Homology Modeling: an Overview of Fundamentals and Tools
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DOI: https://doi.org/10.15866/iremos.v10i2.11412
Abstract
Resolving the three dimensional structure of a protein is a critical step in modern drug discovery today. Homology modeling is a powerful tool that can efficiently predict protein structures from their amino acid sequence. Although it might sound simple enough, homology modeling, in fact, has to pass through several sophisticated steps before it can predict an accurate structure of a protein. These steps include template identification, alignment with the template, model construction and many post-modeling processes. Here, we describe in details these different steps, discuss the strengths and limitations of the methods and list a number of successful homology modelling applications in the literature. The objective of this review is to shed light on this extremely useful tool and highlight many case studies in this area of active research.
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Coleman, J.E. Zinc proteins: enzymes, storage proteins, transcription factors, and replication proteins. Annual review of biochemistry, Vol. 61, pp 897–946. 1992.
http://dx.doi.org/10.1146/annurev.biochem.61.1.897
Simon, M.I.; Strathmann, M.P.; and Gautam, N. Diversity of G proteins in signal transduction. Science (New York, N.Y.), Vol. 252, (Issue 5007), pp 802–8. 1991.
http://dx.doi.org/10.1126/science.1902986
Hille, B. Ion Channel Excitable Membranes. Sunderland Massachusetts USA, pp 1–37. 2001.
http://dx.doi.org/10.1016/0014-5793(92)81020-m
Pabo, C.O.; and Sauer, R.T. Transcription Factors: Structural Families and Principles of DNA Recognition. Annual review of biochemistry. 2003.
http://dx.doi.org/10.1146/annurev.biochem.61.1.1053
Buxbaum, E. Cell skeleton. In Fundamentals of Protein Structure and FunctionBoston, MA: Springer US, 2007, pp. 175–184.
http://dx.doi.org/10.1007/978-0-387-68480-2_11
Kann, M.G. Protein interactions and disease: Computational approaches to uncover the etiology of diseases. Briefings in Bioinformatics, Vol. 8, (Issue 5), pp 333–346. 2007.
http://dx.doi.org/10.1093/bib/bbm031
Yonath, A. X-ray crystallography at the heart of life science. Current Opinion in Structural Biology, Vol. 21, (Issue 5), pp 622–626. October 2011.
http://dx.doi.org/10.1016/j.sbi.2011.07.005
Carpenter, E.P.; Beis, K.; Cameron, A.D.; and Iwata, S. Overcoming the challenges of membrane protein crystallography. Current Opinion in Structural Biology, Vol. 18, (Issue 5), pp 581–586. October 2008.
http://dx.doi.org/10.1016/j.sbi.2008.07.001
Ghosh, E.; Kumari, P.; Jaiman, D.; and Shukla, A.K. Methodological advances: the unsung heroes of the GPCR structural revolution. Nat Rev Mol Cell Biol, Vol. 16, (Issue 2), pp 69–81. February 2015.
http://dx.doi.org/10.1038/nrm3933
Marti-Renom, M.A.; Stuart, A.C.; Fiser, A.; Sanchez, R.; Melo, F.; and Sali, A. Comparative protein structure modeling of genes and genomes. Annual review of biophysics and biomolecular structure, Vol. 29, pp 291–325. 2000.
http://dx.doi.org/10.1146/annurev.biophys.29.1.291
Berman, H.M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T.N.; Weissig, H.; Shindyalov, I.N.; and Bourne, P.E. The Protein Data Bank. Nucleic acids research, Vol. 28, (Issue 1), pp 235–242. 2000.
http://dx.doi.org/10.1093/nar/28.1.235
Mills, C.L.; Beuning, P.J.; and Ondrechen, M.J. Biochemical functional predictions for protein structures of unknown or uncertain function. Computational and Structural Biotechnology Journal, Vol. 13, pp 182–191. February 2015.
http://dx.doi.org/10.1016/j.csbj.2015.02.003
Schwede, T. Protein Modeling: What Happened to the “Protein Structure Gap”? Structure, Vol. 21, (Issue 9), pp 1531–1540. September 2013.
http://dx.doi.org/10.1016/j.str.2013.08.007
Hasani, H.J.; and Barakat, K. Protein-Protein Docking: Methods and Algorithms for Molecular Docking-Based Drug Design and Discovery, pp 173–195.
http://dx.doi.org/10.4018/978-1-5225-0115-2.ch007
Eswar, N. Tools for comparative protein structure modeling and analysis. Nucleic Acids Research, Vol. 31, (Issue 13), pp 3375–3380. 2003.
http://dx.doi.org/10.1093/nar/gkg543
Hongmao, S. Chapter 4 - Homology Modeling and Ligand-Based Molecule Design. In S.B.T.-A.P.G. to R.D.D. Hongmao (ed). A Practical Guide to Rational Drug Design Woodhead Publishing, 2016, pp. 109–160.
http://dx.doi.org/10.1016/b978-0-08-100098-4.00004-1
Lesk, A.M. CASP2: report on ab initio predictions. Proteins, Vol. Suppl 1, pp 151–166. 1997.
http://dx.doi.org/10.1002/(sici)1097-0134(1997)1+%3C151::aid-prot20%3E3.3.co;2-j
Cavasotto, C.N.; and Phatak, S.S. Homology modeling in drug discovery: current trends and applications. Drug discovery today, Vol. 14, (Issue 13–14), pp 676–83. July 2009.
http://dx.doi.org/10.1016/j.drudis.2009.04.006
Fallis, A. Fundamentals of Protein Structure and Function. 2013.
http://dx.doi.org/10.1007/978-3-319-19920-7_2
Taylor, W. Protein Structure Folding and Prediction. In Compact Handbook of Computational Biology CRC Press, 2004, pp. 223–240.
http://dx.doi.org/10.1201/9780203021415.ch6
Korasick, D.A.; and Jez, J.M. Protein Domains: Structure, Function, and Methods. In R.A. Bradshaw, P.D.B.T.-E. of C.B. Stahl (eds).Waltham: Academic Press, 2016, pp. 91–97.
http://dx.doi.org/10.1016/b978-0-12-394447-4.10011-2
Gagneux, P. Protein Structure and Function. Journal of Heredity, Vol. 95, (Issue 3), pp 274–274. May 2004.
http://dx.doi.org/10.1093/jhered/esh040
Ferreira, P.M. Protein structure: By N J Darby and T E Creighton. pp 97. IRL Press, Oxford University Press. 1993. SBN 0-19-963310-X. Biochemical Education, Vol. 23, (Issue 1), pp 46. January 1995.
http://dx.doi.org/10.1016/0307-4412(95)90200-7
Perutz, M. Protein Structure. pp 1–18. 2012.
http://dx.doi.org/10.2210/pdb1mhb/pdb
Zhang, X.; and Cheng, X. Structure of Protein. Vol. 34, pp 978–981.
http://dx.doi.org/10.1016/s0140-6736(02)84783-3
Zorko, M. Protein Folding. In Introduction to Peptides and Proteins CRC Press, 2009, pp. 101–122.
