ZDOCK protocols

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ZDOCK specifications


Unique identifier OMICS_03774
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for ZDOCK

ZDOCK in pipeline

PMCID: 5413048
PMID: 28463985
DOI: 10.1371/journal.pone.0176793

[…] single ligand (fatty acid) to protein (md-2 pdb id#2e56) docking was performed using the swissdock server []. docking of multiple molecules of palmitic acid to md-2 was performed using the zdock server []. docking figures were generated with the ucsf chimera package. chimera was developed by the resource for biocomputing, visualization, and informatics at the university of california, […]

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ZDOCK in publications

PMCID: 5935668
PMID: 29728612
DOI: 10.1038/s41598-018-25279-x

[…] the interactions of these peptides with bmp-2 and bmp-2 receptor (type ia and activin receptor type 2 a). the bmp-2 and bmp-2 receptor structures are from pdb ids 1rew and 2goo and the programs zdock and ftdock were used for the protein-protein docking., all sample conditions were analyzed in triplicates and compared using one-way anova with post-hoc tukey-kramer using instat software […]

PMCID: 5930436
PMID: 29716651
DOI: 10.1186/s12964-018-0231-4

[…] sequence identity, c-score, tm score and rmsd values of template structure., protein-protein interaction studies of tubulins (alpha, beta, gamma) were carried out with hdac8 (pdb id: 1w22_a) using zdock [], which is an interactive online based server for docking protein-protein complexes., hhdac8 (full length) cdna was amplified by using a polymerase chain reaction (pcr) with forward primer: […]

PMCID: 5889503
DOI: 10.22034/ibj.22.3.180

[…] 8.0 professional software[] to further improve the predicted structures., docking was performed using hex 8.0 software, cluspro 2.0 server[] cluspro (https://cluspro.bu.edu/publications.php), zdock (http://zdock.umassmed. edu/)[], and haddock[] at http://haddock.science.uu.nl/services/haddock 2.2/. this scrutiny was used to determine the interaction and orientation between the two […]

PMCID: 5923263
PMID: 29703909
DOI: 10.1038/s41598-018-25077-5

[…] and described in detail in supplementary text and supplementary table . three-dimensional structure predictions were performed using the i-tasser server. docking predictions were performed using the zdock server. foldit standalone was used for manual refinement of predicted structures., , electronic supplementary material , supplementary information accompanies this paper […]

PMCID: 5932393
PMID: 29755968
DOI: 10.3389/fchem.2018.00119

[…] protein data bank (http://www.rcsb.org/pdb; pdb id: 4oha). the missing loop regions were refined by discovery studio 2.5. (accelrys inc. ca, ). molecular docking process was carried out by using zdock module. the rigid-body protein–protein docking program zdock uses the fast fourier transform algorithm to enable an efficient global docking search on a 3d grid, and utilizes a combination […]

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ZDOCK institution(s)
Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA; Bioinformatics Program, Boston University, Boston, MA USA

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