Graphlet signature-based scoring method to estimate protein–ligand binding affinity

Royal Society Open Science

Volumn 1, Issue 4, 2014, Pages

  Singh, Omkar ^a   Sawariya, Kunal ^a   Aparoy, Polamarasetty ^a  

^a CENTRAL UNIVERSITY OF HIMACHAL PRADESH   (India)

Author keywords

Binding affinity; Docking; Graphlet signature; Interaction network

Indexed keywords

EID: 84930191492     PISSN: None     EISSN: 20545703     Source Type: Journal    
DOI: 10.1098/rsos.140306     Document Type: Article

References (24)

1. Aparoy P, Reddy KK, Reddanna P. 2012 Structure and ligand based drug design strategies in the development of novel 5-LOX inhibitors. Curr. Med. Chem. 19, 3763-3778. (doi: 10. 2174/092986712801661112).
2. Cross JB, Thompson DC, Rai BK, Baber JC, Fan KY, Hu Y, Humblet C. 2009 Comparison of several molecular docking programs: pose prediction and virtual screening accuracy. J. Chem. Inf. Model. 49, 1455-1474. (doi: 10. 1021/ci900056c).
3. Uetz P, Finley Jr RL. 2005 From protein networks to biological systems. FEBS Lett. 579, 1821-1827. (doi: 10. 1016/j. febslet. 2005. 02. 001).
4. Bode C, Kovacs IA, Szalay MS, Palotai R, Korcsmaros T, Csermely P. 2007 Network analysis of protein dynamics. FEBS Lett. 581, 2776-2782. (doi: 10. 1016/j. febslet. 2007. 05. 021).
5. Hu Z, Bowen D, Southerland WM, del Sol A, Pan Y, Nussinov R, Ma B. 2007 Ligand binding and circular permutation modify residue interaction network in DHFR. PLoS Comput. Biol. 3, e117. (doi: 10. 1371/journal. pcbi. 0030117).
6. Milenkovic T, Przulj N. 2008 Uncovering biological network function via graphlet degree signatures. Cancer Inform. 6, 257-273.
7. Wang XD, Huang JL, Yang L, Wei DQ, Qi YX, Jiang ZL. 2014 Identification of human disease genes from interactome network using graphlet interaction. PLoS ONE 9, e86142. (doi: 10. 1371/journal. pone. 0086142).
8. Milenkovic T, Memisevic V, Ganesan AK, Przulj N. 2010 Systems-level cancer gene identification from protein interaction network topology applied to melanogenesis-related functional genomics data. J. R. Soc. Interface 7, 423-437. (doi: 10. 1098/rsif. 2009. 0192).
9. Hocevar T, Demsar J. 2014 A combinatorial approach to graphlet counting. Bioinformatics 30, 559-565. (doi: 10. 1093/bioinformatics/btt717).
10. Bernstein FC, Koetzle TF, Williams GJ, Meyer Jr EF, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M. 1978 The Protein Data Bank: a computer-based archival file for macromolecular structures. Arch. Biochem. Biophys. 185, 584-591. (doi: 10. 1016/0003-9861(78)90204-7).
11. Wang JL et al. 2010 The novel benzopyran class of selective cyclooxygenase-2 inhibitors. Part 2. The second clinical candidate having a shorter and favorable human half-life. Bioorg. Med. Chem. Lett. 20, 7159-7163. (doi: 10. 1016/ j. bmcl. 2010. 07. 054).
12. Lagorce D, Pencheva T, Villoutreix BO, Miteva MA. 2009 DG-AMMOS: a new tool to generate 3D conformation of small molecules using distance geometry and automated molecular mechanics optimization for in silico screening. BMC Chem. Biol. 9, 6. (doi: 10. 1186/1472-6769-9-6).
13. Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, Olson AJ. 1998 Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J. Comput. Chem. 19, 1639-1662. (doi: 10. 1002/(SICI)1096-987X (19981115)19: 14<1639:: AID-JCC10>3. 0. CO; 2-B).
14. Alterio V, De Simone G, Monti SM, Scozzafava A, Supuran CT. 2007 Carbonic anhydrase inhibitors: inhibition of human, bacterial, and archaeal isozymes with benzene-1, 3-disulfonamides-solution and crystallographic studies. Bioorg. Med. Chem. Lett. 17, 4201-4207. (doi: 10. 1016/j. bmcl. 2007. 05. 045).
15. Alberto JM, Martin MV, Filippo B, Tomás Di D, IanW, Silvio CET. 2011 RING: networking interacting residues, evolutionary information and energetics in protein structures. Bioinformatics 27, 2003-2005. (doi: 10. 1093/bioinformatics/btr191).
16. Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T. 2111 Cytoscape 2. 8: new features for data integration and network visualization. Bioinformatics 27, 431-432. (doi: 10. 1093/ bioinformatics/btq675).
17. Lindauer K, Bendic C, Suhnel J. 1996 HBexplore-a new tool for identifying and analysing hydrogen bonding patterns in biological macromolecules. Comput. Appl. Biosci. 12, 281-289.
18. Doncheva NT, Assenov Y, Domingues FS, Albrecht M. 2012 Topological analysis and interactive visualization of biological networks and protein structures. Nat. Protoc. 7, 670-685. (doi: 10. 1038/nprot. 2012. 004).
19. Whelan C, Sonmez K. 2012 Computing graphlet signatures of network nodes and motifs in Cytoscape with GraphletCounter. Bioinformatics 28, 290-291. (doi: 10. 1093/bioinformatics/ btr637).
20. Hubbard RE, Kamran Haider M. 2001 Hydrogen bonds in proteins: role and strength. NewYork, NY: JohnWiley & Sons, Ltd.
21. O'Boyle NM, Banck M, James CA, Morley C, Vandermeersch T, Hutchison GR. 2011 Open Babel: an open chemical toolbox. J. Cheminform. 3, 33. (doi: 10. 1186/1758-2946-3-33).
22. Lalanne J-B, François P. 2013 Principles of adaptive sorting revealed by in silico evolution. Phys. Rev. Lett. 110, 218102. (doi: 10. 1103/ PhysRevLett. 110. 218102).
23. Vacic V, Iakoucheva LM, Lonardi S, Radivojac P. 2010 Graphlet kernels for prediction of functional residues in protein structures. J. Comput. Biol. 17, 55-72. (doi: 10. 1089/cmb. 2009. 0029).
24. Bertolazzi P, Guerra C, Liuzzi G. 2014 Predicting protein-ligand and protein-peptide interfaces. Eur. Phys. J. Plus 129, 132. (doi: 10. 1140/epjp/i2014-14132-1).