Browse > Article

구조생물정보학의 신약개발 적용  

Lee, Sael (Purdue University)
Keywords
Citations & Related Records
연도 인용수 순위
  • Reference
1 Fry, H.C. et al., "Computational design and elaboration of a de novo heterotetrameric alpha-helical protein that selectively binds an emissive abiological , (porphinato) zinc chromophore," Journal of the American Chemical Society 132, pp. 3997-4005, 2010.   DOI   ScienceOn
2 Suarez, M. & Jaramillo, A., "Challenges in the computational design of proteins," Journal of the Royal Society Suppl 4, pp. S477-91, 2009.
3 Samish, I. et al., "Theoretical and Computational Protein Design," Annual Review of Physical Chemistry pp. 129-149, 2010.
4 Bolon, D.N. & Mayo, S.L., "Enzyme-like proteins by computational design," Proceedings of the National Academy of Sciences 98, 14274, 2001.   DOI   ScienceOn
5 Chevalier, B.S. et al., "Design, activity, and structure of a highly specific artificial endonuclease," Molecular Cell 10, pp. 895-905, 2002.   DOI   ScienceOn
6 Strop, P. & Mayo, S.L., "Contribution of surface salt bridges to protein stability," Biochemistry 39, pp. 1251-1255, 2000.   DOI   ScienceOn
7 Berezovsky, I.N., Zeldovich, K.B. & Shakhnovich, E.I., "Positive and negative design in stability and thermal adaptation of natural proteins," PLoS Computational Biology 3, e52, 2007.   DOI
8 Villar, H.O. & Hansen, M.R., "Computational techniques in fragment based drug discovery," Current Topics in Medicinal Chemistry 7, pp. 1509-1513, 2007.   DOI   ScienceOn
9 Highsmith, J., "Biologic Therapeutic Drugs: Technologies and Global Markets (BIO079A)," 2011 at
10 Lippow, S.M. & Tidor, B., "Progress in computational protein design," Current Opinion in Biotechnology 18, pp. 305-11, 2007.   DOI   ScienceOn
11 Bellows, M.L. & Floundas, C.A., "Computational methods for de novo protein design and its applications to the human immunodeficiency virus 1, purine nucleoside phosphorylase, ubiquitin specific protease 7, and histone demethylases," Current Drug Target 11, pp. 264-278, 2010.   DOI   ScienceOn
12 Rosenberg, M. & Goldblum, A., "Computational protein design: A novel path to future protein drugs," Current Pharmaceutical Design 12, pp. 3973-97, 2006.   DOI   ScienceOn
13 Ventura, S. et al., "Conformational strain in the hydrophobic core and its implications for protein folding and design," Nature Structural Biology 9, pp. 485-93, 2002.   DOI   ScienceOn
14 Huang, B. & Schroeder, M., "LIGSITEcsc: Predicting ligand binding sites using the Connolly surface and degree of conservation," BMC Structural Biology 6, p.19, 2006.   DOI
15 Xie, L., Xie, L. & Bourne, P.E., "A unified statistical model to support local sequence order independent similarity searching for ligand-binding sites and its application to genome-based drug discovery," Bioinformatics 25, pp.i305-312, 2009.   DOI
16 Alonso, H., Bliznyuk, A. a & Gready, J.E., "Combining docking and molecular dynamic simulations in drug design," Medicinal Research Reviews 26, pp.531-68, 2006.   DOI   ScienceOn
17 Chen, Y. & Shoichet, B.K., "Molecular docking and ligand specificity in fragment-based inhibitor discovery," Nature Chemical Biology 5, pp. 358-64, 2009.   DOI   ScienceOn
18 Sael, L. & Kihara, D., "Binding ligand prediction for proteins using partial matching of local surface patches," International Journal of Molecular Sciences 11, pp. 5009-5026, 2010.   DOI
19 Chikhi, R., Sael, L. & Kihara, D., "Real-time ligand binding pocket database search using local surface descriptors," Proteins 78, pp. 2007-2028, 2010.   DOI   ScienceOn
20 Desjarlais, R.L., "Using computational techniques in fragment-based drug discovery," Methods in Enzymology 493, pp. 137-55, 2011.
