參考文獻 |
Reference
1. Berk A, and S. Lawrence Zipursky: Molecular cell biology. New York: WH Freeman; 2000.
2. Jones S, Thornton JM: Principles of protein-protein interactions. Proceedings of the National Academy of Sciences of the United States of America 1996, 93(1):13-20.
3. McCoy AJ, Chandana Epa V, Colman PM: Electrostatic complementarity at protein/protein interfaces. Journal of molecular biology 1997, 268(2):570-584.
4. Janin J: Elusive affinities. Proteins 1995, 21(1):30-39.
5. Larsen TA, Olson AJ, Goodsell DS: Morphology of protein-protein interfaces. Struct Fold Des 1998, 6(4):421-427.
6. Nadassy K, Wodak SJ, Janin J: Structural features of protein-nucleic acid recognition sites. Biochemistry 1999, 38(7):1999-2017.
7. Clackson T, Wells JA: A hot spot of binding energy in a hormone-receptor interface. Science 1995, 267(5196):383-386.
8. Bogan AA, Thorn KS: Anatomy of hot spots in protein interfaces. Journal of molecular biology 1998, 280(1):1-9.
9. Thorn KS, Bogan AA: ASEdb: a database of alanine mutations and their effects on the free energy of binding in protein interactions. Bioinformatics 2001, 17(3):284-285.
10. DeLano WL: Unraveling hot spots in binding interfaces: progress and challenges. Current opinion in structural biology 2002, 12(1):14-20.
11. Wells JA, McClendon CL: Reaching for high-hanging fruit in drug discovery at protein-protein interfaces. Nature 2007, 450(7172):1001-1009.
12. Stoilova-McPhie S, Ali S, Laezza F: Protein-Protein Interactions as New Targets for Ion Channel Drug Discovery. Austin journal of pharmacology and therapeutics 2013, 1(2).
13. Kessel A, and Nir Ben-Tal: Introduction to proteins: structure, function, and motion. CRC Press; 2010.
14. IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN). Nomenclature and symbolism for amino acids and peptides. Recommendations 1983. European journal of biochemistry / FEBS 1984, 138(1):9-37.
15. Massova I, Kollman PA: Computational alanine scanning to probe protein-protein interactions: A novel approach to evaluate binding free energies. J Am Chem Soc 1999, 121(36):8133-8143.
16. Huo S, Massova I, Kollman PA: Computational alanine scanning of the 1:1 human growth hormone-receptor complex. Journal of computational chemistry 2002, 23(1):15-27.
17. Grosdidier S, Fernandez-Recio J: Identification of hot-spot residues in protein-protein interactions by computational docking. BMC bioinformatics 2008, 9:447.
18. Brenke R, Kozakov D, Chuang GY, Beglov D, Hall D, Landon MR, Mattos C, Vajda S: Fragment-based identification of druggable ′hot spots′ of proteins using Fourier domain correlation techniques. Bioinformatics 2009, 25(5):621-627.
19. Guerois R, Nielsen JE, Serrano L: Predicting changes in the stability of proteins and protein complexes: A study of more than 1000 mutations. Journal of molecular biology 2002, 320(2):369-387.
20. Kortemme T, Baker D: A simple physical model for binding energy hot spots in protein-protein complexes. Proceedings of the National Academy of Sciences of the United States of America 2002, 99(22):14116-14121.
21. Darnell SJ, LeGault L, Mitchell JC: KFC Server: interactive forecasting of protein interaction hot spots. Nucleic acids research 2008, 36(Web Server issue):W265-269.
22. Cho KI, Kim D, Lee D: A feature-based approach to modeling protein-protein interaction hot spots. Nucleic acids research 2009, 37(8):2672-2687.
23. Tuncbag N, Keskin O, Gursoy A: HotPoint: hot spot prediction server for protein interfaces. Nucleic acids research 2010, 38(Web Server issue):W402-406.
24. Xia JF, Zhao XM, Song J, Huang DS: APIS: accurate prediction of hot spots in protein interfaces by combining protrusion index with solvent accessibility. BMC bioinformatics 2010, 11:174.
25. Zhu X, Mitchell JC: KFC2: a knowledge-based hot spot prediction method based on interface solvation, atomic density, and plasticity features. Proteins 2011, 79(9):2671-2683.
26. Deng L, Guan JH, Wei XM, Yi Y, Zhang QC, Zhou SG: Boosting Prediction Performance of Protein-Protein Interaction Hot Spots by Using Structural Neighborhood Properties. J Comput Biol 2013, 20(11):878-891.
27. Mitchell JC, Kerr R, Ten Eyck LF: Rapid atomic density methods for molecular shape characterization. Journal of molecular graphics & modelling 2001, 19(3-4):325-330, 388-390.
28. Chien YT, Huang SW: Accurate prediction of protein catalytic residues by side chain orientation and residue contact density. PloS one 2012, 7(10):e47951.
29. Chen YJ, Lu CT, Su MG, Huang KY, Ching WC, Yang HH, Liao YC, Chen YJ, Lee TY: dbSNO 2.0: a resource for exploring structural environment, functional and disease association and regulatory network of protein S-nitrosylation. Nucleic acids research 2015, 43(Database issue):D503-511.
30. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The Protein Data Bank. Nucleic acids research 2000, 28(1):235-242.
31. Fischer TB, Arunachalam KV, Bailey D, Mangual V, Bakhru S, Russo R, Huang D, Paczkowski M, Lalchandani V, Ramachandra C et al: The binding interface database (BID): a compilation of amino acid hot spots in protein interfaces. Bioinformatics 2003, 19(11):1453-1454.
32. Tuncbag N, Gursoy A, Keskin O: Identification of computational hot spots in protein interfaces: combining solvent accessibility and inter-residue potentials improves the accuracy. Bioinformatics 2009, 25(12):1513-1520.
33. Yu CS, Chen YC, Lu CH, Hwang JK: Prediction of protein subcellular localization. Proteins 2006, 64(3):643-651.
34. Bailey TL, Johnson J, Grant CE, Noble WS: The MEME Suite. Nucleic acids research 2015, 43(W1):W39-49.
35. Chang CC, Lin CJ: LIBSVM: A Library for Support Vector Machines. Acm T Intel Syst Tec 2011, 2(3).
36. Durek P, Schudoma C, Weckwerth W, Selbig J, Walther D: Detection and characterization of 3D-signature phosphorylation site motifs and their contribution towards improved phosphorylation site prediction in proteins. BMC bioinformatics 2009, 10.
|