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HDOCK specifications

Information


Unique identifier OMICS_18439
Name HDOCK
Interface Web user interface
Restrictions to use None
Input data Some sequences and structures proteins.
Input format PDB, FASTA
Output data The docking results include three basic files: i) Receptor file uploaded by users or constructed by the server from the sequence provided by users, ii) Ligand file uploaded by users or constructed by the server from the sequence provided by users and iii) HDOCK Outputs that include 4392 ligand binding modes represented by their transformations.
Output format PDB
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Sheng-You Huang <>

Publication for HDOCK

HDOCK citations

 (3)
library_books

Improved Estimation of Protein Ligand Binding Free Energy by Using the Ligand Entropy and Mobility of Water Molecules

2013
PMCID: 3817721
PMID: 24276169
DOI: 10.3390/ph6050604

[…] than 2 å rmsd for the 132 complexed receptors with the compounds in pdb. the results predicted by our program were almost the same as those predicted by other docking programs []. the docking score (hdock) to estimate the protein-ligand binding free energy was determined as: (15) where nrot, easa, evdw, eele, ehyd, and eintra-vdw represent the number of rotatable bonds of the ligand molecule, […]

library_books

Pro survival effect of Dock180 overexpression on rat derived H9C2 cardiomyocytes

2013
PMCID: 3638688
PMID: 23314417
DOI: 10.12659/MSMBR.883738

[…] is also thought to be involved in the promotion of cell proliferation and survival and anti-apoptosis in the h9c2 cardiomyocytes., rat-derived h9c2 cardiomyocytes were transfected with pcxn2-flag-hdock180, a human dock180 overexpression eukaryotic recombinant plasmid. the rat and human dock180 mrna and protein expression, apoptosis and cell proliferation and survival were analyzed in the h9c2 […]

library_books

Integration of Ligand Based Drug Screening with Structure Based Drug Screening by Combining Maximum Volume Overlapping Score with Ligand Doscking

2012
PMCID: 3816669
PMID: 24281339
DOI: 10.3390/ph5121332

[…] the volume overlap were assessed between the docked compound and the reference ligand that was given a priori. the docking score, scombined-mvo, is the summation of the conventional docking score (hdock), which is the protein-compound interaction energy, and the mvo score (smvo), which is the volume overlap between the docked compound and the reference ligand: (2) where λ is a coupling […]


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HDOCK institution(s)
School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China
HDOCK funding source(s)
Supported by National Natural Science Foundation of China (NSFC) [31670724]; National Key Research and Development Program of China [2016YFC1305800, 2016YFC1305805]; Huazhong University of Science and Technology Startup Grant [2006012126, 3004012104].

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