Comparing Atom-Based with Residue-Based Descriptors in Predicting Binding Site Similarity: Do Backbone Atoms Matter?

References

• Jalencas X , MestresJ. On the origins of drug polypharmacology. Med. Chem. Commun.4 (1), 80–87 (2013).
   Google Scholar
• Weber A , CasiniA, HeineAet al. Unexpected nanomolar inhibition of carbonic anhydrase by COX-2-selective celecoxib: new pharmacological opportunities due to related binding site recognition. J. Med. Chem.47 (3), 550–557 (2004).
   PubMed Web of Science ®Google Scholar
• Kellenberger E , SchalonC, RognanD. How to measure the similarity between protein ligand-binding sites?Curr. Comput. Aided Drug Des.4 (3), 209–220 (2008).
   Web of Science ®Google Scholar
• Kinnings SL , LiuN, BuchmeierN, TongePJ, XieL, BournePE. Drug discovery using chemical systems biology: repositioning the safe medicine comtan to treat multi-drug and extensively drug resistant tuberculosis. PLoS Comput. Biol.5 (7), e1000423 (2009).
   PubMed Web of Science ®Google Scholar
• De Franchi E , SchalonC, MessaM, OnofriF, BenfenatiF, RognanD. Binding of protein kinase inhibitors to synapsin I inferred from pair-wise binding site similarity measurements. PLoS ONE5 (8), e12214 (2010).
   PubMed Web of Science ®Google Scholar
• Ehrt C , BrinkjostT, KochO. Impact of binding site comparisons on medicinal chemistry and rational molecular design. J. Med. Chem.59 (9), 4121–4151 (2016).
   PubMed Web of Science ®Google Scholar
• Schalon C , SurgandJ-S, KellenbergerE, RognanD. A simple and fuzzy method to align and compare druggable ligand-binding sites. Proteins Struct. Funct. Bioinforma.71 (4), 1755–1778 (2008).
   PubMed Web of Science ®Google Scholar
• Sturm N , DesaphyJ, QuinnRJ, RognanD, KellenbergerE. Structural insights into the molecular basis of the ligand promiscuity. J. Chem. Inf. Model.52 (9), 2410–2421 (2012).
   PubMed Web of Science ®Google Scholar
• Desaphy J , BretG, RognanD, KellenbergerE. sc-PDB: a 3D-database of ligandable binding sites – 10 years on. Nucleic Acids Res.43, D399–D404 (2015).
   PubMed Web of Science ®Google Scholar
• Hubbard S , ThorntonJM. NACCESS. Biochemistry and Molecular Biology. University College London, London, UK (1993).
   Google Scholar
• Lee B , RichardsFM. The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol.55 (3), 379–400 (1971).
   PubMed Web of Science ®Google Scholar
• RCSB Protein Data Bank . www.rcsb.org.
   Google Scholar
• Desaphy J , AzdimousaK, KellenbergerE, RognanD. Comparison and druggability prediction of protein–ligand binding sites from pharmacophore-annotated cavity shapes. J. Chem. Inf. Model.52 (8), 2287–2299 (2012).
   PubMed Web of Science ®Google Scholar
• Robin X , TurckN, HainardAet al. pROC: an open-source package for R and S+ to analyze and compare ROC curves. BMC Bioinformatics12, 77 (2011).
   PubMed Web of Science ®Google Scholar
• Laskowski RA , LuscombeNM, SwindellsMB, ThorntonJM. Protein clefts in molecular recognition and function. Protein Sci. Publ. Protein Soc.5 (12), 2438–2452 (1996).
   PubMed Web of Science ®Google Scholar
• Perola E , HermanL, WeissJ. Development of a rule-based method for the assessment of protein druggability. J. Chem. Inf. Model.52 (4), 1027–1038 (2012).
   PubMed Web of Science ®Google Scholar
• Khazanov NA , CarlsonHA. Exploring the composition of protein–ligand binding sites on a large scale. PLOS Comput. Biol.9 (11), e1003321 (2013).
   PubMed Web of Science ®Google Scholar
• Rossi A , Marti-RenomMA, SaliA. Localization of binding sites in protein structures by optimization of a composite scoring function. Protein Sci. Publ. Protein Soc.15 (10), 2366–2380 (2006).
   PubMed Web of Science ®Google Scholar
• Nayal M , HonigB. On the nature of cavities on protein surfaces: application to the identification of drug-binding sites. Proteins63 (4), 892–906 (2006).
