An Algorithm for Describing the Convex and Concave Shape of Protein Surface

1. Pandey, A., Mann, M.: Proteomics to study genes and genomes. Nature. 405(6788), 837–846 (2000)

   Article  Google Scholar 

2. Fleming, K., Kelley, L.A., Islam, S.A., MacCallum, R.M., et al.: The proteome: structure, function and evolution. Philos. Trans. R. Soc. London. 361(1467), 441–451 (2006)

   Article  Google Scholar 

3. Thul, P.J., Åkesson, L., Wiking, M., et al.: A subcellular map of the human proteome. Science. 356(6340) (2017)

   Google Scholar 

4. Burley, S.K., Berman, H.M., Kleywegt, G.J., et al.: Protein Data Bank (PDB): the single global macromolecular structure archive. Methods Mol. Biol. 1607, 627 (2017)

   Article  Google Scholar 

5. Biasini, M., Bienert, S., Waterhouse, A.: SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Res. 42, W252 (2014)

   Article  Google Scholar 

6. Jorgensen, W.L.: Rusting of the lock and key model for protein-ligand binding. Science 254(5034), 954 (1991)

   Article  Google Scholar 

7. Morrison, J.L., Breitling, R., Higham, D.J., et al.: A lock-and-key model for protein-protein interactions. Bioinformatics 22(16), 2012 (2006)

   Article  Google Scholar 

8. Mullard, A.: Protein-protein interaction inhibitors get into the groove. Nat. Rev. Drug Discov. 11(3), 173–5 (2012)

   Article  Google Scholar 

9. Chen, L., Frankel, A.D.: A peptide interaction in the major groove of RNA resembles protein interactions in the minor groove of DNA. Proc. Nat. Acad. Sci. USA 92(11), 5077 (1995)

   Article  Google Scholar 

10. Spola Jr., R.S.: Coupling of local folding to site-specific binding of proteins to DNA. Science 263(5148), 777–84 (1994)

    Article  Google Scholar 

11. Wang, W., Liu, J., Sun, L.: Surface shapes and surrounding environment analysis of single- and double-stranded DNA-binding proteins in protein-DNA interface. Proteins 84(7), 979–989 (2016)

    Article  Google Scholar 

12. Wang, W., Liu, J., Zhou, X.: Identification of single-stranded and double-stranded DNA binding proteins based on protein structure. BMC Bioinf. 15(S12), S4 (2014)

    Article  Google Scholar 

13. Wang, W., Sun, L., Zhang, S., et al.: Analysis and prediction of single-stranded and double-stranded DNA binding proteins based on protein sequences. BMC Bioinf. 18(1), 300 (2017)

    Article  Google Scholar 

14. Coleman, R.G., Burr, M.A., Souvaine, D.L., et al.: An intuitive approach to measuring protein surface curvature. Proteins 61(4), 1068–1074 (2005)

    Article  Google Scholar 

15. Shazman, S., Elber, G., Mandel-Gutfreund, Y.: From face to interface recognition: a differential geometric approach to distinguish DNA from RNA binding surfaces. Nucleic Acids Res. 39(17), 7390–9 (2011)

    Article  Google Scholar 

16. Iwakiri, J., Tateishi, H., Chakraborty, A., et al.: Dissecting the protein-RNA interface: the role of protein surface shapes and RNA secondary structures in protein-RNA recognition. Nucleic Acids Res. 40(8), 3299 (2012)

    Article  Google Scholar 

17. Albou, L.P., Schwarz, B., Poch, O., et al.: Defining and characterizing protein surface using alpha shapes. Proteins 76(1), 1–12 (2009)

    Article  Google Scholar 

18. Kraynov, V., Knudsen, N., Hays Putnam, A.M.A., et al.: Modified interferon beta polypeptides and their uses. US. 8329869 B2[P] (2012)

    Google Scholar 

19. Xia, J.F., Zhao, X.M., Song, J., et al.: APIS: accurate prediction of hot spots in protein interfaces by combining protrusion index with solvent accessibility. BMC Bioinf. 11(1), 174 (2010)

    Article  Google Scholar 

20. Sikić, M., Tomić, S., Vlahovicek, K.: Prediction of protein-protein interaction sites in sequences and 3D structures by random forests. PLoS Comput. Biol. 5(1), e1000278 (2009)

    Article  Google Scholar 

21. Wang, W., Liu, J., Sun, L.: Surface shapes and surrounding environment analysis of single-and double-stranded DNA-binding proteins in protein-DNA interface. Proteins 84(7), 979–989 (2016)

    Article  Google Scholar 

22. Pintar, A., Carugo, O., Pongor, S.: CX, an algorithm that identifies protruding atoms in proteins. Bioinformatics 18(7), 980–984 (2002)

    Article  Google Scholar 

23. Duan, J., Dixon, S.L., Lowrie, J.F., et al.: Analysis and comparison of 2D fingerprints: Insights into database screening performance using eight fingerprint methods. J. Mol. Graph. Model. 29(2), 157–170 (2010)

    Article  Google Scholar 

24. Harinder, S., Singh, C.J., Michael, G.M., et al.: ccPDB: compilation and creation of data sets from Protein Data Bank. Nucleic Acids Res. 40, 486–9 (2012)

    Article  Google Scholar 

25. Carter, P., Andersen, C.A., Rost, B.: DSSPcont: continuous secondary structure assignments for proteins. Nucleic Acids Res. 31(13), 3293–3295 (2003)

    Article  Google Scholar 

26. Touw, W.G., Baakman, C., Black, J., et al.: A series of PDB-related databanks for everyday needs. Nucleic Acids Res. 43, 364–8 (2015)

    Article  Google Scholar 

27. Kim, H., Park, H.: Prediction of protein relative solvent accessibility with support vector machines and long-range interaction 3D local descriptor. Proteins 54(3), 557 (2004)

    Article  Google Scholar 

28. Janin, J., Bahadur, R.P.: Relating macromolecular function and association: the structural basis of protein-DNA and RNA recognition. Cell. Mol. Bioeng. 1(4), 327–338 (2008)

    Article  Google Scholar 

29. Yang, J., Wang, Y., Zhang, Y.: ResQ: an approach to unified estimation of B-factor and residue-specific error in protein structure prediction. J. Mol. Biol. 428(4), 693–701 (2016)

    Article  Google Scholar 

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