

2 references