http://dx.doi.org/10.1201/b15106-11
Saxena, A.; Sangwan, R.S.; and Mishra, S. Fundamentals of Homology Modeling Steps and Comparison among Important Bioinformatics Tools: An Overview. Science International, pp 237–252. 2013.
http://dx.doi.org/10.17311/sciintl.2013.237.252
Vyas, V.; Ukawala, R.; Chintha, C.; and Ghate, M. Homology modeling a fast tool for drug discovery: Current perspectives. Indian Journal of Pharmaceutical Sciences, Vol. 74, (Issue 1), pp 1. 2012.
http://dx.doi.org/10.4103/0250-474x.102537
Nayeem, A.; Sitkoff, D.; and Krystek, S. A comparative study of available software for high-accuracy homology modeling: from sequence alignments to structural models. Protein science : a publication of the Protein Society, Vol. 15, (Issue 4), pp 808–824. 2006.
http://dx.doi.org/10.1110/ps.051892906
Ginalski, K. Comparative modeling for protein structure prediction. Current Opinion in Structural Biology, Vol. 16, (Issue 2), pp 172–177. 2006.
http://dx.doi.org/10.1016/j.sbi.2006.02.003
Hillisch, A.; Pineda, L.F.; and Hilgenfeld, R. Utility of homology models in the drug discovery process. Drug discovery today, Vol. 9, (Issue 15), pp 659–69. August 2004.
http://dx.doi.org/10.1016/s1359-6446(04)03196-4
Fiser, a; Fiser, a; Do, R.K.; Do, R.K.; Sali, a; and Sali, a. Modeling of loops in protein structures. Protein science : a publication of the Protein Society, Vol. 9, (Issue 9), pp 1753–73. 2000.
http://dx.doi.org/10.1110/ps.9.9.1753
Orengo, C.A.; Bray, J.E.; Buchan, D.W.A.; Harrison, A.; Lee, D.; Pearl, F.M.G.; Sillitoe, I.; Todd, A.E.; and Thornton, J.M. The CATH protein family database: a resource for structural and functional annotation of genomes. Proteomics, Vol. 2, (Issue 1), pp 11–21. January 2002.
http://dx.doi.org/10.1002/1615-9861(200201)2:1%3C11::aid-prot11%3E3.0.co;2-t
Murzin, A.G.; Brenner, S.E.; Hubbard, T.; and Chothia, C. SCOP: A structural classification of proteins database for the investigation of sequences and structures. Journal of Molecular Biology, Vol. 247, (Issue 4), pp 536–540. April 1995.
http://dx.doi.org/10.1016/s0022-2836(05)80134-2
Holm, L.; and Rosenström, P. Dali server: conservation mapping in 3D. Nucleic Acids Research, Vol. 38, (Issue suppl 2), pp W545–W549. July 2010.
http://dx.doi.org/10.1093/nar/gkq366
Benson, D.A.; Karsch-Mizrachi, I.; Lipman, D.J.; Ostell, J.; and Wheeler, D.L. GenBank. Nucleic Acids Research, Vol. 33, (Issue Database issue), pp D34–D38. January 2005.
http://dx.doi.org/10.1093/nar/gki063
Pieper, U.; Eswar, N.; Davis, F.P.; Braberg, H.; Madhusudhan, M.S.; Rossi, A.; Marti-Renom, M.; Karchin, R.; Webb, B.M.; Eramian, D.; Shen, M.-Y.; Kelly, L.; Melo, F.; and Sali, A. MODBASE: a database of annotated comparative protein structure models and associated resources. Nucleic acids research, Vol. 34, (Issue Database issue), pp D291-5. January 2006.
http://dx.doi.org/10.1093/nar/gkn791
Gerstein, M. A structural census of genomes: comparing bacterial, eukaryotic, and archaeal genomes in terms of protein structure. Journal of molecular biology, Vol. 274, (Issue 4), pp 562–576. December 1997.
http://dx.doi.org/10.1006/jmbi.1997.1412
Bairoch, A.; and Apweiler, R. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic acids research, Vol. 28, (Issue 1), pp 45–48. January 2000.
http://dx.doi.org/10.1093/nar/28.1.45
Pearson, W.R. Rapid and sensitive sequence comparison with FASTP and FASTA. Methods in enzymology, Vol. 183, pp 63–98. 1990.
http://dx.doi.org/10.1016/0076-6879(90)83007-v
Altschul, S.F.; Gish, W.; Miller, W.; Myers, E.W.; and Lipman, D.J. Basic local alignment search tool. Journal of Molecular Biology, Vol. 215, (Issue 3), pp 403–410. 1990.
http://dx.doi.org/10.1016/s0022-2836(05)80360-2
Jones, D.T.; Taylor, W.R.; and Thornton, J.M. A new approach to protein fold recognition. Nature, Vol. 358, (Issue 6381), pp 86–89. July 1992.
http://dx.doi.org/10.1038/358086a0
Larkin, M.A.; Blackshields, G. Brown, N.P. Chenna, R. McGettigan, P.A. McWilliam, H. Valentin, F. Wallace, I.M. Wilm, A. Lopez, R. Thompson, J.D. Gibson, T.J. and Higgins, D.G. Clustal W and Clustal X version 2.0. Bioinformatics, Vol. 23, (Issue 21), pp 2947–2948. 2007.
http://dx.doi.org/10.1093/bioinformatics/btm404
Corpet, F. Multiple sequence alignment with hierarchical clustering. Nucleic acids research, Vol. 16, (Issue 22), pp 10881–10890. November 1988.
http://dx.doi.org/10.1093/nar/16.22.10881
Notredame, C.; Higgins, D.G.; and Heringa, J. T-Coffee: A novel method for fast and accurate multiple sequence alignment. Journal of molecular biology, Vol. 302, (Issue 1), pp 205—217. September 2000.
http://dx.doi.org/10.1006/jmbi.2000.4042
Krissinel, E.; and Henrick, K. Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. ActaCrystallographica Section D, Vol. 60, (Issue 12 Part 1), pp 2256–2268. December 2004.
http://dx.doi.org/10.1107/s0907444904026460
Kim, D.E.; Chivian, D.; and Baker, D. Protein structure prediction and analysis using the Robetta server. Nucleic acids research, Vol. 32, (Issue Web Server issue), pp W526-31. July 2004.
http://dx.doi.org/10.1093/nar/gkh468
Abagyan, R.; Totrov, M.; and Kuznetsov, D. ICM - A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation. Journal of Computational Chemistry, Vol. 15, (Issue 5), pp 488–506. 1994.
http://dx.doi.org/10.1002/jcc.540150503
Šali, A.; and Blundell, T.L. Comparative Protein Modelling by Satisfaction of Spatial Restraints. Journal of Molecular Biology, Vol. 234, (Issue 3), pp 779–815. December 1993.
