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sc-PDB specifications

Information


Unique identifier OMICS_03834
Name sc-PDB
Restrictions to use None
Maintained Yes

Publications for sc-PDB

sc-PDB citations

 (7)
library_books

Docking based inverse virtual screening: methods, applications, and challenges

2018
Biophysics Rep
PMCID: 5860130
PMID: 29577065
DOI: 10.1007/s41048-017-0045-8

[…] present (16th March 2017), the number of protein entries in the PDB has reached up to 118,663, which provides an abundant resource for constructing a sub-database for IVS.For example, screening-PDB (sc-PDB) (Kellenberger et al. ) is a sub-database extracted from the PDB for the purpose of virtual screening. sc-PDB collects all the high-resolution crystal structures of protein–ligand complexes in […]

library_books

Mapping the 3D structures of small molecule binding sites

2016
J Cheminform
PMCID: 5395517
DOI: 10.1186/s13321-016-0180-0

[…] ward to BSC if the fpocket Score is ≥16.8, corresponding to the Score above which 95% of the ligand-bound cavities from the PDBBind-refined set are identified.Applying fpocket cavity detection to the sc-PDB dataset (2013) to assess the impact of incorporating objective and unbiased cavity detection to BSC compared with only defining binding sites that surround exemplified bound ligands. Using Site […]

library_books

Predicting Subtype Selectivity for Adenosine Receptor Ligands with Three Dimensional Biologically Relevant Spectrum (BRS 3D)

2016
Sci Rep
PMCID: 5095671
PMID: 27812030
DOI: 10.1038/srep36595

[…] amed after our previous two-dimensional approach. The procedure of using BRS-3D in QSAR study was illustrated in .First, a database was constructed with 300 ligands which were diversely selected from sc-PDB (version 2011, http://bioinfo-pharma.u-strasbg.fr/scPDB/). This database was named 3D bio-relevance representative compounds database (BRCD-3D). We used sc-PDB because it is a focused “drug-lik […]

library_books

Identification of gefitinib off targets using a structure based systems biology approach; their validation with reverse docking and retrospective data mining

2016
Sci Rep
PMCID: 5032012
PMID: 27653775
DOI: 10.1038/srep33949

[…] DB id 4WKQ; 1.85 Å) was selected as query protein. The binding pocket at the distance of 3 Å around gefitinib was cropped using GetCleft tool and subsequently used for MIF similarities search against Sc-PDB database. The parameters used for analysis were as follows: grid spacing 1.5 Å and geometric distance threshold 3.0 Å. Structures were ranked by Tanimoto score and designated as MIF rank. Top 1 […]

library_books

Simple Ligand–Receptor Interaction Descriptor (SILIRID) for alignment free binding site comparison

2014
Comput Struct Biotechnol J
PMCID: 4151984
PMID: 25210596
DOI: 10.1016/j.csbj.2014.05.004

[…] SILIRIDs are calculated from the IFP described by Marcou and Rognan and stored in the sc-PDB database (version 2011) . Every IFP consists of 8 bits per amino acid: hydrophobic, aromatic face to face, aromatic edge to face, hydrogen bond donated by the protein, hydrogen bond donated by […]

library_books

Identification of Nucleotide Binding Sites in Protein Structures: A Novel Approach Based on Nucleotide Modularity

2012
PLoS One
PMCID: 3507729
PMID: 23209685
DOI: 10.1371/journal.pone.0050240

[…] ins that do not bind nucleotides. In order to properly test the method we built a “negative” dataset of protein structures that do not bind nucleotides containing the same number of structures of the sc-PDB dataset. The structures were obtained from BLASTClust homology-based groups of protein chains (non-redundant at 30% of sequence identity), by randomly choosing 924 groups that do not include an […]

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sc-PDB institution(s)
Laboratoire d'innovation thérapeutique, Medalis Drug Discovery Center, UMR7200 CNRS-Université de Strasbourg, Illkirch, France

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