TY - JOUR AU - Kumar, R. AU - Jangir, D. K. AU - Verma, G. AU - Shekhar, S. AU - Hanpude, P. AU - Kumar, S. PY - 2017 DA - 2017// TI - S-nitrosylation of UCHL1 induces its structural instability and promotes α-synuclein aggregation JO - Sci Rep VL - 7 UR - https://doi.org/10.1038/srep44558 DO - 10.1038/srep44558 ID - Kumar2017 ER - TY - JOUR AU - Siddiqui, I. J. AU - Pervaiz, N. AU - Abbasi, A. A. PY - 2016 DA - 2016// TI - The Parkinson disease gene SNCA: evolutionary and structural insights with pathological implication JO - Sci Rep VL - 6 UR - https://doi.org/10.1038/srep24475 DO - 10.1038/srep24475 ID - Siddiqui2016 ER - TY - JOUR AU - Lee Y-T, C. AU - Hsu S-T, D. PY - 2017 DA - 2017// TI - Familial mutations and post-translational modifications of UCH-L1 in Parkinson's disease and neurodegenerative disorders JO - Curr Protein Pept Sci VL - 18 UR - https://doi.org/10.2174/1389203717666160217143721 DO - 10.2174/1389203717666160217143721 ID - Lee Y-T2017 ER - TY - JOUR AU - Virgilio, A. AU - Greco, A. AU - Fabbrini, G. AU - Inghilleri, M. AU - Rizzo, M. I. AU - Gallo, A. PY - 2016 DA - 2016// TI - Parkinson's disease: autoimmunity and neuroinflammation JO - Autoimmun Rev VL - 15 UR - https://doi.org/10.1016/j.autrev.2016.07.022 DO - 10.1016/j.autrev.2016.07.022 ID - Virgilio2016 ER - TY - JOUR AU - Lunati, A. AU - Lesage, S. AU - Brice, A. PY - 2018 DA - 2018// TI - The genetic landscape of Parkinson’s disease JO - Rev Neurol VL - 174 UR - https://doi.org/10.1016/j.neurol.2018.08.004 DO - 10.1016/j.neurol.2018.08.004 ID - Lunati2018 ER - TY - JOUR AU - Zhang, M. AU - Cai, F. AU - Zhang, S. AU - Zhang, S. AU - Song, W. PY - 2014 DA - 2014// TI - Overexpression of ubiquitin carboxyl-terminal hydrolase L1 (UCHL1) delays Alzheimer's progression in vivo JO - Sci Rep VL - 4 UR - https://doi.org/10.1038/srep07298 DO - 10.1038/srep07298 ID - Zhang2014 ER - TY - JOUR AU - Bilguvar, K. AU - Tyagi, N. K. AU - Ozkara, C. AU - Tuysuz, B. AU - Bakircioglu, M. AU - Choi, M. PY - 2013 DA - 2013// TI - Recessive loss of function of the neuronal ubiquitin hydrolase UCHL1 leads to early-onset progressive neurodegeneration JO - Proc Natl Acad Sci U S A VL - 110 UR - https://doi.org/10.1073/pnas.1222732110 DO - 10.1073/pnas.1222732110 ID - Bilguvar2013 ER - TY - JOUR AU - Nazé, P. AU - Vuillaume, I. AU - Destée, A. AU - Pasquier, F. AU - Sablonnière, B. PY - 2002 DA - 2002// TI - Mutation analysis and association studies of the ubiquitin carboxy-terminal hydrolase L1 gene in Huntington's disease JO - Neurosci Lett VL - 328 UR - https://doi.org/10.1016/S0304-3940(02)00231-8 DO - 10.1016/S0304-3940(02)00231-8 ID - Nazé2002 ER - TY - JOUR AU - Belin, A. C. AU - Westerlund, M. AU - Bergman, O. AU - Nissbrandt, H. AU - Lind, C. AU - Sydow, O. PY - 2007 DA - 2007// TI - S18Y in ubiquitin carboxy-terminal hydrolase L1 (UCH-L1) associated with decreased risk of Parkinson's