TY - JOUR AU - Ovchinnikov, S. AU - Park, H. AU - Varghese, N. AU - Huang, P. -. S. AU - Pavlopoulos, G. A. AU - Kim, D. E. PY - 2017 DA - 2017// TI - Protein structure determination using metagenome sequence data JO - Science. VL - 355 UR - https://doi.org/10.1126/science.aah4043 DO - 10.1126/science.aah4043 ID - Ovchinnikov2017 ER - TY - JOUR AU - Ayyer, K. AU - Yefanov, O. M. AU - Oberthür, D. AU - Roy-Chowdhury, S. AU - Galli, L. AU - Mariani, V. PY - 2016 DA - 2016// TI - Macromolecular diffractive imaging using imperfect crystals JO - Nature. VL - 530 UR - https://doi.org/10.1038/nature16949 DO - 10.1038/nature16949 ID - Ayyer2016 ER - TY - JOUR AU - Bai, X. -. C. AU - McMullan, G. AU - Scheres, S. H. PY - 2015 DA - 2015// TI - How cryo-EM is revolutionizing structural biology JO - Trends Biochem Sci VL - 40 UR - https://doi.org/10.1016/j.tibs.2014.10.005 DO - 10.1016/j.tibs.2014.10.005 ID - Bai2015 ER - TY - JOUR AU - Marks, D. S. AU - Hopf, T. A. AU - Sander, C. PY - 2012 DA - 2012// TI - Protein structure prediction from sequence variation JO - Nat Biotechnol VL - 30 UR - https://doi.org/10.1038/nbt.2419 DO - 10.1038/nbt.2419 ID - Marks2012 ER - TY - JOUR AU - Simons, K. T. AU - Strauss, C. AU - Baker, D. PY - 2001 DA - 2001// TI - Prospects for ab initio protein structural genomics JO - J Mol Biol VL - 306 UR - https://doi.org/10.1006/jmbi.2000.4459 DO - 10.1006/jmbi.2000.4459 ID - Simons2001 ER - TY - JOUR AU - Das, R. AU - Baker, D. PY - 2008 DA - 2008// TI - Macromolecular modeling with rosetta JO - Annu Rev Biochem VL - 77 UR - https://doi.org/10.1146/annurev.biochem.77.062906.171838 DO - 10.1146/annurev.biochem.77.062906.171838 ID - Das2008 ER - TY - JOUR AU - Baker, D. AU - Sali, A. PY - 2001 DA - 2001// TI - Protein structure prediction and structural genomics JO - Science. VL - 294 UR - https://doi.org/10.1126/science.1065659 DO - 10.1126/science.1065659 ID - Baker2001 ER - TY - JOUR AU - Bradley, P. AU - Malmström, L. AU - Qian, B. AU - Schonbrun, J. AU - Chivian, D. AU - Kim, D. E. PY - 2005 DA - 2005// TI - Free modeling with Rosetta in CASP6 JO - Proteins: Struct, Funct, Bioinformatics VL - 61 UR - https://doi.org/10.1002/prot.20729 DO - 10.1002/prot.20729 ID - Bradley2005 ER - TY - JOUR AU - Uziela, K. AU - Shu, N. AU - Wallner, B. AU - Elofsson, A. PY - 2016 DA - 2016// TI - ProQ3: improved model quality assessments using Rosetta energy terms JO - Sci Rep VL - 6 UR - https://doi.org/10.1038/srep33509 DO - 10.1038/srep33509 ID - Uziela2016 ER - TY - JOUR AU - Cao, R. AU - Bhattacharya, D. AU - Hou, J. AU - Cheng, J. PY - 2016 DA - 2016// TI - DeepQA: improving the estimation of single protein model quality with deep belief networks JO - BMC bioinformatics VL - 17 UR - https://doi.org/10.1186/s12859-016-1405-y DO - 10.1186/s12859-016-1405-y ID - Cao2016 ER - TY - JOUR AU - Kryshtafovych, A. AU - Monastyrskyy, B. AU - Fidelis, K. AU - Moult, J. AU - Schwede, T. AU - Tramontano, A. PY - 2018 DA - 2018// TI - Evaluation of the template-based modeling in CASP12 JO - Proteins: Struct, Funct, Bioinformatics VL - 86 UR - https://doi.org/10.1002/prot.25425 DO - 10.1002/prot.25425 ID - Kryshtafovych2018 ER - TY - STD TI - Yang J, Anishchenko I, Park H, Peng Z, Ovchinnikov S, Baker D. Improved protein structure prediction using predicted interresidue orientations. Proc Natl Acad Sci. 2020. ID - ref12 ER - TY - JOUR AU - Shen, M. AU - Sali, A. PY - 2006 DA - 2006// TI - Statistical potential for assessment and prediction of protein structures JO - Protein Sci VL - 15 UR - https://doi.org/10.1110/ps.062416606 