A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation

By Michal Brylinski, Jeffrey Skolnick. 2008

329 citations recorded by the source corpus.

Subfields: Computational Theory and Mathematics, Materials Chemistry, Molecular Biology

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Citations in the corpus

I-TASSER server: new development for protein structure and function predictions (2015, methodology): “Starting from the computational structure modeling, a number of methods have been proposed to anno-tate the biological function of protein molecules, with examples including COFACTROR (8,9), COACH (10), Con-Cavity (11), FINDSITE (12), Firestar (13) and 3DLigand-Site (14), among many others.”
Protein-ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment (2013, methodology): “The second structure-based approach is to infer ligand-binding information from the known template proteins, which have similar global and/or local structure to the query (Brylinski and Skolnick, 2008; Roche et al., 2011; Roy et al., 2012; Roy and Zhang, 2012; Wass et al., 2010).”
Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure (2009, background): “, Theoretical Microscopic Titration Curves (THEMATICS) [35], binding site similarity [36], phage display libraries [37], and residue interaction graphs [38]).”
3DLigandSite: predicting ligand-binding sites using similar structures (2010, background): “3DLigandSite performance has been assessed on two sets of proteins; the CASP8 targets, and a set of 617 proteins from the FINDSITE test set (11).”
Computer-Aided Drug Design Methods (2017, background): “Other programs for binding site identification include FINDSITE (47) and ConCavity (48).”
Recognizing protein-ligand binding sites by global structural alignment and local geometry refinement (2012, unknown): “The results are controlled by two recently developed structure-based methods, FINDSITE (Brylinski and Skolnick, 2008) and Con- Cavity (Capra et al., 2009).”
Protein Structure Prediction: Is It Useful? (2009, unknown): “The authors found that 62–87% of binding residues could be correctly recovered using deformed receptor structures with a RMSD of 1–3 Å by Q-DOCK, a knowledge-based reduced docking approach guided by binding restraints from threading algorithms [12].”
Protein interface conservation across structure space (2010, background): “Remote similarities such as these have been exploited in a wide range of applications including the prediction of protein-ligand interactions (24), protein-protein interactions (10), and function annotation (11, 25).”
The FTMap family of web servers for determining and characterizing ligand binding hot spots of proteins (2015, methodology): “These methods include 3DLigandSite 61 and FINDSITE 62 .”
DoGSiteScorer: a web server for automatic binding site prediction, analysis and druggability assessment (2012, methodology): “Some servers exist that allow— besides binding site prediction—for their analysis and functional classification, e.g. FINDSITE (Brylinski and Skolnick, 2008), SplitPocket (Tseng et al., 2009), fPOP (Tseng et al., 2010), ProBis (Konc and Janezic, 2010) and SiteComp (Lin et al., 2012).”
I-TASSER: a unified platform for automated protein structure and function prediction (2010, background): “, which in many cases can be directly used to infer functio”
Assessment of ligand binding site predictions in CASP10 (2014, methodology): “Firestar10 bases its predictions on homology transfer of functionally important residues, found by local evolutionary sequence conservation; SP-ALIGN, an update to FINDSITE,11 is a threading based method to detect ligand binding sites by the employment of remote template identification and super-imp”