PatchDock statistics

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Citations per year

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

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

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Protocols

PatchDock specifications

Information


Unique identifier OMICS_03777
Name PatchDock
Interface Web user interface
Restrictions to use Academic or non-commercial use
Input data Receptor protein and ligand protein
Input format PDB
Output data A list of candidate complexes between user specified receptor and ligand molecule. The geometric score, the desolvation energy, the interface area size and the actual rigid transformation of each candidate are shown.
Output format ZIP, PDB
Computer skills Basic
Version 1.3
Stability Beta
Maintained Yes

Documentation


Maintainer


  • person_outline Dina Schneidman-Duhovny

Information


Unique identifier OMICS_03777
Name PatchDock
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input data Receptor protein and ligand protein
Input format PDB
Output data A list of candidate complexes between user specified receptor and ligand molecule. The geometric score, the desolvation energy, the interface area size and the actual rigid transformation of each candidate are shown.
Output format ZIP, PDB
Operating system Unix/Linux, Mac OS
Computer skills Advanced
Version 1.3
Stability Beta
Maintained Yes

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Versioning


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Documentation


Maintainer


  • person_outline Dina Schneidman-Duhovny

Publications for PatchDock

PatchDock citations

 (162)
library_books

Investigation of immunogenic properties of Hemolin from silkworm, Bombyx mori as carrier protein: an immunoinformatic approach

2018
Sci Rep
PMCID: 5934409
PMID: 29725106
DOI: 10.1038/s41598-018-25374-z

[…] Molecular docking was performed to check the interaction between hemolin protein and TLR-3 and TLR4-myeloid differentiation factor 4 (MD4) using PatchDock (http://bioinfo3d.cs.tau.ac.il/PatchDock/) server. Patchdock is a fully automated protein - protein docking online server. Algorithm of PatchDock is divided into three different stages; the […]

library_books

Computational identification, characterization and validation of potential antigenic peptide vaccines from hrHPVs E6 proteins using immunoinformatics and computational systems biology approaches

2018
PLoS One
PMCID: 5929558
PMID: 29715318
DOI: 10.1371/journal.pone.0196484

[…] a. Afterward, the best peptide coordinates were docked to the class I MHC molecules HLA-A*0101 (PDB ID 4NQV), HLA-B*1501 (PDB ID 1XR9), HLA-B*5801 (PDB ID 5IM7) and HLA-C*0801 (PDB ID 4NT6) using the PatchDock rigid-body docking server based on the defined threshold []. PatchDock uses a geometry based docking algorithm to find docking transformations with good molecular shape complementarity []. S […]

call_split

Evolutionary Analysis Provides Insight Into the Origin and Adaptation of HCV

2018
Front Microbiol
PMCID: 5938362
PMID: 29765366
DOI: 10.3389/fmicb.2018.00854
call_split See protocol

[…] . The 1b subtype was used in the original study describing interaction between OAS1 and NS5A (). Two docking methods were applied and their results compared for consistency. Specifically, we used the PatchDock server () and imposed that the F37 residue in NS5A is located at the binding interface, as described (). We next used ClusPro (; ) without any assumption on the residues involved in binding. […]

call_split

Yeast aconitase mitochondrial import is modulated by interactions of its C and N terminal domains and Ssa1/2 (Hsp70)

2018
Sci Rep
PMCID: 5897410
PMID: 29651044
DOI: 10.1038/s41598-018-24068-w
call_split See protocol

[…] o) were generated using I-TASSER. The models with the highest probability score among the provided models were selected for further investigation. Docking of Ssa1 to aconitase was performed using the PatchDock software, with the structural models as input. These models were further refined with the RosettaDock local refinement algorithm to generate models with atomistic detail of the interaction. […]

call_split

Preferential binding of fullerene and fullerenol with the N terminal and middle regions of amyloid beta peptide: an in silico investigation

2018
PMCID: 5863620
PMID: 29593399
DOI: 10.2147/IJN.S125011
call_split See protocol

[…] er for 50 ns using GROMACS (Version 4.5.5) to generate an ensemble of Aβ conformations using g_cluster algorithm. Nineteen dominant conformations of Aβ were docked with fullerene and fullerenol using PatchDock server to predict the most probable binding site of fullerene and fullerenol in Aβ. Fullerene and fullerenol were generated using GaussView. The docking results were analyzed using PyMOL and […]

library_books

Structural Studies of Predicted Ligand Binding Sites and Molecular Docking Analysis of Slc2a4 as a Therapeutic Target for the Treatment of Cancer

2018
Int J Mol Sci
PMCID: 5855608
PMID: 29382080
DOI: 10.3390/ijms19020386

[…] ctions during angiogenesis in tumour formation and this can serve as another novel therapeutic agent for the treatment and management of cancer.In this study, online protein-protein interaction tools PatchDock and FireDock server were used as docking tool for our putative anticancer AMPs (RAB1- RAB7) with Slc2a4 protein. The generated 3D structure of the seven-novel anticancer putative AMPs serves […]


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PatchDock institution(s)
School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel; Sackler Institute of Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Basic Research Program, SAIC-Frederick Inc., Laboratory of Experimental and Computational Biology NCI-Frederick, Frederick, MD, USA
PatchDock funding source(s)
This research has been supported by the Center of Excellence in Geometric Computing and its Applications funded by the Israel Science Foundation. It was also funded by the Hermann Minkowski-Minerva Center for Geometry at Tel Aviv University; the Eshkol Fellowship funded by the Israeli Ministry of Science; Federal funds from the National Cancer Institute, National Institutes of Health, under contract number NO1-CO-12400.

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