disease in Sweden JO - Parkinsonism Relat Disord VL - 13 UR - https://doi.org/10.1016/j.parkreldis.2006.12.002 DO - 10.1016/j.parkreldis.2006.12.002 ID - Belin2007 ER - TY - JOUR AU - Leroy, E. AU - Boyer, R. AU - Auburger, G. AU - Leube, B. AU - Ulm, G. AU - Mezey, E. PY - 1998 DA - 1998// TI - The ubiquitin pathway in Parkinson's disease JO - Nature. VL - 395 UR - https://doi.org/10.1038/26652 DO - 10.1038/26652 ID - Leroy1998 ER - TY - JOUR AU - Rydning, S. L. AU - Backe, P. H. AU - Sousa, M. M. AU - Iqbal, Z. AU - Øye, A. -. M. AU - Sheng, Y. PY - 2016 DA - 2016// TI - Novel UCHL1 mutations reveal new insights into ubiquitin processing JO - Hum Mol Genet VL - 26 ID - Rydning2016 ER - TY - JOUR AU - Das, C. AU - Hoang, Q. Q. AU - Kreinbring, C. A. AU - Luchansky, S. J. AU - Meray, R. K. AU - Ray, S. S. PY - 2006 DA - 2006// TI - Structural basis for conformational plasticity of the Parkinson's disease-associated ubiquitin hydrolase UCH-L1 JO - Proc Natl Acad Sci U S A VL - 103 UR - https://doi.org/10.1073/pnas.0510403103 DO - 10.1073/pnas.0510403103 ID - Das2006 ER - TY - JOUR AU - Ragland, M. AU - Hutter, C. AU - Zabetian, C. AU - Edwards, K. PY - 2009 DA - 2009// TI - Association between the ubiquitin carboxyl-terminal esterase L1 gene (UCHL1) S18Y variant and Parkinson's disease: a HuGE review and meta-analysis JO - Am J Epidemiol VL - 170 UR - https://doi.org/10.1093/aje/kwp288 DO - 10.1093/aje/kwp288 ID - Ragland2009 ER - TY - JOUR AU - Sasaki, H. AU - Yukiue, H. AU - Moiriyama, S. AU - Kobayashi, Y. AU - Nakashima, Y. AU - Kaji, M. PY - 2001 DA - 2001// TI - Clinical significance of matrix metalloproteinase-7 and Ets-1 gene expression in patients with lung cancer JO - J Surg Res VL - 101 UR - https://doi.org/10.1006/jsre.2001.6279 DO - 10.1006/jsre.2001.6279 ID - Sasaki2001 ER - TY - JOUR AU - Yamazaki, T. AU - Hibi, K. AU - Takase, T. AU - Tezel, E. AU - Nakayama, H. AU - Kasai, Y. PY - 2002 DA - 2002// TI - PGP9. 5 as a marker for invasive colorectal cancer JO - Clin Cancer Res VL - 8 ID - Yamazaki2002 ER - TY - JOUR AU - Kabuta, T. AU - Furuta, A. AU - Aoki, S. AU - Furuta, K. AU - Wada, K. PY - 2008 DA - 2008// TI - Aberrant interaction between Parkinson disease-associated mutant UCH-L1 and the lysosomal receptor for chaperone-mediated autophagy JO - J Biol Chem VL - 283 UR - https://doi.org/10.1074/jbc.M801918200 DO - 10.1074/jbc.M801918200 ID - Kabuta2008 ER - TY - JOUR AU - Li, H. AU - Kiyama, H. AU - Osaka, H. AU - Kimura, I. AU - Nishikawa, K. AU - Namikawa, K. PY - 2003 DA - 2003// TI - Ubiquitin carboxy-terminal hydrolase L1 binds to and stabilizes monoubiquitin in neuron JO - Hum Mol Genet VL - 12 UR - https://doi.org/10.1093/hmg/ddg218 DO - 10.1093/hmg/ddg218 ID - Li2003 ER - TY - JOUR AU - Nishikawa, K. AU - Li, H. AU - Kawamura, R. AU - Osaka, H. AU - Wang, Y. -. L. AU - Hara, Y. PY - 2003 DA - 2003// TI - Alterations of