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SwarmDock specifications


Unique identifier OMICS_03780
Name SwarmDock
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for SwarmDock

SwarmDock citations


Immune Informatic Analysis and Design of Peptide Vaccine From Multi epitopes Against Corynebacterium pseudotuberculosis

Bioinform Biol Insights
PMCID: 5954444
PMID: 29780242
DOI: 10.1177/1177932218755337
call_split See protocol

[…] To verify the anchoring between the protein and the toll-like receptor type 2 (TLR2) the SwarmDock software (http://bmm.crick.ac.uk/~SwarmDock/index.html) was used. This software uses a flexible protein-protein complex model. The server is divided into the following stages:Entrance struct […]


Plasmodium UIS3 sequesters host LC3 to avoid elimination by autophagy in hepatocytes

Nat Microbiol
PMCID: 5739284
PMID: 29109477
DOI: 10.1038/s41564-017-0054-x

[…] ented in ModRefiner software. Experimental and homology-derived protein coordinates were then used to construct models of the human and mouse UIS3-LC3 complexes by flexible molecular docking with the Swarmdock algorithm. LC3 proteins were considered as receptors and UIS3 as ligands. For each complex, an initial set of 100 ligand starting positions was generated in the space around the receptor, be […]


Anaplasma phagocytophilum MSP4 and HSP70 Proteins Are Involved in Interactions with Host Cells during Pathogen Infection

PMCID: 5496961
PMID: 28725639
DOI: 10.3389/fcimb.2017.00307

[…] y the OPM database (Lomize et al., ) and generated using the Desmond systems builder (Bowers et al., ) as part of the Schrodinger's Maestro package. The protein-protein docking was assessed using the SwarmDock server (Torchala et al., ) that incorporates flexible docking by exploring in proximity to the Cartesian center of mass of the target protein. Minimization steps are included for the whole s […]


Functions of tryptophan residues in EWGWS insert of Plasmodium falciparum enolase

FEBS Open Bio
PMCID: 5494301
PMID: 28680804
DOI: 10.1002/2211-5463.12242

[…] ve.For exploring the effect of mutations on oligomeric structure of Pfeno, rigid body docking between two monomers of Pfeno (modeled using TgEno1 structure as template; pdb: 3OTR) was performed using SwarmDock algorithm . In brief, SwarmDock uses a combination of local docking and particle swarm optimization to find in the docked complex low energy positions and orientations . Visualization of the […]


Cysteine residues 244 and 458–459 within the catalytic subunit of Na,K ATPase control the enzyme's hydrolytic and signaling function under hypoxic conditions

Redox Biol
PMCID: 5470536
PMID: 28601781
DOI: 10.1016/j.redox.2017.05.021

[…] Src kinase (PDB id 2src). Docking was performed using Na,K-ATPase NBD (377–588 residues) and kinase domain of Src kinase (residues 267–520). Global docking of these domains has been carried out with SwarmDock, GRAMM_X, ZDock and ClusPro servers. Thereafter the full-size protein structures were reconstructed. Qasdom server (http://qasdom.eimb.ru/qasdom.html) was used to identify interactions betwe […]


Applications of contact predictions to structural biology

PMCID: 5414403
PMID: 28512576
DOI: 10.1107/S2052252517005115

[…] ranking intermolecular contacts are present in poses from some top-performing servers such as ClusPro (Comeau et al., 2004) or servers specialized for the flexible docking of protein partners such as SwarmDock (Torchala et al., 2013). Finally, it is worth reiterating here the additional difficulties of contact prediction between two different proteins: a concatenated alignment in which orthologues […]


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SwarmDock institution(s)
Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, London, UK

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