http://dx.doi.org/10.1006/jmbi.1993.1626
Roy, A.; Kucukural, A.; and Zhang, Y. I-TASSER: a unified platform for automated protein structure and function prediction. Nature protocols, Vol. 5, (Issue 4), pp 725–738. 2010.
http://dx.doi.org/10.1038/nprot.2010.5
Zhang, Y. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics, Vol. 9, (Issue 1), pp 40. 2008.
http://dx.doi.org/10.1186/1471-2105-9-40
Bates, P.A.; Kelley, L.A.; MacCallum, R.M.; and Sternberg, M.J. Enhancement of protein modeling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM. Proteins, Vol. Suppl 5, pp 39–46. January 2001.
http://dx.doi.org/10.1002/prot.1168
Ginalski, K.; Elofsson, A.; Fischer, D.; and Rychlewski, L. 3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics (Oxford, England), Vol. 19, (Issue 8), pp 1015–1018. May 2003.
http://dx.doi.org/10.1093/bioinformatics/btg124
Buchan, D.W.A.; Minneci, F.; Nugent, T.C.O.; Bryson, K.; and Jones, D.T. Scalable web services for the PSIPRED Protein Analysis Workbench. Nucleic acids research, Vol. 41, (Issue Web Server issue), pp W349-57. July 2013.
http://dx.doi.org/10.1093/nar/gkt381
Jones, D.T. Protein secondary structure prediction based on position-specific scoring matrices. Journal of molecular biology, Vol. 292, (Issue 2), pp 195–202. September 1999.
http://dx.doi.org/10.1006/jmbi.1999.3091
Källberg, M.; Wang, H.; Wang, S.; Peng, J.; Wang, Z.; Lu, H.; and Xu, J. Template-based protein structure modeling using the RaptorX web server. Nat. Protocols, Vol. 7, (Issue 8), pp 1511–1522. August 2012.
http://dx.doi.org/10.1038/nprot.2012.085
Kelley, L.A.; Mezulis, S.; Yates, C.M.; Wass, M.N.; and Sternberg, M.J.E. The Phyre2 web portal for protein modeling, prediction and analysis. Nat. Protocols, Vol. 10, (Issue 6), pp 845–858. June 2015.
http://dx.doi.org/10.1038/nprot.2015.053
Schwede, T.; Kopp, J.; Guex, N.; and Peitsch, M.C. SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Research , Vol. 31, (Issue 13), pp 3381–3385. July 2003.
http://dx.doi.org/10.1093/nar/gkg520
Vriend, G. WHAT IF: a molecular modeling and drug design program. Journal of molecular graphics, Vol. 8, (Issue 1), pp 29,52-56. March 1990.
http://dx.doi.org/10.1016/0263-7855(90)80070-v
Aszodi, A.; and Taylor, W.R. Homology modelling by distance geometry. Folding & design, Vol. 1, (Issue 5), pp 325–334. 1996.
http://dx.doi.org/10.1016/s1359-0278(96)00048-x
Krivov, G.G.; Shapovalov, M. V.; and Dunbrack, R.L. Improved prediction of protein side-chain conformations with SCWRL4. Proteins: Structure, Function and Bioinformatics, Vol. 77, (Issue 4), pp 778–795. 2009.
http://dx.doi.org/10.1002/prot.22488
Melo, F.; Devos, D.; Depiereux, E.; and Feytmans, E. ANOLEA: a www server to assess protein structures. Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology, Vol. 5, pp 187–190. 1997.
http://dx.doi.org/10.2172/378839
Laskowski, R.A.; Rullmannn, J.A.; MacArthur, M.W.; Kaptein, R.; and Thornton, J.M. AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. Journal of biomolecular NMR, Vol. 8, (Issue 4), pp 477–486. December 1996.
http://dx.doi.org/10.1007/bf00228148
Colovos, C.; and Yeates, T.O. Verification of protein structures: patterns of nonbonded atomic interactions. Protein science : a publication of the Protein Society, Vol. 2, (Issue 9), pp 1511–1519. September 1993.
http://dx.doi.org/10.1002/pro.5560020916
Laskowski, R.A.; MacArthur, M.W.; Moss, D.S.; and Thornton, J.M. PROCHECK: a program to check the stereochemical quality of protein structures. Journal of Applied Crystallography, Vol. 26, (Issue C), pp 283–291. 1993.
http://dx.doi.org/10.1107/s0021889892009944
Hooft, R.W.; Vriend, G.; Sander, C.; and Abola, E.E. Errors in protein structures. Nature, Vol. 381, (Issue 6580), pp 272. May 1996.
http://dx.doi.org/10.1038/381272a0
Bowie, J.U.; Luthy, R.; and Eisenberg, D. A method to identify protein sequences that fold into a known three-dimensional structure. Science (New York, N.Y.), Vol. 253, (Issue 5016), pp 164–170. July 1991.
http://dx.doi.org/10.1126/science.1853201
Wiederstein, M.; and Sippl, M.J. ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic acids research, Vol. 35, (Issue Web Server issue), pp W407-10. July 2007.
http://dx.doi.org/10.1093/nar/gkm290
Pearson, W.R. Empirical statistical estimates for sequence similarity searches. Journal of molecular biology, Vol. 276, (Issue 1), pp 71–84. February 1998.
http://dx.doi.org/10.1006/jmbi.1997.1525
Gribskov, M.; McLachlan, A.D.; and Eisenberg, D. Profile analysis: detection of distantly related proteins. Proceedings of the National Academy of Sciences of the United States of America, Vol. 84, (Issue 13), pp 4355–4358. July 1987.
http://dx.doi.org/10.1073/pnas.84.13.4355
Yona, G.; and Levitt, M. Within the twilight zone: a sensitive profile-profile comparison tool based on information theory. Journal of molecular biology, Vol. 315, (Issue 5), pp 1257–1275. February 2002.
http://dx.doi.org/10.1006/jmbi.2001.5293
Rychlewski, L.; Jaroszewski, L.; Li, W.; and Godzik, A. Comparison of sequence profiles. Strategies for structural predictions using sequence information. Protein science : a publication of the Protein Society, Vol. 9, (Issue 2), pp 232–241. February 2000.
http://dx.doi.org/10.1110/ps.9.2.232
Eddy, S.R. Profile hidden Markov models. Bioinformatics (Oxford, England), Vol. 14, (Issue 9), pp 755–763. 1998.
http://dx.doi.org/10.1093/bioinformatics/14.9.755
Karplus, K.; Barrett, C.; and Hughey, R. Hidden Markov models for detecting remote protein homologies. Bioinformatics (Oxford, England), Vol. 14, (Issue 10), pp 846–856. 1998.
http://dx.doi.org/10.1093/bioinformatics/14.10.846
Teichmann, S.A.; Chothia, C.; Church, G.M.; and Park, J. Fast assignment of protein structures to sequences using the intermediate sequence library PDB-ISL. Bioinformatics (Oxford, England), Vol. 16, (Issue 2), pp 117–124. February 2000.
