Surflex-Dock protocols

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Surflex-Dock specifications

Information


Unique identifier OMICS_03808
Name Surflex-Dock
Alternative name Surflex
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input data A ligand to the protomol.
Output data Some putative alignments of fragments.
Operating system Unix/Linux
License Commercial
Computer skills Advanced
Stability No
Maintained Yes

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https://www.certara.com/citations/surflex-dock-2-1-robust-performance-from-ligand-energetic-modeling-ring-flexibility-and-knowledge-based-search/

Publications for Surflex-Dock

Surflex-Dock in pipeline

2015
PMCID: 4393300
PMID: 25860348
DOI: 10.1371/journal.pone.0122223

[…] minimized by amber (version10.0) []. stereochemical properties of modeled protein structure were validated by procheck [], verify3d [] and errat []. molecular docking experiments were conducted by surflex-dock implemented in sybyl (version 7.3) [], fred (version 2.2.5) [] and gold (version 2.5) []. ucsf chimera [–] and moe [] were used for visualization purpose. the flowchart of work plan […]


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Surflex-Dock in publications

 (114)
PMCID: 5845645
PMID: 29559909
DOI: 10.3389/fphar.2018.00146

[…] scientific software, santa fe, nm, united states2)., compounds were submitted to three different molecular alignments: (i) alignment based on the morphological similarity function implemented in surflex-sim, accessible in sybyl-x 1.2 (sybyl-x 1.2, tripos international, st. louis, mo, united states); (ii) shape-based alignment from rocs 3.2.1.4 software (; rocs 3.2.1.4: openeye scientific […]

PMCID: 5825354
PMID: 29476294
DOI: 10.1186/s13065-018-0389-2

[…] the degradation and molecular modification of pcbs., crystal structures of nine types of bpha (pdb ids: 1ulj [], 1wql [], 2yfj [], 2yfl [], 2gbx [], 2xsh [], 2e4p [], 3gzx [], and 3gzy []) used in surflex-dock were obtained from the protein data bank (http://www.rcsb.org/pdb/). the catalytic activities these bpha were different. the active sites were determined by the amino acid residues […]

PMCID: 5796112
PMID: 29320397
DOI: 10.3390/ijms19010163

[…] plot and errat suggested that all models of mglurs could be applied for future studies. the homology modeling models and the ramachandran plots are shown in ., the molecular docking algorithm of surflex-dock was used to further refine the pharmacophore screening results. surflex-dock is a fully automatic flexible molecular docking algorithm that combines the scoring function […]

PMCID: 5715071
PMID: 29203791
DOI: 10.1038/s41598-017-17122-6

[…] structure of the activated irtk in complex with the grb14 bps domain (pdb id: 2auh, resolution 3.2 å) was used for in silico screening. a multi-step docking/scoring protocol employing ms-dock and surflex was used. two binding pockets could be identified at the surface of the ir and the compound collection was docked on these two different pockets. the chembridge database (the starting […]

PMCID: 5715060
PMID: 29203785
DOI: 10.1038/s41598-017-17050-5

[…] mode by sybyl 7.3 software. the molecular conformations of z11-16:ald and z9-16:ald were constructed by sketch mode and optimized using the tripos force field and gasteiger-hückel charge. the surflex-dock module of sybyl 7.3 was employed to perform the molecular docking modeling. the binding cavity was set as “automatic” and the total score was used to evaluate the binding affinity […]


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Surflex-Dock institution(s)
UCSF Cancer Research Institute, Department of Biopharmaceutical Sciences, and Department of Laboratory Medicine, University of California, San Francisco, CA, USA
Surflex-Dock funding source(s)
Supported by the NIH (grant GM070481).

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