21 Blundell, T.L. et al., "Structural biology and bioinformatics in drug design: Opportunities and challenges for target identification and lead discovery," Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 361, pp.413-23, 2006.   DOI   ScienceOn
22 Rohl, C. et al., "Modeling structurally variable regions in homologous proteins with Rosetta," Proteins 55, pp.656-77, 2004.   DOI   ScienceOn
23 Chen, H. & Kihara, D., "Effect of using suboptimal alignments in template-based protein structure prediction," Proteins 79, pp. 315-34, 2011.   DOI   ScienceOn
24 Zhou, H. & Skolnick, J., "Improving threading algorithms for remote homology modeling by combining fragment and template comparisons," Proteins 78, pp. 2041-8, 2010.
25 Peng, J. & Xu, J., "Low-homology protein threading," Bioinformatics 26, pp.i294-300, 2010.   DOI
26 Kolinski, A., "Protein modeling and structure prediction with a reduced representation," Acta Biochimica Polonica 51, pp. 349-71, 2004.
27 Li, B. et al., "Characterization of local geometry of protein surfaces with the visibility criterion," Proteins 71, pp. 670-683, 2008.   DOI   ScienceOn
28 Kalidas, Y. & Chandra, N., "PocketDepth: A new depth based algorithm for identification of ligand binding sites in proteins," Journal of Structural Biology 161, pp. 31-42, 2008.   DOI   ScienceOn
29 Ratti, E. & Trist, D., "The continuing evolution of the drug discovery process in the pharmaceutical industry," Farmaco 56, pp.13-9, 2001.   DOI   ScienceOn
30 Chen, Y., Li, Z. & Ung, C., "Computational method for drug target search and application in drug discovery," Molecular Engineering of Biological and Chemical Systems (MEBCS) pp.1-8, 2003.
31 Bolon, D.N. et al., "Specificity versus stability in computational protein design," Proceedings of the National Academy of Sciences 102, pp. 12724-9, 2005.   DOI   ScienceOn
32 Rothlisberger, D. et al., "Kemp elimination catalysts by computational enzyme design," Nature 453, pp. 190-5, 2008.   DOI   ScienceOn
33 Khersonsky, O. et al., "Evolutionary optimization of computationally designed enzymes: Kemp eliminases of the KE07 series," Journal of Molecular Biology 396, 1025-42, 2010.   DOI   ScienceOn
34 Sircar, A. & Gray, J.J., "SnugDock: Paratope structural optimization during antibody-antigen docking compensates for errors in antibody homology models," PLoS Computational Biology 6, e1000644, 2010.   DOI
35 Reichert, J. & Pavlou, A., "From the analystʼs couch: Monoclonal antibodies market," Nature Reviews Drug Discovery 3, pp. 383-384, 2004.   DOI   ScienceOn
36 Schwede, T. et al., "Outcome of a workshop on applications of protein models in biomedical research," Structure 17, pp. 151-9, 2009.   DOI   ScienceOn
37 Kuhlman, B. et al., "Design of a novel globular protein fold with atomic-level accuracy," Science 302, pp. 1364-8, 2003.   DOI
38 Bender, G.M. et al., "De novo design of a single-chain diphenylporphyrin metalloprotein," Journal of the American Chemical Society 129, pp. 10732-40, 2007.   DOI   ScienceOn
39 Jiang, L. et al., "De novo computational design of retro-aldol enzymes," Science 319, pp. 1387-91(2008).   DOI
40 Filikov, A.V. et al., "Computational stabilization of human growth hormone," Protein Science 11, pp. 1452-1461, 2002.   DOI   ScienceOn
41 Malakauskas, S.M. & Mayo, S.L., "Design, structure and stability of a hyperthermophilic protein variant," Nature Structural Biology 5, pp. 470-475, 1998.   DOI   ScienceOn
42 Slovic, A.M. et al., "Computational design of watersoluble analogues of the potassium channel KcsA," Proceedings of the National Academy of Sciences 101, pp. 1828-33, 2004.   DOI   ScienceOn
43 Slovic, A.M. et al., "Computational design of a watersoluble analog of phospholamban," Protein Science 12, pp. 337-48, 2003.   DOI   ScienceOn
44 Mandell, D.J. & Kortemme, T., "Backbone flexibility in computational protein design," Currrent Opinion in Biotechnology 20, pp.420-8, 2009.   DOI   ScienceOn
45 Altman, R.B. & Dugan, J.M., "Defining bioinformatics and structural bioinformatics," Structural Bioinformatics pp. 3-14, 2005.
46 Weigelt, J., "Structural genomics-impact on biomedicine and drug discovery," Experimental Cell Research 316, pp.1332-8, 2010.   DOI   ScienceOn