http://dx.doi.org/10.1093/bioinformatics/16.2.117
Altschul, S.F.; Madden, T.L.; Schaffer, A.A.; Zhang, J.; Zhang, Z.; Miller, W.; and Lipman, D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic acids research, Vol. 25, (Issue 17), pp 3389–3402. September 1997.
http://dx.doi.org/10.1093/nar/25.17.3389
Karplus, K.; Karchin, R.; Draper, J.; Casper, J.; Mandel-Gutfreund, Y.; Diekhans, M.; and Hughey, R. Combining local-structure, fold-recognition, and new fold methods for protein structure prediction. Proteins, Vol. 53 Suppl 6, pp 491–496. 2003.
http://dx.doi.org/10.1002/prot.10540
Muller, A.; MacCallum, R.M.; and Sternberg, M.J. Benchmarking PSI-BLAST in genome annotation. Journal of molecular biology, Vol. 293, (Issue 5), pp 1257–1271. November 1999.
http://dx.doi.org/10.1006/jmbi.1999.3233
Soding, J.; Biegert, A.; and Lupas, A.N. The HHpred interactive server for protein homology detection and structure prediction. Nucleic acids research, Vol. 33, (Issue Web Server issue), pp W244-8. July 2005.
http://dx.doi.org/10.1093/nar/gki408
Godzik, A.; Kolinski, A.; and Skolnick, J. Topology fingerprint approach to the inverse protein folding problem. Journal of Molecular Biology, Vol. 227, (Issue 1), pp 227–238. 1992.
http://dx.doi.org/10.1016/0022-2836(92)90693-e
Peng, J.; and Xu, J. A multiple-template approach to protein threading. Proteins: Structure, Function, and Bioinformatics, Vol. 79, (Issue 6), pp 1930–1939. June 2011.
http://dx.doi.org/10.1002/prot.23016
Kelley, L.A.; MacCallum, R.M.; and Sternberg, M.J.E. Enhanced genome annotation using structural profiles in the program 3D-PSSM1. Journal of Molecular Biology, Vol. 299, (Issue 2), pp 501–522. June 2000.
http://dx.doi.org/10.1006/jmbi.2000.3741
Yang, Y.; Faraggi, E.; Zhao, H.; and Zhou, Y. Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of query and corresponding native properties of templates. Bioinformatics (Oxford, England), Vol. 27, (Issue 15), pp 2076–2082. August 2011.
http://dx.doi.org/10.1093/bioinformatics/btr350
Deane, C.M.; and Blundell, T.L. 27 - Protein Comparative Modelling and Drug Discovery. In C.G.B.T.-T.P. of M.C. (Second E. Wermuth (ed).London: Academic Press, 2003, pp. 445–458.
http://dx.doi.org/10.1016/b978-012744481-9/50031-3
Ma, J.; and Wang, S. Chapter Five - Algorithms, Applications, and Challenges of Protein Structure Alignment. In R.D.B.T.-A. in P.C. and S. Biology (ed).Academic Press, 2014, pp. 121–175.
http://dx.doi.org/10.1016/b978-0-12-800168-4.00005-6
Johnson, M.S.; and Overington, J.P. A structural basis for sequence comparisons. An evaluation of scoring methodologies. Journal of molecular biology, Vol. 233, (Issue 4), pp 716–738. October 1993.
http://dx.doi.org/10.1006/jmbi.1993.1548
Larsson, P.; Wallner, B.; Lindahl, E.; and Elofsson, A. Using multiple templates to improve quality of homology models in automated homology modeling. Protein science : a publication of the Protein Society, Vol. 17, (Issue 6), pp 990–1002. June 2008.
http://dx.doi.org/10.1110/ps.073344908
Sanchez, R.; and Sali, A. Evaluation of comparative protein structure modeling by MODELLER-3. Proteins, Vol. Suppl 1, pp 50–58. 1997.
http://dx.doi.org/10.1002/(sici)1097-0134(1997)1+%3C50::aid-prot8%3E3.3.co;2-w
Blundell, T.L.; Sibanda, B.L.; Sternberg, M.J.E.; and Thornton, J.M. Knowledge-based prediction of protein structures and the design of novel molecules. Nature, Vol. 326, (Issue 6111), pp 347–352. March 1987.
http://dx.doi.org/10.1038/326347a0
Sutcliffe, M.J.; Haneef, I.; Carney, D.; and Blundell, T.L. Knowledge based modelling of homologous proteins, Part I: Three-dimensional frameworks derived from the simultaneous superposition of multiple structures. Protein engineering, Vol. 1, (Issue 5), pp 377–384. 1987.
http://dx.doi.org/10.1093/protein/1.5.377
Holm, L.; and Sander, C. Database algorithm for generating protein backbone and side-chain co-ordinates from a C alpha trace application to model building and detection of co-ordinate errors. Journal of molecular biology, Vol. 218, (Issue 1), pp 183–194. March 1991.
http://dx.doi.org/10.1016/0022-2836(91)90883-8
vanGelder, C.W.; Leusen, F.J.; Leunissen, J.A.; and Noordik, J.H. A molecular dynamics approach for the generation of complete protein structures from limited coordinate data. Proteins, Vol. 18, (Issue 2), pp 174–185. February 1994.
http://dx.doi.org/10.1002/prot.340180209
Iwata, Y.; Kasuya, A.; and Miyamoto, S. An efficient method for reconstructing protein backbones from alpha-carbon coordinates. Journal of molecular graphics & modelling, Vol. 21, (Issue 2), pp 119–128. October 2002.
http://dx.doi.org/10.1016/s1093-3263(02)00142-0
Levitt, M. Accurate modeling of protein conformation by automatic segment matching. Journal of Molecular Biology, Vol. 226, (Issue 2), pp 507–533. 1992.
http://dx.doi.org/10.1016/0022-2836(92)90964-l
Aszodi, A.; and Taylor, W.R. Secondary structure formation in model polypeptide chains. Protein Eng, Vol. 7, (Issue 5), pp 633–644. 1994.
http://dx.doi.org/10.1093/protein/7.5.633
Allison, J.R.; Hertig, S.; Missimer, J.H.; Smith, L.J.; Steinmetz, M.O.; and Dolenc, J. Probing the structure and dynamics of proteins by combining molecular dynamics simulations and experimental NMR data. Journal of Chemical Theory and Computation, Vol. 8, (Issue 10), pp 3430–3444. 2012.
http://dx.doi.org/10.1021/ct300393b
Kahraman, A.; Herzog, F.; Leitner, A.; Rosenberger, G.; Aebersold, R.; and Malmström, L. Cross-Link Guided Molecular Modeling with ROSETTA. PLoS ONE, Vol. 8, (Issue 9), pp e73411. September 2013.
http://dx.doi.org/10.1371/journal.pone.0073411
Rappsilber, J. The beginning of a beautiful friendship: Cross-linking/mass spectrometry and modelling of proteins and multi-protein complexes. Journal of Structural Biology, Vol. 173, (Issue 3), pp 530–540. March 2011.
