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Protocols

SwissDock specifications

Information


Unique identifier OMICS_05432
Name SwissDock
Interface Web user interface
Restrictions to use Academic or non-commercial use
Input data A protein structure, one or several putative ligands and docking parameters
Input format PDB
Programming languages Perl, PHP, Python
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Olivier Michielin

Information


Unique identifier OMICS_05432
Name SwissDock
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input data A protein structure, one or several putative ligands and docking parameters
Input format PDB
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes

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No version available

Maintainer


  • person_outline Olivier Michielin

Publication for SwissDock

SwissDock citations

 (74)
library_books

Direct neurotransmitter activation of voltage gated potassium channels

2018
Nat Commun
PMCID: 5945843
PMID: 29748663
DOI: 10.1038/s41467-018-04266-w

[…] tated sequences are shown to illustrate the otherwise high sequence identity in these stretches. Unguided docking of GABA, retigabine, and ML-213, to predict native binding sites, was performed using SwissDock with CHARMM forcefields. Phylogenetic analysis was performed using BLAST searching of predicted or known protein sequences from multiple genomes (where available) from each clade; KCNQ5 sequ […]

library_books

Identification of a novel fused gene family implicates convergent evolution in eukaryotic calcium signaling

2018
BMC Genomics
PMCID: 5924475
PMID: 29703146
DOI: 10.1186/s12864-018-4685-y

[…] ted by MEME (meme-suite.org). The three-dimensional structure of the SCAMK protein was de novo modeled using the online I-TASSER server []. Protein-ligand docking was modeled relying on online server SwissDock []. […]

library_books

Dehydroepiandrosterone Antagonizes Pain Stress Induced Suppression of Testosterone Production in Male Rats

2018
Front Pharmacol
PMCID: 5911460
PMID: 29713278
DOI: 10.3389/fphar.2018.00322

[…] ever, the crystal structure of rat HSD11B1 was not available. The structures of cortisone and DHEA were obtained from PubChem as ligands. Molecular docking simulation calculations were performed with SwissDock, a docking algorithm based on the docking software EADock DSS (). The free energy was calculated. The docked file was visualized using a program Chimera 1.1.1 (San Francisco, CA, United Stat […]

library_books

A Computational Approach Using Bioinformatics to Screening Drug Targets for Leishmania infantum Species

2018
PMCID: 5896251
PMID: 29785196
DOI: 10.1155/2018/6813467

[…] iProt ID: A4I8D6), which presented a drug score and a simple score of 0.81 and 0.62, respectively, showed the best results (). To confirm these findings, a docking analysis was performed by using the SwissDock server, in which the FullFitness and Gibbs free energy (ΔG) parameters were evaluated. The results showed that strychnobiflavone showed affinity with a highest druggability score and a FullF […]

call_split

Inhibition of Protein Aggregation by Several Antioxidants

2018
PMCID: 5889867
PMID: 29765505
DOI: 10.1155/2018/8613209
call_split See protocol

[…] The molecular docking study was performed using the SwissDock server http://www.swissdock.ch/. SwissDock is based on the docking software EADock DSS, whose algorithm consists of many steps []. The target molecules were provided as PDB files (stB wt PDB […]

library_books

Expansions, diversification, and interindividual copy number variations of AID/APOBEC family cytidine deaminase genes in lampreys

2018
Proc Natl Acad Sci U S A
PMCID: 5889659
PMID: 29555777
DOI: 10.1073/pnas.1720871115

[…] atalytic residues. Protein charge and pI were predicted for each protein structure using the PARSE force field in PROPKA 3.0. DNA substrates were docked to each AID or CDA model using Swiss-Dock (www.swissdock.ch). Each substrate was constructed in Marvin Sketch v.5.11.5 (www.chemaxon.com/products/marvin/marvinsketch/), while surface topology and docking parameters were generated using Swiss-Param […]

Citations

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SwissDock institution(s)
Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland; Ludwig Institute for Cancer Research, Lausanne, Switzerland; Pluridisciplinary Center for Clinical Oncology (CePO), Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
SwissDock funding source(s)
Swiss Institute of Bioinformatics; Swiss National Science Foundation (SCORE 3232B0-103172, 3200B0-103173 and 310030-130857); Oncosuisse (OCS 01381-08-2003 and OCS 02555-02-2010). National Center of Competence in Research (NCCR) Molecular Oncology, a research instrument of the Swiss National Science Foundation; National Institutes of Health (P41 RR001081) for Molecular graphics images.

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