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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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No version available

Documentation


Maintainer


  • person_outline Dina Schneidman-Duhovny

Publications for PatchDock

PatchDock citations

 (174)
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

[…] 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 []. […]

library_books

Evolutionary Analysis Provides Insight Into the Origin and Adaptation of HCV

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

[…] 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 […]

library_books

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

[…] interaction further, we generated a model of the structure of this complex, based on homology models of the individual partners (see methods). among the top 20 interaction models generated by patchdock,, the first and third model positioned the c terminal (last 12 residues) helix at the interface. these models were further refined with the rosettadock local refinement algorithm […]

library_books

A Highly Sensitive Detection System based on Proximity dependent Hybridization with Computer aided Affinity Maturation of a scFv Antibody

2018
Sci Rep
PMCID: 5832849
PMID: 29497069
DOI: 10.1038/s41598-018-22111-4

[…] predicted using i-tasser. the server generated five models and the best one was selected based on the c-score. all the predicted models were viewed and analysed in pymol viewer., web based server ‘patchdock’ was used for the peptide-scfv docking studies. molecular models of scfv and pres1 peptide were used as input for the antigen-antibody docking algorithm. twenty models were generated […]

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

[…] was validated using procheck. subsequently, the probable motifs and active site of the protein were forecasted. also, the molecular interaction between the amps and slc2a4 was ascertained using patchdock. the result revealed that, all the amps are good slc2a4 inhibitors with rab1 having the highest binding affinity of 12,392 and binding energy of −39.13 kcal/mol. hence, this study reveals […]

library_books

Computational and Pharmacological Evaluation of Ferrocene Based Acyl Ureas and Homoleptic Cadmium Carboxylate Derivatives for Anti diabetic Potential

2018
Front Pharmacol
PMCID: 5776112
PMID: 29387011
DOI: 10.3389/fphar.2017.01001

[…] 1b (ptp-1b, pdb id: 2f70). by using same software, water molecules and ligands were removed and polar h-atoms were added, followed by saving in pdb format. molecular docking was performed by patchdock server, which is an online, geometry based automatic docking tool (duhovny et al., ). we selected root mean square deviation clustering value at 2.0 to discard the redundant solutions […]


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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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