http://dx.doi.org/10.1016/j.jsb.2010.10.014
Venselaar, H.; Joosten, R.P.; Vroling, B.; Baakman, C.A.B.; Hekkelman, M.L.; Krieger, E.; and Vriend, G. Homology modelling and spectroscopy, a never-ending love story. European Biophysics Journal, Vol. 39, (Issue 4), pp 551–563. March 2010.
http://dx.doi.org/10.1007/s00249-009-0531-0
Petrey, D.; Xiang, Z.; Tang, C.L.; Xie, L.; Gimpelev, M.; Mitros, T.; Soto, C.S.; Goldsmith-Fischman, S.; Kernytsky, A.; Schlessinger, A.; Koh, I.Y.Y.; Alexov, E.; and Honig, B. Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling. Proteins, Vol. 53 Suppl 6, pp 430–435. 2003.
http://dx.doi.org/10.1002/prot.10550
Xiang, Z. Advances in homology protein structure modeling. Current protein & peptide science, Vol. 7, (Issue 3), pp 217–227. June 2006.
http://dx.doi.org/10.2174/138920306777452312
Fiser, A.; Do, R.; and Sali, A. Modeling of loops in protein structures. PRS, Vol. 9, (Issue 9), pp 1753–1773. 2000.
http://dx.doi.org/10.1110/ps.9.9.1753
Sali, A.; Potterton, L.; Yuan, F.; van Vlijmen, H.; and Karplus, M. Evaluation of comparative protein modeling by MODELLER. Proteins, Vol. 23, (Issue 3), pp 318–326. November 1995.
http://dx.doi.org/10.1002/prot.340230306
Guex, N.; and Peitsch, M.C. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis, Vol. 18, (Issue 15), pp 2714–2723. December 1997.
http://dx.doi.org/10.1002/elps.1150181505
Tappura, K. Influence of rotational energy barriers to the conformational search of protein loops in molecular dynamics and ranking the conformations. Proteins, Vol. 44, (Issue 3), pp 167–179. August 2001.
http://dx.doi.org/10.1002/prot.1082
vanVlijmen, H.W.; and Karplus, M. PDB-based protein loop prediction: parameters for selection and methods for optimization. Journal of molecular biology, Vol. 267, (Issue 4), pp 975–1001. April 1997.
http://dx.doi.org/10.1006/jmbi.1996.0857
Xiang, Z.; Soto, C.S.; and Honig, B. Evaluating conformational free energies: The colony energy and its application to the problem of loop prediction. Proceedings of the National Academy of Sciences of the United States of America, Vol. 99, (Issue 11), pp 7432–7437. May 2002.
http://dx.doi.org/10.1073/pnas.102179699
Deane, C.M.; and Blundell, T.L. CODA: a combined algorithm for predicting the structurally variable regions of protein models. Protein science : a publication of the Protein Society, Vol. 10, (Issue 3), pp 599–612. March 2001.
http://dx.doi.org/10.1110/ps.37601
Johnson, M.S.; Srinivasan, N.; Sowdhamini, R.; and Blundell, T.L. Knowledge-based protein modeling. Critical reviews in biochemistry and molecular biology, Vol. 29, (Issue 1), pp 1–68. 1994.
http://dx.doi.org/10.3109/10409239409086797
Francis-Lyon, P.; and Koehl, P. Protein side-chain modeling with a protein-dependent optimized rotamer library. Proteins: Structure, Function and Bioinformatics, Vol. 82, (Issue 9), pp 2000–2017. 2014.
http://dx.doi.org/10.1002/prot.24555
Stites, W.E.; Meeker, A.K.; and Shortle, D. Evidence for strained interactions between side-chains and the polypeptide backbone. Journal of molecular biology, Vol. 235, (Issue 1), pp 27–32. January 1994.
http://dx.doi.org/10.1016/s0022-2836(05)80008-7
Dunbrack, R.L.J.; and Karplus, M. Conformational analysis of the backbone-dependent rotamer preferences of protein sidechains. Nature structural biology, Vol. 1, (Issue 5), pp 334–340. May 1994.
http://dx.doi.org/10.1038/nsb0594-334
Canutescu, A.A.; Shelenkov, A.A.; and Dunbrack, R.L.J. A graph-theory algorithm for rapid protein side-chain prediction. Protein science : a publication of the Protein Society, Vol. 12, (Issue 9), pp 2001–2014. September 2003.
http://dx.doi.org/10.1110/ps.03154503
Xu, J.; and Berger, B. Fast and accurate algorithms for protein side-chain packing. Journal of the ACM, Vol. 53, (Issue 4), pp 533–557. 2006.
http://dx.doi.org/10.1145/1162349.1162350
Wallner, B.; and Elofsson, A. All are not equal: a benchmark of different homology modeling programs. Protein science : a publication of the Protein Society, Vol. 14, (Issue 5), pp 1315–27. May 2005.
http://dx.doi.org/10.1110/ps.041253405
Xiang, Z.; and Honig, B. Extending the accuracy limits of prediction for side-chain conformations. Journal of molecular biology, Vol. 311, (Issue 2), pp 421–430. August 2001.
http://dx.doi.org/10.1006/jmbi.2001.4865
Liang, S.; and Grishin, N. V. Side-chain modeling with an optimized scoring function. Protein science : a publication of the Protein Society, Vol. 11, (Issue 2), pp 322–331. February 2002.
http://dx.doi.org/10.1110/ps.24902
Samudrala, R.; and Moult, J. Determinants of side chain conformational preferences in protein structures. Protein engineering, Vol. 11, (Issue 11), pp 991–997. November 1998.
http://dx.doi.org/10.1093/protein/11.11.991
Krieger, E.; Nabuurs, S.B.; and Vriend, G. Homology Modeling. In Structural Bioinformatics John Wiley & Sons, Inc., 2003, pp. 509–523.
http://dx.doi.org/10.1002/0471721204.ch25
Xun, S.; Jiang, F.; and Wu, Y.D. Significant refinement of protein structure models using a residue-specific force field. Journal of Chemical Theory and Computation, Vol. 11, (Issue 4), pp 1949–1956. 2015.
http://dx.doi.org/10.1021/acs.jctc.5b00029
Lu, H.; and Skolnick, J. Application of statistical potentials to protein structure refinement from low resolution ab initio models. Biopolymers, Vol. 70, (Issue 4), pp 575–584. 2003.
http://dx.doi.org/10.1002/bip.10537
Han, R.; Leo-Macias, A.; Zerbino, D.; Bastolla, U.; Contreras-Moreira, B.; and Ortiz, A.R. An efficient conformational sampling method for homology modeling. Proteins, Vol. 71, (Issue 1), pp 175–88. April 2008.
http://dx.doi.org/10.1002/prot.21672
Ishitani, R.; Terada, T.; and Shimizu, K. Refinement of comparative models of protein structure by using multicanonical molecular dynamics simulations. Molecular Simulation, Vol. 34, (Issue 3), pp 327–336. March 2008.