   PubMed Web of Science ®Google Scholar
• Biswal HS . Hydrogen bonds involving sulfur: new insights from ab initio calculations and gas phase laser spectroscopy [Internet]. In : Noncovalent Forces. ScheinerS ( Ed.). Springer International Publishing, Cham, Switzerland, 15–45 (2015).
   Google Scholar
• Weill N , RognanD. Alignment-free ultra-high-throughput comparison of druggable protein–ligand binding sites. J. Chem. Inf. Model.50 (1), 123–135 (2010).
   PubMed Web of Science ®Google Scholar
• Haupt VJ , DaminelliS, SchroederM. Drug promiscuity in PDB: protein binding site similarity is key. PLoS ONE8 (6), e65894 (2013).
   PubMed Web of Science ®Google Scholar
• Barelier S , SterlingT, O'MearaMJ, ShoichetBK. The recognition of identical ligands by unrelated proteins. ACS Chem. Biol.10 (12), 2772–2784 (2015).
   PubMed Web of Science ®Google Scholar
• Shindyalov IN , BournePE. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng.11 (9), 739–747 (1998).
   PubMedGoogle Scholar
• Gao M , SkolnickJ. APoc: large-scale identification of similar protein pockets. Bioinformatics29, 597–604 (2013).
   PubMed Web of Science ®Google Scholar
• Fober T , GlincaG, KlebeG, HullermeierE. Superposition and alignment of labeled point clouds. IEEE/ACM Trans. Comput. Biol. Bioinform.8 (6), 1653–1666 (2011).
   PubMed Web of Science ®Google Scholar
• Krotzky T , RickmeyerT, FoberT, KlebeG. Extraction of protein binding pockets in close neighborhood of bound ligands makes comparisons simple due to inherent shape similarity. J. Chem. Inf. Model.54 (11), 3229–3237 (2014).
   PubMed Web of Science ®Google Scholar
• Mills CL , BeuningPJ, OndrechenMJ. Biochemical functional predictions for protein structures of unknown or uncertain function. Comput. Struct. Biotechnol. J.13, 182–191 (2015).
   PubMed Web of Science ®Google Scholar
• Cammer SA , HoffmanBT, SpeirJAet al. Structure-based active site profiles for genome analysis and functional family subclassification. J. Mol. Biol.334 (3), 387–401 (2003).
   PubMed Web of Science ®Google Scholar
• Wang Z , YinP, LeeJS, ParasuramR, SomarowthuS, OndrechenMJ. Protein function annotation with Structurally Aligned Local Sites of Activity (SALSAs). BMC Bioinformatics14 (3), 1–9 (2013).
   PubMedGoogle Scholar
• Leuthaeuser JB , KnutsonST, KumarK, BabbittPC, FetrowJS. Comparison of topological clustering within protein networks using edge metrics that evaluate full sequence, full structure, and active site microenvironment similarity. Protein Sci. Publ. Protein Soc.24 (9), 1423–1439 (2015).
   PubMed Web of Science ®Google Scholar
• Sturm N , QuinnRJ, KellenbergerE. Similarity between flavonoid biosynthetic enzymes and flavonoid protein targets captured by three-dimensional computing approach. Planta Med.81 (6), 467–473 (2015).
   PubMed Web of Science ®Google Scholar
• Ma B , NussinovR. Druggable orthosteric and allosteric hot spots to target protein–protein interactions. Curr. Pharm. Des.20 (8), 1293–1301 (2014).
   PubMed Web of Science ®Google Scholar
• Hall DR , KozakovD, WhittyA, VajdaS. Lessons from hot spot analysis for fragment-based drug discovery. Trends Pharmacol. Sci.36 (11), 724–736 (2015).
   PubMed Web of Science ®Google Scholar
• Kalliokoski T , OlssonTSG, VulpettiA. Subpocket analysis method for fragment-based drug discovery. J. Chem. Inf. Model.53 (1), 131–141 (2013).
   PubMed Web of Science ®Google Scholar
• Jalencas X , MestresJ. Chemoisosterism in the proteome. J. Chem. Inf. Model.53 (2), 279–292 (2013).
   PubMed Web of Science ®Google Scholar
• Jadhav PK , AlaP, WoernerFJet al. Cyclic urea amides: HIV-1 protease inhibitors with low nanomolar potency against both wild type and protease inhibitor resistant mutants of HIV. J. Med. Chem.40 (2), 181–191 (1997).
   PubMed Web of Science ®Google Scholar