structure and hydrolase activity of parkinsonism-associated human ubiquitin carboxyl-terminal hydrolase L1 variants JO - Biochem Biophys Res Commun VL - 304 UR - https://doi.org/10.1016/S0006-291X(03)00555-2 DO - 10.1016/S0006-291X(03)00555-2 ID - Nishikawa2003 ER - TY - JOUR AU - Setsuie, R. AU - Wang, Y. -. L. AU - Mochizuki, H. AU - Osaka, H. AU - Hayakawa, H. AU - Ichihara, N. PY - 2007 DA - 2007// TI - Dopaminergic neuronal loss in transgenic mice expressing the Parkinson's disease-associated UCH-L1 I93M mutant JO - Neurochem Int VL - 50 UR - https://doi.org/10.1016/j.neuint.2006.07.015 DO - 10.1016/j.neuint.2006.07.015 ID - Setsuie2007 ER - TY - JOUR AU - Setsuie, R. AU - Wada, K. PY - 2007 DA - 2007// TI - The functions of UCH-L1 and its relation to neurodegenerative diseases JO - Neurochem Int VL - 51 UR - https://doi.org/10.1016/j.neuint.2007.05.007 DO - 10.1016/j.neuint.2007.05.007 ID - Setsuie2007 ER - TY - JOUR AU - Cartier, A. E. AU - Ubhi, K. AU - Spencer, B. AU - Vazquez-Roque, R. A. AU - Kosberg, K. A. AU - Fourgeaud, L. PY - 2012 DA - 2012// TI - Differential effects of UCHL1 modulation on alpha-synuclein in PD-like models of alpha-synucleinopathy JO - PLoS One VL - 7 UR - https://doi.org/10.1371/journal.pone.0034713 DO - 10.1371/journal.pone.0034713 ID - Cartier2012 ER - TY - JOUR AU - Mellick, G. AU - Silburn, P. PY - 2000 DA - 2000// TI - The ubiquitin carboxy-terminal hydrolase-L1 gene S18Y polymorphism does not confer protection against idiopathic Parkinson's disease JO - Neurosci Lett VL - 293 UR - https://doi.org/10.1016/S0304-3940(00)01510-X DO - 10.1016/S0304-3940(00)01510-X ID - Mellick2000 ER - TY - JOUR AU - Miyake, Y. AU - Tanaka, K. AU - Fukushima, W. AU - Kiyohara, C. AU - Sasaki, S. AU - Tsuboi, Y. PY - 2012 DA - 2012// TI - UCHL1 S18Y variant is a risk factor for Parkinson’s disease in Japan JO - BMC Neurol VL - 12 UR - https://doi.org/10.1186/1471-2377-12-62 DO - 10.1186/1471-2377-12-62 ID - Miyake2012 ER - TY - JOUR AU - Yousaf, A. AU - Sohail Raza, M. AU - Ali, A. A. PY - 2015 DA - 2015// TI - The evolution of bony vertebrate enhancers at odds with their coding sequence landscape JO - Genome Biol Evol VL - 7 UR - https://doi.org/10.1093/gbe/evv146 DO - 10.1093/gbe/evv146 ID - Yousaf2015 ER - TY - JOUR AU - Tamura, K. AU - Peterson, D. AU - Peterson, N. AU - Stecher, G. AU - Nei, M. AU - Kumar, S. PY - 2011 DA - 2011// TI - MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods JO - Mol Biol Evol VL - 28 UR - https://doi.org/10.1093/molbev/msr121 DO - 10.1093/molbev/msr121 ID - Tamura2011 ER - TY - JOUR AU - Abbasi, A. A. PY - 2011 DA - 2011// TI - Molecular evolution of HR, a gene that regulates the postnatal cycle of the hair follicle JO - Sci Rep VL - 1 UR - https://doi.org/10.1038/srep00032 DO - 10.1038/srep00032 ID - Abbasi2011 ER - TY - JOUR AU - Abbasi, A. A. AU - Goode, D. K. AU - Amir, S. AU - Grzeschik, K. -. H. PY - 2009 DA - 2009// TI - Evolution and functional diversification of the GLI family of transcription factors in vertebrates JO - Evol Bioinforma VL - 5 UR - https://doi.org/10.4137/EBO.S2322 DO - 10.4137/EBO.S2322 ID - Abbasi2009 ER - TY - JOUR AU - Punta, M. AU - Coggill, P. C. AU - Eberhardt, R. Y. AU - Mistry, J. AU - Tate, J. AU - Boursnell, C. PY - 2011 DA - 2011// TI - The Pfam protein families database JO - Nucleic Acids Res VL - 40 UR - https://doi.org/10.1093/nar/gkr1065 DO - 10.1093/nar/gkr1065 ID - Punta2011 ER - TY - JOUR AU - Pagni, M. AU - Ioannidis, V. AU - Cerutti, L. AU - Zahn-Zabal, M. AU - Jongeneel, C. V. AU - Falquet, L. PY - 2004 DA - 2004// TI - MyHits: a new interactive resource for protein annotation and domain identification JO - Nucleic Acids Res VL - 32 UR - https://doi.org/10.1093/nar/gkh479 DO - 10.1093/nar/gkh479 ID - Pagni2004 ER - TY - JOUR AU - Bett, J. S. AU - Ritorto, M. S. AU - Ewan, R. AU - Jaffray, E. G. AU - Virdee, S. AU - Chin, J. W. PY - 2015 DA - 2015// TI - Ubiquitin C-terminal hydrolases cleave isopeptide-and peptide-linked ubiquitin from structured proteins but do not edit ubiquitin homopolymers JO - Biochem J VL - 466 UR - https://doi.org/10.1042/BJ20141349 DO - 10.1042/BJ20141349 ID - Bett2015 ER - TY - JOUR AU - Konya, C. AU - Hatanaka, Y. AU - Fujiwara, Y. AU - Uchida, K. AU - Nagai, Y. AU - Wada, K. PY - 2011 DA - 2011// TI - Parkinson’s disease-associated mutations in α-synuclein and UCH-L1 inhibit the unconventional secretion of UCH-L1 JO - Neurochem Int VL - 59 UR - https://doi.org/10.1016/j.neuint.2011.05.012 DO - 10.1016/j.neuint.2011.05.012 ID - Konya2011 ER - TY - JOUR AU - Liu, Z. AU - Meray, R. K. AU - Grammatopoulos, T. N. AU - Fredenburg, R. A. AU - Cookson, M. R. AU - Liu, Y. PY - 2009 DA - 2009// TI - Membrane-associated farnesylated UCH-L1 promotes α-synuclein neurotoxicity and is a therapeutic target for Parkinson's disease JO - Proc Natl Acad Sci VL - 106 UR - https://doi.org/10.1073/pnas.0806474106 DO - 10.1073/pnas.0806474106 ID - Liu2009 ER - TY - JOUR AU - Ortlund, E. A. AU - Bridgham, J. T. AU - Redinbo, M. R. AU - Thornton, J. W. PY - 2007 DA - 2007// TI - Crystal structure of an ancient protein: evolution by conformational epistasis JO - Science. VL - 317 UR - https://doi.org/10.1126/science.1142819 DO - 10.1126/science.1142819 ID - Ortlund2007 ER - TY - JOUR AU - Lim, K. -. L. AU - Tan, J. M. PY - 2007 DA - 2007// TI - Role of the ubiquitin proteasome system in Parkinson's disease JO - BMC Biochem VL - 8 UR - https://doi.org/10.1186/1471-2091-8-1 DO - 10.1186/1471-2091-8-1 ID - Lim2007 ER - TY - JOUR AU - Szklarczyk, D. AU - Morris, J. H. AU - Cook, H. AU - Kuhn, M. AU - Wyder, S. AU - Simonovic, M. PY - 2016 DA - 2016// TI - The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible JO - Nucleic Acids Res VL - 1 ID - Szklarczyk2016 ER - TY - JOUR AU - Trempe, J. -. F. AU - Sauvé, V. AU - Grenier, K. AU - Seirafi, M. AU - Tang, M. Y. AU - Ménade, M. PY - 2013 DA - 2013// TI - Structure of parkin reveals mechanisms for ubiquitin ligase activation JO - Science. VL - 340 UR - https://doi.org/10.1126/science.1237908 DO - 10.1126/science.1237908 ID - Trempe2013 ER - TY - JOUR AU - Ciechanover, A. AU - Kwon, Y. T. PY - 2015 DA - 2015// TI - Degradation of misfolded proteins in neurodegenerative diseases: therapeutic targets and strategies JO - Exp Mol Med VL - 47 UR - https://doi.org/10.1038/emm.2014.117 DO - 10.1038/emm.2014.117 ID - Ciechanover2015 ER - TY - JOUR AU - Sulistio, Y. A. AU - Heese, K. PY - 2016 DA - 2016// TI - The ubiquitin-proteasome system and molecular chaperone deregulation in Alzheimer’s disease JO - Mol Neurobiol VL - 53 UR - https://doi.org/10.1007/s12035-014-9063-4 DO - 10.1007/s12035-014-9063-4 ID - Sulistio2016 ER - TY - JOUR AU - Huang, Q. AU - Figueiredo-Pereira, M. E. PY - 2010 DA - 2010// TI - Ubiquitin/proteasome pathway impairment in neurodegeneration: therapeutic implications JO - Apoptosis. VL - 15 UR - https://doi.org/10.1007/s10495-010-0466-z DO - 10.1007/s10495-010-0466-z ID - Huang2010 ER - TY - JOUR AU - Schwartz, A. L. AU - Ciechanover, A. PY - 2009 DA - 2009// TI - Targeting proteins for destruction by the ubiquitin system: implications for human pathobiology JO - Annu Rev Pharmacol Toxicol VL - 49 UR - https://doi.org/10.1146/annurev.pharmtox.051208.165340 DO - 10.1146/annurev.pharmtox.051208.165340 ID - Schwartz2009 ER - TY - JOUR AU - Tramutola, A. AU - Domenico, F. AU - Barone, E. AU - Perluigi, M. AU - Butterfield, D. A. PY - 2016 DA - 2016// TI - It is all about (U) biquitin: role of altered ubiquitin-proteasome system and UCHL1 in Alzheimer disease JO - Oxidative Med Cell Longev VL - 2016 UR - https://doi.org/10.1155/2016/2756068 DO - 10.1155/2016/2756068 ID - Tramutola2016 ER - TY - JOUR AU - Gadhave, K. AU - Bolshette, N. AU - Ahire, A. AU - Pardeshi, R. AU - Thakur, K. AU - Trandafir, C. PY - 2016 DA - 2016// TI - The ubiquitin proteasomal system: a potential target for the management of Alzheimer's disease JO - J Cell Mol Med VL - 20 UR - https://doi.org/10.1111/jcmm.12817 DO - 10.1111/jcmm.12817 ID - Gadhave2016 ER - TY - JOUR AU - McNaught, K. S. P. AU - Jenner, P. PY - 2001 DA - 2001// TI - Proteasomal function is impaired in substantia nigra in Parkinson's disease JO - Neurosci Lett VL - 297 UR - https://doi.org/10.1016/S0304-3940(00)01701-8 DO - 10.1016/S0304-3940(00)01701-8 ID - McNaught2001 ER - TY - JOUR AU - Ma, S. AU - Attarwala, I. Y. AU - Xie, X. -. Q. PY - 2019 DA - 2019// TI - SQSTM1/p62: a potential target for neurodegenerative disease JO - ACS Chem Neurosci VL - 10 UR - https://doi.org/10.1021/acschemneuro.8b00516 DO - 10.1021/acschemneuro.8b00516 ID - Ma2019 ER - TY - JOUR AU - Kyratzi, E. AU - Pavlaki, M. AU - Stefanis, L. PY - 