http://dx.doi.org/10.1080/08927020801930539
Fan, H. Refinement of homology-based protein structures by molecular dynamics simulation techniques. Protein Science, Vol. 13, (Issue 1), pp 211–220. January 2004.
http://dx.doi.org/10.1110/ps.03381404
Kannan, S.; and Zacharias, M. Application of biasing-potential replica-exchange simulations for loop modeling and refinement of proteins in explicit solvent. Proteins, Vol. 78, (Issue 13), pp 2809–19. October 2010.
http://dx.doi.org/10.1002/prot.22796
Zhu, J.; Fan, H.; Periole, X.; Honig, B.; and Mark, A.E. Refining Homology Models by Combining Replica-Exchange Molecular Dynamics and Statistical Potentials. Proteins, Vol. 72, (Issue 4), pp 1171–1188. September 2008.
http://dx.doi.org/10.1002/prot.22005
Qian, B.; Ortiz, A.R.; and Baker, D. Improvement of comparative model accuracy by free-energy optimization along principal components of natural structural variation. Proceedings of the National Academy of Sciences of the United States of America, Vol. 101, (Issue 43), pp 15346–15351. October 2004.
http://dx.doi.org/10.1073/pnas.0404703101
Raval, A.; Piana, S.; Eastwood, M.P.; Dror, R.O.; and Shaw, D.E. Refinement of protein structure homology models via long, all-atom molecular dynamics simulations. Proteins, Vol. 80, (Issue 8), pp 2071–9. August 2012.
http://dx.doi.org/10.1002/prot.24098
Xu, D.; and Zhang, Y. Improving the physical realism and structural accuracy of protein models by a two-step atomic-level energy minimization. Biophysical journal, Vol. 101, (Issue 10), pp 2525–2534. November 2011.
http://dx.doi.org/10.1016/j.bpj.2011.10.024
Laskowski, R.A.; and Swaminathan, G.J. Problems of Protein Three-Dimensional Structures. Elsevier Inc., 2013.
http://dx.doi.org/10.1016/b0-08-045044-x/00097-3
Dalton, J.A.R.; and Jackson, R.M. An evaluation of automated homology modelling methods at low target-template sequence similarity. Bioinformatics, Vol. 23, (Issue 15), pp 1901–1908. 2007.
http://dx.doi.org/10.1093/bioinformatics/btm262
Rodriguez, R.; Chinea, G.; Lopez, N.; Pons, T.; and Vriend, G. Homology modeling, model and software evaluation: three related resources. Bioinformatics (Oxford, England), Vol. 14, (Issue 6), pp 523–528. 1998.
http://dx.doi.org/10.1093/bioinformatics/14.6.523
MacKerell, A.D.; Bashford, D.; Bellott, M.; Dunbrack, R.L.; Evanseck, J.D.; Field, M.J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F.T.; et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. The journal of physical chemistry. B, Vol. 102, (Issue 18), pp 3586–3616. April 1998.
http://dx.doi.org/10.1021/jp973084f
Sali, A.; and Overington, J.P. Derivation of rules for comparative protein modeling from a database of protein structure alignments. Protein science : a publication of the Protein Society, Vol. 3, (Issue 9), pp 1582–1596. September 1994.
http://dx.doi.org/10.1002/pro.5560030923
Kiefer, F.; Arnold, K.; Kunzli, M.; Bordoli, L.; and Schwede, T. The SWISS-MODEL Repository and associated resources. Nucleic acids research, Vol. 37, (Issue Database issue), pp D387-92. January 2009.
http://dx.doi.org/10.1093/nar/gkn750
Brooks, B.R.; Bruccoleri, R.E.; Olafson, B.D.; States, D.J.; Swaminathan, S.; and Karplus, M. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. Journal of Computational Chemistry, Vol. 4, (Issue 2), pp 187–217. 1983.
http://dx.doi.org/10.1002/jcc.540040211
Song, Y.; DiMaio, F.; Wang, R.Y.-R.; Kim, D.; Miles, C.; Brunette, T.; Thompson, J.; and Baker, D. High-resolution comparative modeling with RosettaCM. Structure (London, England: 1993), Vol. 21, (Issue 10), pp 1735–1742. October 2013.
http://dx.doi.org/10.1016/j.str.2013.08.005
Rohl, C.A.; Strauss, C.E.M.; Chivian, D.; and Baker, D. Modeling structurally variable regions in homologous proteins with rosetta. Proteins, Vol. 55, (Issue 3), pp 656–677. May 2004.
http://dx.doi.org/10.1002/prot.10629
Ortiz, A.R.; Strauss, C.E.M.; and Olmea, O. MAMMOTH (matching molecular models obtained from theory): an automated method for model comparison. Protein science: a publication of the Protein Society, Vol. 11, (Issue 11), pp 2606–2621. November 2002.
http://dx.doi.org/10.1110/ps.0215902
Sircar, A.; Kim, E.T.; and Gray, J.J. RosettaAntibody: antibody variable region homology modeling server. Nucleic acids research, Vol. 37, (Issue Web Server issue), pp W474-9. July 2009.
http://dx.doi.org/10.1093/nar/gkp387
Moult, J.; Pedersen, J.T.; Judson, R.; and Fidelis, K. A large-scale experiment to assess protein structure prediction methods. Proteins, Vol. 23, (Issue 3), pp ii–v. November 1995.
http://dx.doi.org/10.1002/prot.340230303
Haas, J.; Roth, S.; Arnold, K.; Kiefer, F.; Schmidt, T.; Bordoli, L.; and Schwede, T. The Protein Model Portal--a comprehensive resource for protein structure and model information. Database : the journal of biological databases and curation, Vol. 2013, pp bat031. 2013.
http://dx.doi.org/10.1093/database/bat031
Bujnicki, J.M.; Elofsson, A.; Fischer, D.; and Rychlewski, L. LiveBench-2: large-scale automated evaluation of protein structure prediction servers. Proteins, Vol. Suppl 5, pp 184–91. January 2001.
http://dx.doi.org/10.1002/prot.10039
Koh, I.Y.Y.; Eyrich, V.A.; Marti-Renom, M.A.; Przybylski, D.; Madhusudhan, M.S.; Eswar, N.; Grana, O.; Pazos, F.; Valencia, A.; Sali, A.; and Rost, B. EVA: Evaluation of protein structure prediction servers. Nucleic acids research, Vol. 31, (Issue 13), pp 3311–3315. July 2003.
http://dx.doi.org/10.1093/nar/gkg619
Eyrich, V.A.; Marti-Renom, M.A.; Przybylski, D.; Madhusudhan, M.S.; Fiser, A.; Pazos, F.; Valencia, A.; Sali, A.; and Rost, B. EVA: continuous automatic evaluation of protein structure prediction servers. Bioinformatics (Oxford, England), Vol. 17, (Issue 12), pp 1242–1243. December 2001.
http://dx.doi.org/10.1093/bioinformatics/17.12.1242
Yang, J.; Yan, R.; Roy, A.; Xu, D.; Poisson, J.; and Zhang, Y. The I-TASSER Suite: protein structure and function prediction. Nature Methods, Vol. 12, (Issue 1), pp 7–8. 2014.
