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SIFt specifications

Information


Unique identifier OMICS_23867
Name SIFt
Alternative name Structural Interaction Fingerprint
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages MATLAB
Computer skills Advanced
Maintained No

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Publication for Structural Interaction Fingerprint

SIFt citations

 (8)
library_books

A novel interaction fingerprint derived from per atom score contributions: exhaustive evaluation of interaction fingerprint performance in docking based virtual screening

2018
J Cheminform
PMCID: 5856854
PMID: 29549526
DOI: 10.1186/s13321-018-0264-0

[…] ost processing of docking poses. For a detailed overview and description of methods, the interested reader may refer to literature such as [].One of the first and well-established fingerprints is the structural interaction fingerprint (SIFt) []. It is a binary fingerprint build up from a seven bit vector for each amino acid that encodes if an interaction with the ligand occurs, whether main chain […]

call_split

Ligand guided homology modelling of the GABAB2 subunit of the GABAB receptor

2017
PLoS One
PMCID: 5360267
PMID: 28323850
DOI: 10.1371/journal.pone.0173889
call_split See protocol

[…] Structural Interaction Fingerprints (SIFt) were used to map the allosteric binding site of GABAB2 subunit in the eight selected homology models [,]. The residues around each docked ligand and the type of interaction was determined based […]

library_books

Structural basis for PPAR partial or full activation revealed by a novel ligand binding mode

2016
Sci Rep
PMCID: 5052532
PMID: 27708429
DOI: 10.1038/srep34792

[…] screened compounds with high accuracy. To eliminate false-positive results, the best 20% of thriving compounds from SP docking were further incorporated for XP docking mode using advanced scoring.The SIFt method was used to identify amino acids that interact with the complexed ligand. SIFts were calculated by using the user interface (GUI) script implemented in Schrodinger’s Small Molecule Drug Di […]

library_books

Multiple conformational states in retrospective virtual screening – homology models vs. crystal structures: beta 2 adrenergic receptor case study

2015
J Cheminform
PMCID: 4420846
PMID: 25949744
DOI: 10.1186/s13321-015-0062-x

[…] ata Bank (PDB), making this receptor a strong base for in silico structural studies.Our previous study applying Machine Learning (ML) to post-docking analysis used Structural Interaction Fingerprint (SIFt) profiles created upon three different crystalline conformations of receptors [,]. It showed the applicability of this approach to ligand-protein complexes evaluation for Virtual Screening (VS). […]

library_books

CREDO: a structural interactomics database for drug discovery

2013
PMCID: 3715132
PMID: 23868908
DOI: 10.1093/database/bat049

[…] similarity but large difference in shape—this would indicate that not all ligand atoms are contributing to the interaction and that the remaining atoms are sticking into the bulk solvent. The UniProt SIFt clusters, as they are called in CREDO, can be visualized dynamically as circular phylogenetic trees through the web interface. The open-source JavaScript library jsPhyloSVG () is used to render t […]

library_books

Bimolecular Complementation to Visualize Filovirus VP40 Host Complexes in Live Mammalian Cells: Toward the Identification of Budding Inhibitors

2011
PMCID: 3217271
PMID: 22102845
DOI: 10.1155/2011/341816

[…] inhibitors. Compound 5539-0062 could potentially be optimized to improve binding affinity by either searching for chemically similar molecules in the commercially available databases, or by using the structural interaction fingerprint method which involves selecting compounds which are predicted to have the same protein-ligand interactions as 5539-0062 []. One advantage of L-domain inhibitors is t […]

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SIFt institution(s)
Department of Structural Informatics, Biogen, Inc., Cambridge, MA, USA

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