2008 DA - 2008// TI - The S18Y polymorphic variant of UCH-L1 confers an antioxidant function to neuronal cells JO - Hum Mol Genet VL - 17 UR - https://doi.org/10.1093/hmg/ddn115 DO - 10.1093/hmg/ddn115 ID - Kyratzi2008 ER - TY - JOUR AU - Bishop, P. AU - Rocca, D. AU - Henley, J. M. PY - 2016 DA - 2016// TI - Ubiquitin C-terminal hydrolase L1 (UCH-L1): structure, distribution and roles in brain function and dysfunction JO - Biochem J VL - 473 UR - https://doi.org/10.1042/BCJ20160082 DO - 10.1042/BCJ20160082 ID - Bishop2016 ER - TY - JOUR AU - Kim, H. -. J. AU - Kim, H. J. AU - Jeong, J. -. E. AU - Baek, J. Y. AU - Jeong, J. AU - Kim, S. PY - 2014 DA - 2014// TI - N-terminal truncated UCH-L1 prevents Parkinson's disease associated damage JO - PLoS One VL - 9 UR - https://doi.org/10.1371/journal.pone.0099654 DO - 10.1371/journal.pone.0099654 ID - Kim2014 ER - TY - JOUR AU - Sułkowska, J. I. AU - Rawdon, E. J. AU - Millett, K. C. AU - Onuchic, J. N. AU - Stasiak, A. PY - 2012 DA - 2012// TI - Conservation of complex knotting and slipknotting patterns in proteins JO - Proc Natl Acad Sci U S A VL - 109 UR - https://doi.org/10.1073/pnas.1205918109 DO - 10.1073/pnas.1205918109 ID - Sułkowska2012 ER - TY - JOUR AU - Bishop, P. AU - Rubin, P. AU - Thomson, A. R. AU - Rocca, D. AU - Henley, J. M. PY - 2014 DA - 2014// TI - The ubiquitin C-terminal hydrolase L1 (UCH-L1) C terminus plays a key role in protein stability, but its farnesylation is not required for membrane association in primary neurons JO - J Biol Chem VL - 289 UR - https://doi.org/10.1074/jbc.M114.557124 DO - 10.1074/jbc.M114.557124 ID - Bishop2014 ER - TY - JOUR AU - Zerbino, D. R. AU - Achuthan, P. AU - Akanni, W. AU - Amode, M. R. AU - Barrell, D. AU - Bhai, J. PY - 2017 DA - 2017// TI - Ensembl 2018 JO - Nucleic Acids Res VL - 46 UR - https://doi.org/10.1093/nar/gkx1098 DO - 10.1093/nar/gkx1098 ID - Zerbino2017 ER - TY - JOUR AU - Wheeler, D. L. AU - Barrett, T. AU - Benson, D. A. AU - Bryant, S. H. AU - Canese, K. AU - Chetvernin, V. PY - 2007 DA - 2007// TI - Database resources of the national center for biotechnology information JO - Nucleic Acids Res VL - 36 UR - https://doi.org/10.1093/nar/gkm1000 DO - 10.1093/nar/gkm1000 ID - Wheeler2007 ER - TY - JOUR AU - Altschul, S. F. AU - Gish, W. AU - Miller, W. AU - Myers, E. W. AU - Lipman, D. J. PY - 1990 DA - 1990// TI - Basic local alignment search tool JO - J Mol Biol VL - 215 UR - https://doi.org/10.1016/S0022-2836(05)80360-2 DO - 10.1016/S0022-2836(05)80360-2 ID - Altschul1990 ER - TY - JOUR AU - Pervaiz, N. AU - Shakeel, N. AU - Qasim, A. AU - Zehra, R. AU - Anwar, S. AU - Rana, N. PY - 2019 DA - 2019// TI - Evolutionary history of the human multigene families reveals widespread gene duplications throughout the history of animals JO - BMC Evol Biol VL - 19 UR - https://doi.org/10.1186/s12862-019-1441-0 DO - 10.1186/s12862-019-1441-0 