DO - 10.1110/ps.062416606 ID - Shen2006 ER - TY - JOUR AU - Zhou, H. AU - Skolnick, J. PY - 2011 DA - 2011// TI - GOAP: a generalized orientation-dependent, all-atom statistical potential for protein structure prediction JO - Biophys J VL - 101 UR - https://doi.org/10.1016/j.bpj.2011.09.012 DO - 10.1016/j.bpj.2011.09.012 ID - Zhou2011 ER - TY - JOUR AU - Yan, R. AU - Xu, D. AU - Yang, J. AU - Walker, S. AU - Zhang, Y. PY - 2013 DA - 2013// TI - A comparative assessment and analysis of 20 representative sequence alignment methods for protein structure prediction JO - Sci Rep VL - 3 ID - Yan2013 ER - TY - JOUR AU - Yang, J. AU - Yan, R. AU - Roy, A. AU - Xu, D. AU - Poisson, J. AU - Zhang, Y. PY - 2015 DA - 2015// TI - The I-TASSER suite: protein structure and function prediction JO - Nat Methods VL - 12 UR - https://doi.org/10.1038/nmeth.3213 DO - 10.1038/nmeth.3213 ID - Yang2015 ER - TY - JOUR AU - Cheng, J. AU - Randall, A. Z. AU - Sweredoski, M. J. AU - Baldi, P. PY - 2005 DA - 2005// TI - SCRATCH: a protein structure and structural feature prediction server JO - Nucleic Acid Res VL - 33 UR - https://doi.org/10.1093/nar/gki396 DO - 10.1093/nar/gki396 ID - Cheng2005 ER - TY - JOUR AU - Pollastri, G. AU - Baldi, P. AU - Fariselli, P. AU - Casadio, R. PY - 2002 DA - 2002// TI - Prediction of coordination number and relative solvent accessibility in proteins JO - Proteins: Struct, Funct, Bioinformatics. VL - 47 UR - https://doi.org/10.1002/prot.10069 DO - 10.1002/prot.10069 ID - Pollastri2002 ER - TY - JOUR AU - Wang, S. AU - Sun, S. AU - Li, Z. AU - Zhang, R. AU - Xu, J. PY - 2017 DA - 2017// TI - Accurate de novo prediction of protein contact map by ultra-deep learning model JO - PLoS Comput Biol VL - 13 UR - https://doi.org/10.1371/journal.pcbi.1005324 DO - 10.1371/journal.pcbi.1005324 ID - Wang2017 ER - TY - JOUR AU - Wang, S. AU - Li, Z. AU - Yu, Y. AU - Xu, J. PY - 2017 DA - 2017// TI - Folding membrane proteins by deep transfer learning JO - Cell Syst VL - 5 UR - https://doi.org/10.1016/j.cels.2017.09.001 DO - 10.1016/j.cels.2017.09.001 ID - Wang2017 ER - TY - JOUR AU - Wang, S. AU - Sun, S. AU - Xu, J. PY - 2018 DA - 2018// TI - Analysis of deep learning methods for blind protein contact prediction in CASP12 JO - Proteins: Struct, Funct, Bioinormatics. VL - 86 UR - https://doi.org/10.1002/prot.25377 DO - 10.1002/prot.25377 ID - Wang2018 ER - TY - JOUR AU - Wang, S. AU - Li, W. AU - Zhang, R. AU - Liu, S. AU - Xu, J. PY - 2016 DA - 2016// TI - CoinFold: a web server for protein contact prediction and contact-assisted protein folding JO - Nucleic Acids Res VL - 44 UR - https://doi.org/10.1093/nar/gkw307 DO - 10.1093/nar/gkw307 ID - Wang2016 ER - TY - JOUR AU - Li, J. AU - Cao, R. AU - Cheng, J. PY - 2015 DA - 2015// TI - A large-scale conformation sampling and evaluation server for protein tertiary structure prediction and its assessment in CASP11 JO - BMC bioinformatics. VL - 16 UR - https://doi.org/10.1186/s12859-015-0775-x DO - 10.1186/s12859-015-0775-x ID - Li2015 ER - TY - JOUR AU - Zhang, Y. AU - Skolnick, J. PY - 2004 DA - 2004// TI - Scoring function for automated assessment of protein structure template quality JO - Proteins: Struct, Funct, Bioinformatics. VL - 57 UR - https://doi.org/10.1002/prot.20264 DO - 10.1002/prot.20264 ID - Zhang2004 ER - TY - JOUR AU - Zemla, A. PY - 2003 DA - 2003// TI - LGA: a method for finding 3D similarities in protein structures JO - Nucleic Acids Res VL - 31 UR - https://doi.org/10.1093/nar/gkg571 DO - 10.1093/nar/gkg571 ID - Zemla2003 ER -