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H++ specifications

Information


Unique identifier OMICS_10698
Name H++
Interface Web user interface
Restrictions to use None
Input data Two input formats are supported by the H++ website, PDB and PQR.
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


Publication for H++

H++ citations

 (80)
library_books

Modulation of nucleosomal DNA accessibility via charge altering post translational modifications in histone core

2018
PMCID: 5856334
PMID: 29548294
DOI: 10.1186/s13072-018-0181-5

[…] te for all of the nucleosome states considered here is the atomistic structure of the nucleosome core particle (PDB ID 1KX5) []. The protonation states of the ionizable residues were computed via the H++ server [, ] which employs the standard continuum electrostatics methodology for determining the pKs of amino acid residues []. We set the following parameters for estimating the protonation state […]

library_books

High affinity ligands of the colchicine domain in tubulin based on a structure guided design

2018
Sci Rep
PMCID: 5844890
PMID: 29523799
DOI: 10.1038/s41598-018-22382-x

[…] ut with cGRILL,,, a computational tool formally equivalent to Goodford´s program GRID. Hydrogen atoms, atom point charges and radii for all atoms in the complexes were calculated by submission to the H++ server (http://biophysics.cs.vt.edu) in order to obtain their pqr format files. Grid center was defined by selecting the corresponding ligand and a cubic box of 50 × 50 × 50 points and a grid spac […]

call_split

L718Q mutant EGFR escapes covalent inhibition by stabilizing a non reactive conformation of the lung cancer drug osimertinib† †Electronic supplementary information (ESI) available: pKa shift for Cys797; geometries of TSs identified with QM/MM calculations; analysis of the minimum free energy path for Cys797 alkylation; analysis of MD replicas; convergence for US simulations; replica of simulation of Cys797 alkylation; conformational FESs obtained from each MD replica. See DOI: 10.1039/c7sc04761d

2018
PMCID: 5911825
PMID: 29732058
DOI: 10.1039/c7sc04761d
call_split See protocol

[…] rom the 10 ns MD trajectories for EGFR T790M–osimertinib and EGFR T790M/L718Q–osimertinib complexes. The structures were exported as PDB files and submitted to pKa calculations using Propka3.0 () and H++ ) software using default settings. Individual ΔpKa values were calculated as Cys797 pKa of EGFR T790M minus Cys797 pKa of EGFR T790M/L718Q, while the final values reported in main text resulted fr […]

library_books

Correlation of structure, function and protein dynamics in GH7 cellobiohydrolases from Trichoderma atroviride, T. reesei and T. harzianum

2018
Biotechnol Biofuels
PMCID: 5766984
PMID: 29344086
DOI: 10.1186/s13068-017-1006-7

[…] glycans attached to the catalytic domains were omitted from the models, as they have relatively limited effects on the protein dynamics over MD-simulation time scales []. pKa calculations, using the H++ webserver, and visual inspection were used to determine the protonation states of the titratable residues at pH 5.0 with internal and external dielectrics of 10 and 80, respectively [–]. Disulfide […]

call_split

Membrane binding of the insertion sequence of Proteus vulgaris L amino acid deaminase stabilizes protein structure and increases catalytic activity

2017
Sci Rep
PMCID: 5651824
PMID: 29057984
DOI: 10.1038/s41598-017-14238-7
call_split See protocol

[…] code 5hxw) was used as the initial model, and prepared using Molecule Operating Environment (MOE, Chemical Computing Group Inc.) package. The protonation states of charged residues were determined by H++ program, and then the model was neutralized by adding Na+ or Cl− ions at protein surface using Amber. The model was solvated into a box with a 10 Å buffer distance between the solvent box wall and […]

library_books

Molecular motion regulates the activity of the Mitochondrial Serine Protease HtrA2

2017
PMCID: 5759095
PMID: 29022916
DOI: 10.1038/cddis.2017.487

[…] ore distant from the protease domain, whereas in the S306A crystal structure the PDZ domain is significantly closer to the protease domain.The protonation states of the residues were checked with the H++ and PROPKA webservers, and visually confirmed afterwards, with all residues falling under the standard protonation states except residues H170, H389, H403 (which were modeled as positively charged […]

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H++ institution(s)
Department of Computer Science, Virginia Tech Blacksburg, VA, USA

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