ID - Pervaiz2019 ER - TY - JOUR AU - Seemab, S. AU - Pervaiz, N. AU - Zehra, R. AU - Anwar, S. AU - Bao, Y. AU - Abbasi, A. A. PY - 2019 DA - 2019// TI - Molecular evolutionary and structural analysis of familial exudative vitreoretinopathy associated FZD4 gene JO - BMC Evol Biol VL - 19 UR - https://doi.org/10.1186/s12862-019-1400-9 DO - 10.1186/s12862-019-1400-9 ID - Seemab2019 ER - TY - JOUR AU - Saitou, N. AU - Nei, M. PY - 1987 DA - 1987// TI - The neighbor-joining method: a new method for reconstructing phylogenetic trees JO - Mol Biol Evol VL - 4 ID - Saitou1987 ER - TY - JOUR AU - Russo, C. PY - 1997 DA - 1997// TI - Efficiencies of different statistical tests in supporting a known vertebrate phylogeny JO - Mol Biol Evol VL - 14 UR - https://doi.org/10.1093/oxfordjournals.molbev.a025714 DO - 10.1093/oxfordjournals.molbev.a025714 ID - Russo1997 ER - TY - JOUR AU - Tamura, K. AU - Nei, M. AU - Kumar, S. PY - 2004 DA - 2004// TI - Prospects for inferring very large phylogenies by using the neighbor-joining method JO - Proc Natl Acad Sci U S A VL - 101 UR - https://doi.org/10.1073/pnas.0404206101 DO - 10.1073/pnas.0404206101 ID - Tamura2004 ER - TY - JOUR AU - Whelan, S. AU - Goldman, N. PY - 2001 DA - 2001// TI - A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach JO - Mol Biol Evol VL - 18 UR - https://doi.org/10.1093/oxfordjournals.molbev.a003851 DO - 10.1093/oxfordjournals.molbev.a003851 ID - Whelan2001 ER - TY - JOUR AU - Felsenstein, J. PY - 1985 DA - 1985// TI - Confidence limits on phylogenies: an approach using the bootstrap JO - Evolution. VL - 39 UR - https://doi.org/10.1111/j.1558-5646.1985.tb00420.x DO - 10.1111/j.1558-5646.1985.tb00420.x ID - Felsenstein1985 ER - TY - JOUR AU - Goldman, N. AU - Yang, Z. PY - 1994 DA - 1994// TI - A codon-based model of nucleotide substitution for protein-coding DNA sequences JO - Mol Biol Evol VL - 11 ID - Goldman1994 ER - TY - JOUR AU - Sievers, F. AU - Wilm, A. AU - Dineen, D. AU - Gibson, T. J. AU - Karplus, K. AU - Li, W. PY - 2011 DA - 2011// TI - Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal omega JO - Mol Syst Biol VL - 7 UR - https://doi.org/10.1038/msb.2011.75 DO - 10.1038/msb.2011.75 ID - Sievers2011 ER - TY - JOUR AU - Grantham, R. PY - 1974 DA - 1974// TI - Amino acid difference formula to help explain protein evolution JO - Science. VL - 185 UR - https://doi.org/10.1126/science.185.4154.862 DO - 10.1126/science.185.4154.862 ID - Grantham1974 ER - TY - JOUR AU - Betts, M. J. AU - Russell, R. B. PY - 2003 DA - 2003// TI - Amino acid properties and consequences of substitutions JO - Bioinformatics Genet VL - 1 UR - https://doi.org/10.1002/0470867302.ch14 DO - 10.1002/0470867302.ch14 ID - Betts2003 ER - TY - JOUR AU - Berman, H. M. AU - Westbrook, J. AU - Feng, Z. AU - Gilliland, G. AU - Bhat, T. N. AU - Weissig, H. PY - 2000 DA - 2000// TI - The protein data Bank JO - Nucleic Acids Res VL - 28 UR - https://doi.org/10.1093/nar/28.1.235 DO - 10.1093/nar/28.1.235 ID - Berman2000 ER - TY - JOUR AU - Webb, B. AU - Sali, A. PY - 2014 DA - 2014// TI - Comparative protein structure modeling using MODELLER JO - Curr Protoc Bioinformatics VL - 47 UR - https://doi.org/10.1002/0471250953.bi0506s47 DO - 10.1002/0471250953.bi0506s47 ID - Webb2014 ER - TY - JOUR AU - Krieger, E. AU - Joo, K. AU - Lee, J. AU - Lee, J. AU - Raman, S. AU - Thompson, J. PY - 2009 DA - 2009// TI - Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: four approaches that performed well in CASP8 JO - Proteins VL - 77 UR - https://doi.org/10.1002/prot.22570 DO - 10.1002/prot.22570 ID - Krieger2009 ER - TY - JOUR AU - Lovell, S. C. AU - Davis, I. W. AU - Arendall, W. B. AU - Bakker, P. I. AU - Word, J. M. AU - Prisant, M. G. PY - 2003 DA - 2003// TI - Structure validation by Cα geometry: ϕ, ψ and Cβ deviation JO - Proteins VL - 50 UR - https://doi.org/10.1002/prot.10286 DO - 10.1002/prot.10286 ID - Lovell2003 ER - TY - JOUR AU - Colovos, C. PY - 1993 DA - 1993// TI - Verification of protein structures: patterns of nonbonded atomic interactions JO - Protein Sci VL - 2 UR - https://doi.org/10.1002/pro.5560020916 DO - 10.1002/pro.5560020916 ID - Colovos1993 ER - TY - JOUR AU - Cheng, J. AU - Randall, A. AU - Baldi, P. PY - 2006 DA - 2006// TI - Prediction of protein stability changes for single-site mutations using support vector machines JO - Proteins VL - 62 UR - https://doi.org/10.1002/prot.20810 DO - 10.1002/prot.20810 ID - Cheng2006 ER - TY - JOUR AU - Yang, J. AU - Zhang, Y. PY - 2015 DA - 2015// TI - I-TASSER server: new development for protein structure and function predictions JO - Nucleic Acids Res VL - 43 UR - https://doi.org/10.1093/nar/gkv342 DO - 10.1093/nar/gkv342 ID - Yang2015 ER - TY - JOUR AU - Pettersen, E. F. AU - Goddard, T. D. AU - Huang, C. C. AU - Couch, G. S. AU - Greenblatt, D. M. AU - Meng, E. C. PY - 2004 DA - 2004// TI - UCSF chimera—a visualization system for exploratory research and analysis JO - J Comput Chem VL - 25 UR - https://doi.org/10.1002/jcc.20084 DO - 10.1002/jcc.20084 ID - Pettersen2004 ER - TY - JOUR AU - Comeau, S. R. AU - Gatchell, D. W. AU - Vajda, S. AU - Camacho, C. J. PY - 2004 DA - 2004// TI - ClusPro: a fully automated algorithm for protein–protein docking JO - Nucleic Acids Res VL - 32 UR - https://doi.org/10.1093/nar/gkh354 DO - 10.1093/nar/gkh354 ID - Comeau2004 ER - TY - JOUR AU - Wallace, A. C. AU - Laskowski, R. A. AU - Thornton, J. M. PY - 1995 DA - 1995// TI - LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions JO - Protein Eng Des Sel VL - 8 UR - https://doi.org/10.1093/protein/8.2.127 DO - 10.1093/protein/8.2.127 ID - Wallace1995 ER - TY - BOOK AU - DeLano, W. PY - 2010 DA - 2010// TI - The PyMOL molecular graphics system, version 1.3 r1. Schrödinger, LLC, New York ID - DeLano2010 ER -