http://dx.doi.org/10.1038/nmeth.3213
Hildebrand, A.; Remmert, M.; Biegert, A.; and Soding, J. Fast and accurate automatic structure prediction with HHpred. Proteins, Vol. 77 Suppl 9, pp 128–132. 2009.
http://dx.doi.org/10.1002/prot.22499
McGuffin, L.J.; Atkins, J.D.; Salehe, B.R.; Shuid, A.N.; and Roche, D.B. IntFOLD: an integrated server for modelling protein structures and functions from amino acid sequences. Nucleic acids research, Vol. 43, (Issue W1), pp W169-73. July 2015.
http://dx.doi.org/10.1093/nar/gkv236
Saxena, A.; Sangwan, R.S.; and Mishra, S. Fundamentals of Homology Modeling Steps and Comparison among Important Bioinformatics Tools: An Overview. Science International. 2013.
http://dx.doi.org/10.17311/sciintl.2013.237.252
Lundstrom, K. Structural genomics and drug discovery. Journal of cellular and molecular medicine, Vol. 11, (Issue 2), pp 224–238. 2007.
http://dx.doi.org/10.1111/j.1582-4934.2007.00028.x
Williamson, A.R. Creating a structural genomics consortium. Nat StructMolBiol, Vol. 7, (Issue 953). 2000.
http://dx.doi.org/10.1038/80726
Rajapaksha, H.; and Petrovsky, N. In SilicoStructural Homology Modelling and Docking for Assessment of Pandemic Potential of a Novel H7N9 Influenza Virus and Its Ability to Be Neutralized by Existing Anti-Hemagglutinin Antibodies. PLoS ONE, Vol. 9, (Issue 7), pp e102618. July 2014.
http://dx.doi.org/10.1371/journal.pone.0102618
Zhu, K.; Day, T.; Warshaviak, D.; Murrett, C.; Friesner, R.; and Pearlman, D. Antibody structure determination using a combination of homology modeling, energy-based refinement, and loop prediction. Proteins, Vol. 82, (Issue 8), pp 1646–55. August 2014.
http://dx.doi.org/10.1002/prot.24551
Ngo, T.; Kufareva, I.; Coleman, J.L.; Graham, R.M.; Abagyan, R.; and Smith, N.J. Identifying ligands at orphan GPCRs: Current status using structure-based approaches. British Journal of Pharmacology. 2016.
http://dx.doi.org/10.1111/bph.13452
Heifetz, A.; James, T.; Morao, I.; Bodkin, M.J.; and Biggin, P.C. Guiding lead optimization with GPCR structure modeling and molecular dynamics. Current Opinion in Pharmacology, Vol. 30, pp 14–21. October 2016.
http://dx.doi.org/10.1016/j.coph.2016.06.004
Evers, A.; and Klabunde, T. Structure-based Drug Discovery Using GPCR Homology Modeling: Successful Virtual Screening for Antagonists of the Alpha1A Adrenergic Receptor. Journal of Medicinal Chemistry, Vol. 48, (Issue 4), pp 1088–1097. February 2005.
http://dx.doi.org/10.1021/jm0491804
Perry, S.R.; Xu, W.; Wirija, A.; Lim, J.; Yau, M.-K.; Stoermer, M.J.; Lucke, A.J.; and Fairlie, D.P. Three Homology Models of PAR2 Derived from Different Templates: Application to Antagonist Discovery. Journal of Chemical Information and Modeling, Vol. 55, (Issue 6), pp 1181–1191. June 2015.
http://dx.doi.org/10.1021/acs.jcim.5b00087
Trujillo, K.; Paoletta, S.; Kiselev, E.; and Jacobson, K.A. Molecular modeling of the human P2Y14 receptor: A template for structure-based design of selective agonist ligands. Bioorganic & Medicinal Chemistry, Vol. 23, (Issue 14), pp 4056–4064. July 2015.
http://dx.doi.org/10.1016/j.bmc.2015.03.042
Shehata, M.A.; Belcik Christensen, H.; Isberg, V.; Sejer Pedersen, D.; Bender, A.; Brauner-Osborne, H.; and Gloriam, D.E. Identification of the first surrogate agonists for the G protein-coupled receptor GPR132. RSC Advances, Vol. 5, (Issue 60), pp 48551–48557. 2015.
http://dx.doi.org/10.1039/c5ra04804d
Arafat, A.S.Y.; Arun, A.; Ilamathi, M.; Asha, J.; Sivashankari, P.R.; D’Souza, C.J.M.; Sivaramakrishnan, V.; and Dhananjaya, B.L. Homology modeling, molecular dynamics and atomic level interaction study of snake venom 5’ nucleotidase. Journal of molecular modeling, Vol. 20, (Issue 3), pp 2156. March 2014.
http://dx.doi.org/10.1007/s00894-014-2156-1
Tian, W.; and Skolnick, J. How well is enzyme function conserved as a function of pairwise sequence identity? Journal of molecular biology, Vol. 333, (Issue 4), pp 863–882. October 2003.
http://dx.doi.org/10.1016/j.jmb.2003.08.057
Launay, G.; and Simonson, T. Homology modelling of protein-protein complexes: a simple method and its possibilities and limitations. BMC bioinformatics, Vol. 9, pp 427. 2008.
http://dx.doi.org/10.1186/1471-2105-9-427
Szilagyi, A.; and Zhang, Y. Template-based structure modeling of protein–protein interactions. Current Opinion in Structural Biology, Vol. 24, pp 10–23. February 2014.
http://dx.doi.org/10.1016/j.sbi.2013.11.005
Villoutreix, B.O.; Kuenemann, M. a.; Poyet, J.L.; Bruzzoni-Giovanelli, H.; Labbé, C.; Lagorce, D.; Sperandio, O.; and Miteva, M. a. Drug-like protein-protein interaction modulators: Challenges and opportunities for drug discovery and chemical biology. Molecular Informatics, Vol. 33, (Issue 6–7), pp 414–437. 2014.
http://dx.doi.org/10.1002/minf.201400040
Waksman, G.; and Sansom, C. Introduction: Proteomics and Protein – Protein Interactions: Biology , Chemistry , Bioinformatics , and Drug Design. In G. Waksman (ed). Proteomics and Protein – Protein Interactions: Biology , Chemistry , Bioinformatics , and Drug Design New York: Springer, 2005, pp. 1–18.
http://dx.doi.org/10.1007/0-387-24532-4_1
Xu, Y.; Wang, Y.; Meng, X.; Zhang, M.; Jiang, M.; Cui, M.; and Tseng, G. Building KCNQ1 / KCNE1 Channel Models and Probing their Interactions by Molecular-Dynamics Simulations. Vol. 105, (Issue December), pp 2461–2473. 2013.
