HYDE statistics

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Citations per year

Number of citations per year for the bioinformatics software tool HYDE
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Tool usage distribution map

This map represents all the scientific publications referring to HYDE per scientific context
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Associated diseases

This word cloud represents HYDE usage per disease context
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Popular tool citations

chevron_left Structure-based virtual screening Binding affinity prediction chevron_right
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Protocols

HYDE specifications

Information


Unique identifier OMICS_20180
Name HYDE
Alternative name HYdrogen bond and DEhydration energies
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Stability Stable
Registration required Yes
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Matthias Rarey

Additional information


HYDE is also embedded in SeeSAR.

Publication for HYdrogen bond and DEhydration energies

HYDE citations

 (7)
library_books

Molecular dynamic simulations reveal structural insights into substrate and inhibitor binding modes and functionality of Ecto Nucleoside Triphosphate Diphosphohydrolases

2018
Sci Rep
PMCID: 5803232
PMID: 29416085
DOI: 10.1038/s41598-018-20971-4

[…] for docking studies. Hybrid enthalpy and entropy approach of docking was used with all other default parameters. Top ranking 50 poses for each ligand molecule were kept and validated further through HYDE visual affinity assessment which is a function of two parameters namely, hydrogen bonding affinity and dehydration energy estimation. For each docked pose binding affinity (ΔG) was determined. Po […]

call_split

The protein kinase promiscuities in the cancer preventive mechanisms of NSAIDs

2015
PMCID: 4885542
PMID: 25714784
DOI: 10.1097/CEJ.0000000000000129
call_split See protocol

[…] Docking of the drugs into targets was performed using LeadIT software from BioSolveIT (LeadIT; http://www.biosolveit.de/LeadIT). The best docking poses were evaluated using the Hyde method to determine the contribution of hydration. Targets of the chemotherapeutics were identified according to the data in DrugBank and their corresponding structures were retrieved from the RS […]

library_books

Deciphering the signaling mechanisms of the plant cell wall degradation machinery in Aspergillus oryzae

2015
BMC Syst Biol
PMCID: 4647334
PMID: 26573537
DOI: 10.1186/s12918-015-0224-5

[…] pot file is calculated prior to the docking procedure. The poses are pruned and a final optimization step is performed before the poses are scored []. To shortlist the strong binding metabolites, the HYDE scoring function in the LeadIT software suite was employed. LeadIT version 2.0.1 is an interactive graphical user interface, which embeds both docking and fragment-based design tools, FlexX and R […]

library_books

Identification and Validation of a Potent Dual Inhibitor of the P. falciparum M1 and M17 Aminopeptidases Using Virtual Screening

2015
PLoS One
PMCID: 4583420
PMID: 26406322
DOI: 10.1371/journal.pone.0138957

[…] 7 drug-like molecules showed comparable poses when docked with both MVD and FlexX (RMSD < 2.0 Å on superposed heavy atoms) in PfA-M1 and PfA-M17 binding sites. To rank the 37 virtual hits we used the Hyde scoring function [] to predict the binding affinity of each compound to PfA-M1 and PfA-M17 (Table A in ). This scoring function takes into account the zinc coordination geometry contribution in t […]

library_books

Structure Based Optimization of Inhibitors of the Aspartic Protease Endothiapepsin

2015
Int J Mol Sci
PMCID: 4581293
PMID: 26287174
DOI: 10.3390/ijms160819184

[…] ΔGEXPT (2) = −31.3 kJ·mol−1) and ligand efficiencies (LE (2) = 0.28), obtained from the IC50 values using the Cheng–Prusoff equation [], correlate with the calculated value using the scoring function HYDE in the LeadIT suite ΔGHYDE (2) = −32.0 kJ·mol−1 [,]. This correlation is also valid for other acylhydrazones, except for 3, 6 and 7 ().When the para-methyl group of the mesityl substituent of 1 i […]

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Novel Histone Deacetylase Class IIa Selective Substrate Radiotracers for PET Imaging of Epigenetic Regulation in the Brain

2015
PLoS One
PMCID: 4526562
PMID: 26244761
DOI: 10.1371/journal.pone.0133512
call_split See protocol

[…] s performed with the ligands AHA, FAHA, DFAHA, and TFAHA. Top 20 poses based on the docking score of each docking run were saved and the top 10 poses were used for binding affinity calculations using Hyde software (BioSolveIT GmbH, Germany) [,]. […]


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HYDE institution(s)
Center for Bioinformatics, University of Hamburg, Hamburg, Germany; Bayer CropScience AG, Frankfurt am Main, Germany; BioSolveIT GmbH, St. Augustin, Germany
HYDE funding source(s)
Supported by Bayer CropScience AG and Bayer Pharma AG.

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