PatchDock protocols

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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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Documentation


Maintainer


  • person_outline Dina Schneidman-Duhovny <>

Publications for PatchDock

PatchDock in pipelines

 (4)
2014
PMCID: 4030036
PMID: 24885928
DOI: 10.1186/1476-4598-13-103

[…] with ucsf chimera []. homology models of dclk1 isoform 2 (dclk-long-α) and 4 (dclk-long-β) were generated using sparksx fold recognition software []. docking analyses were carried out with patchdock [] and results were visualized with ucsf chimera and ligplot +  []. model predictions were checked for reasonable precision by repeating the modeling procedures using swissmodel []., […]

2013
PMCID: 3669323
PMID: 23741320
DOI: 10.1371/journal.pone.0064364

[…] positions forms the most accessible cavity regions for ligand interaction. to examine the change in binding affinity in native and mutant protein, we further conducted complimentarity analysis using patchdock tool. in patchdock results the total docking score of mutant with ligand were found to be lower as compared to native structure ()., molecular docking analysis was conducted using autodock […]

2012
PMCID: 3524943
PMID: 23275691
DOI: 10.6026/97320630008980

[…] of the 267 compounds from 7 different plants are shown in the (see supplementary material). the top 10 compounds were further docked against aldose reductase using 5 others docking programs gold, patchdock, ehits, medock and autodock vina. the docking scores of the 10 best compounds attained using different software are listed in (see supplementary material). each docking program is listing […]

2012
PMCID: 3524943
PMID: 23275691
DOI: 10.6026/97320630008980

[…] scoring is a widely used approach to improve the scoring reliability and hit rate in virtual screening and four standalone programs (gold, molegro, autodock and e-hits) and two online servers (patchdock and medock) are utilized to rank top hits. allium38 ranked high and reported to be the best compound that can bind with high affinity to aldose reductase enzyme. allium38 resulted in best […]


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PatchDock in publications

 (174)
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 []. […]

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 […]

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 […]

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 […]

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 […]


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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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