http://dx.doi.org/10.1016/j.bpj.2013.09.058
Xu, Y.; Wang, Y.; Zhang, M.; Jiang, M.; Rosenhouse-Dantsker, A.; Wassenaar, T.; and Tseng, G.-N. Probing Binding Sites and Mechanisms of Action of an IKs Activator by Computations and Experiments. Biophysical Journal, Vol. 108, (Issue 1), pp 62–75. 2015.
http://dx.doi.org/10.1016/j.bpj.2014.10.059
Dhanavade, M.J.; Jalkute, C.B.; Barage, S.H.; and Sonawane, K.D. Homology modeling, molecular docking and MD simulation studies to investigate role of cysteine protease from Xanthomonascampestris in degradation of Aβ peptide. Computers in Biology and Medicine, Vol. 43, (Issue 12), pp 2063–2070. December 2013.
http://dx.doi.org/10.1016/j.compbiomed.2013.09.021
Merlino, A.; Vieites, M.; Gambino, D.; and Laura Coitiño, E. Homology modeling of T. cruzi and L. major NADH-dependent fumaratereductases: Ligand docking, molecular dynamics validation, and insights on their binding modes. Journal of Molecular Graphics and Modelling, Vol. 48, pp 47–59. March 2014.
http://dx.doi.org/10.1016/j.jmgm.2013.12.001
Brannigan, J. a; and Wilkinson, A.J. Protein engineering 20 years on. Nature reviews. Molecular cell biology, Vol. 3, (Issue 12), pp 964–70. 2002.
http://dx.doi.org/10.1038/nrm975
Antikainen, N.M.; and Martin, S.F. Altering protein specificity: techniques and applications. Bioorganic & medicinal chemistry, Vol. 13, (Issue 8), pp 2701–2716. April 2005.
http://dx.doi.org/10.1016/j.bmc.2005.01.059
Gagnidze, K.; Sachchidanand; Rozenfeld, R.; Mezei, M.; Zhou, M.-M.; and Devi, L.A. Homology Modeling and Site-directed Mutagenesis to Identify Selective Inhibitors of Endothelin-Converting Enzyme-2. Journal of medicinal chemistry, Vol. 51, (Issue 12), pp 3378–3387. June 2008.
http://dx.doi.org/10.1021/jm7015478
Szklarz, G.D.; and Halpert, J.R. Use of homology modeling in conjunction with site-directed mutagenesis for analysis of structure-function relationships of mammalian cytochromes P450. Life sciences, Vol. 61, (Issue 26), pp 2507–2520. 1997.
http://dx.doi.org/10.1016/s0024-3205(97)00717-0
Silvestrov, P.; Müller, T.A.; Clark, K.N.; Hausinger, R.P.; and Cisneros, G.A. Homology modeling, molecular dynamics, and site-directed mutagenesis study of AlkB human homolog 1 (ALKBH1). Journal of Molecular Graphics and Modelling, Vol. 54, pp 123–130. November 2014.
http://dx.doi.org/10.1016/j.jmgm.2014.10.013
Anwar-Mohamed, A.; Barakat, K.H.; Bhat, R.; Noskov, S.Y.; Tyrrell, D.L.; Tuszynski, J. a.; and Houghton, M. A human ether-á-go-go-related (hERG) ion channel atomistic model generated by long supercomputer molecular dynamics simulations and its use in predicting drug cardiotoxicity. Toxicology Letters, Vol. 230, (Issue 3), pp 382–392. 2014.
http://dx.doi.org/10.1016/j.toxlet.2014.08.007
Lerche, C.; Bruhova, I.; Lerche, H.; Steinmeyer, K.; Wei, A.D.; Strutz-Seebohm, N.; Lang, F.; Busch, A.E.; Zhorov, B.S.; and Seebohm, G. Chromanol 293B binding in KCNQ1 (Kv7.1) channels involves electrostatic interactions with a potassium ion in the selectivity filter. Molecular pharmacology, Vol. 71, pp 1503–1511. 2007.
http://dx.doi.org/10.1124/mol.106.031682
Szklarz, G.D.; Ornstein, R.L.; and Halpert, J.R. Application of 3-dimensional homology modeling of cytochrome P450 2B1 for interpretation of site-directed mutagenesis results. Journal of biomolecular structure & dynamics, Vol. 12, (Issue 1), pp 61–78. August 1994.
http://dx.doi.org/10.1080/07391102.1994.10508088
Ismail, A.M.; Sharma, O.P.; Kumar, M.S.; Kannangai, R.; and Abraham, P. Impact of rtI233V mutation in hepatitis B virus polymerase protein and adefovir efficacy: Homology modeling and molecular docking studies. Bioinformation, Vol. 9, (Issue 3), pp 121–125. 2013.
http://dx.doi.org/10.6026/97320630009121
Li, M.; and Wang, B. Homology modeling and examination of the effect of the D92E mutation on the H5N1 nonstructural protein NS1 effector domain. Journal of Molecular Modeling, Vol. 13, (Issue 12), pp 1237–1244. 2007.
http://dx.doi.org/10.1007/s00894-007-0245-0
Rodrigues, J.P.G.L.M.; Melquiond, A.S.J.; Karaca, E.; Trellet, M.; Van Dijk, M.; Van Zundert, G.C.P.; Schmitz, C.; De Vries, S.J.; Bordogna, A.; Bonati, L.; Kastritis, P.L.; and Bonvin, A.M.J.J. Defining the limits of homology modeling in information-driven protein docking. Proteins: Structure, Function and Bioinformatics, Vol. 81, (Issue 12), pp 2119–2128. 2013.
http://dx.doi.org/10.1002/prot.24382
Hardin, C.; Pogorelov, T. V.; and Luthey-Schulten, Z. Ab initio protein structure prediction. Current Opinion in Structural Biology, Vol. 12, (Issue 2), pp 176–181. 2002.
http://dx.doi.org/10.1016/s0959-440x(02)00306-8
Krieger, E.; Joo, K.; Lee, J.; Lee, J.; Raman, S.; Thompson, J.; Tyka, M.; Baker, D.; and Karplus, K. Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8. Proteins: Structure, Function and Bioinformatics, Vol. 77, (Issue SUPPL. 9), pp 114–122. 2009.
http://dx.doi.org/10.1002/prot.22570
Li, Y.; and Zhang, Y. REMO: A new protocol to refine full atomic protein models from C-alpha traces by optimizing hydrogen-bonding networks. Proteins: Structure, Function and Bioinformatics, Vol. 76, (Issue 3), pp 665–676. 2009.
http://dx.doi.org/10.1002/prot.22380
Fisher, C.K.; Huang, A.; and Stultz, C.M. Modeling intrinsically disordered proteins with Bayesian statistics. Journal of the American Chemical Society, Vol. 132, (Issue 42), pp 14919–14927. 2010.
http://dx.doi.org/10.1021/ja105832g
Chen, C.Y.-C.; and Tou, W. leong. How to design a drug for the disordered proteins? Drug Discovery Today, Vol. 18, (Issue 19–20), pp 910–915. 2013.
http://dx.doi.org/10.1016/j.drudis.2013.04.008
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