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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 citations


Identification of the effector domain of biglycan that facilitates BMP 2 osteogenic function

Sci Rep
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 […]


Overexpressed HDAC8 in cervical cancer cells shows functional redundancy of tubulin deacetylation with HDAC6

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: […]


Ofatumumab Monoclonal Antibody Affinity Maturation Through in silico Modeling

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 […]


Interaction of the GntR family transcription factor Sll1961 with thioredoxin in the cyanobacterium Synechocystis sp. PCC 6803

Sci Rep
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 […]


Exploring the Interaction Mechanism Between Cyclopeptide DC3 and Androgen Receptor Using Molecular Dynamics Simulations and Free Energy Calculations

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 […]


Lipophosphoglycan 3 From Leishmania infantum chagasi Binds Heparin With Micromolar Affinity

Bioinform Biol Insights
PMCID: 5858678
PMID: 29568220
DOI: 10.1177/1177932218763363

[…] the steric clashes between residues. the high quality of model was evaluated by procheck and prosa softwares. the protein-protein docking to tetrameric complex modeling was performed using m-zdock, web server. the top 10 models of this program were compared and the most repetitive structure with smaller root-mean-square deviation against other models was selected as the consensus model. […]

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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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