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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

[…] study 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. […]


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

[…] of HDAC8 respectively [Fig. (b)]. Gamma-tubulin residues such as Tyr82, Ala370, Glu327, Asn79, Gln227 were found to be interacting with Pro273, Ser150, Tyr100, Cys352, Gln232 of HDAC8 [Fig. (c)]. The ZDOCK score of the tubulins are provided in (Table. ). All the Figures related to protein-protein interaction studies were generated using Discovery Studio Visualizer version 4.1.Further in silico mut […]


Ofatumumab Monoclonal Antibody Affinity Maturation Through in silico Modeling

PMCID: 5889503
DOI: 10.22034/ibj.22.3.180

[…] 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 molecule […]


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
call_split See protocol

[…] 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. […]


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

[…] Molecular docking was then performed to explore the possible binding site and binding mechanism of DC3-AR complex. As a result, 2,000 poses of 60 clusters were generated by ZDOCK module. The pose amount of each cluster, ZRank Score, ZDock Score, and the rationality of binding mode were combined to assess the poses. The ZRank Score represents the extent of energy contribu […]


Meet U: Educating through research immersion

PLoS Comput Biol
PMCID: 5854232
PMID: 29543809
DOI: 10.1371/journal.pcbi.1005992

[…] etermination and modeling. At the end of the course, all 6 teams managed to deliver a finalized end product, and some of the results were comparable to those of state-of-the-art docking tools such as ZDOCK [] and ATTRACT [] (). The closing meeting day (https://storify.com/pierrepo/colloque-meet-u) gathered about 100 attendees, among whom were the participating students, the pedagogical teams, and […]


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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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