Improved protein structure prediction using potentials from deep learning
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Demis Hassabis | Karen Simonyan | David T. Jones | David Silver | Andrew W. Senior | Richard Evans | John Jumper | James Kirkpatrick | Laurent Sifre | Tim Green | Chongli Qin | Augustin Žídek | Alexander W. R. Nelson | Alex Bridgland | Hugo Penedones | Stig Petersen | Steve Crossan | Pushmeet Kohli | Koray Kavukcuoglu | David T. Jones | David C. Jones | L. Sifre | K. Kavukcuoglu | D. Hassabis | A. Senior | Stig Petersen | Pushmeet Kohli | Augustin Zídek | K. Simonyan | J. Kirkpatrick | Tim Green | J. Jumper | Chongli Qin | Richard Evans | Alex Bridgland | Hugo Penedones | Steve Crossan | David Silver | A. W. R. Nelson | Augustin Žídek
[1] Marco Biasini,et al. lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests , 2013, Bioinform..
[2] David E. Kim,et al. Improved de novo structure prediction in CASP11 by incorporating coevolution information into Rosetta , 2016, Proteins.
[3] David C. Jones. Predicting novel protein folds by using FRAGFOLD , 2001, Proteins.
[4] Petr Popov,et al. Crystal structure of misoprostol bound to the labor inducer prostaglandin E2 receptor , 2018, Nature Chemical Biology.
[5] Jian Sun,et al. Deep Residual Learning for Image Recognition , 2015, 2016 IEEE Conference on Computer Vision and Pattern Recognition (CVPR).
[6] David Baker,et al. Macromolecular modeling with rosetta. , 2008, Annual review of biochemistry.
[7] T. N. Bhat,et al. The Protein Data Bank , 2000, Nucleic Acids Res..
[8] Matteo Dal Peraro,et al. A further leap of improvement in tertiary structure prediction in CASP13 prompts new routes for future assessments , 2019, Proteins.
[9] Lloyd Allison,et al. Minimum message length inference of secondary structure from protein coordinate data , 2012, Bioinform..
[10] Maria Jesus Martin,et al. Uniclust databases of clustered and deeply annotated protein sequences and alignments , 2016, Nucleic Acids Res..
[11] Thomas L. Madden,et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.
[12] C Kooperberg,et al. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. , 1997, Journal of molecular biology.
[13] A. Lesk,et al. Correlation of co-ordinated amino acid substitutions with function in viruses related to tobacco mosaic virus. , 1987, Journal of molecular biology.
[14] Yang Zhang. Protein structure prediction: when is it useful? , 2009, Current opinion in structural biology.
[15] C. Sander,et al. Direct-coupling analysis of residue coevolution captures native contacts across many protein families , 2011, Proceedings of the National Academy of Sciences.
[16] Nitish Srivastava,et al. Dropout: a simple way to prevent neural networks from overfitting , 2014, J. Mach. Learn. Res..
[17] C Venclovas,et al. Processing and analysis of CASP3 protein structure predictions , 1999, Proteins.
[18] Jinbo Xu,et al. A position-specific distance-dependent statistical potential for protein structure and functional study. , 2012, Structure.
[19] Yuan Yu,et al. TensorFlow: A system for large-scale machine learning , 2016, OSDI.
[20] Marcin J. Skwark,et al. Improved Contact Predictions Using the Recognition of Protein Like Contact Patterns , 2014, PLoS Comput. Biol..
[21] David A. Lee,et al. CATH: an expanded resource to predict protein function through structure and sequence , 2016, Nucleic Acids Res..
[22] K. Dill,et al. The Protein-Folding Problem, 50 Years On , 2012, Science.
[23] Jimin Pei,et al. An automatic method for CASP9 free modeling structure prediction assessment , 2011, Bioinform..
[24] C. D. Gelatt,et al. Optimization by Simulated Annealing , 1983, Science.
[25] Yang Zhang,et al. Ensembling multiple raw coevolutionary features with deep residual neural networks for contact‐map prediction in CASP13 , 2019, Proteins.
[26] Pushmeet Kohli,et al. Protein structure prediction using multiple deep neural networks in the 13th Critical Assessment of Protein Structure Prediction (CASP13) , 2019, Proteins.
[27] Vladlen Koltun,et al. Multi-Scale Context Aggregation by Dilated Convolutions , 2015, ICLR.
[28] David T Jones,et al. Prediction of interresidue contacts with DeepMetaPSICOV in CASP13 , 2019, Proteins.
[29] K. Dill,et al. The protein folding problem. , 1993, Annual review of biophysics.
[30] Heiga Zen,et al. WaveNet: A Generative Model for Raw Audio , 2016, SSW.
[31] Sepp Hochreiter,et al. Fast and Accurate Deep Network Learning by Exponential Linear Units (ELUs) , 2015, ICLR.
[32] Johannes Söding,et al. The HHpred interactive server for protein homology detection and structure prediction , 2005, Nucleic Acids Res..
[33] James Scott-Brown,et al. Visualization and analysis of non-covalent contacts using the Protein Contacts Atlas , 2018, Nature structural & molecular biology.
[34] David T. Jones,et al. MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins , 2014, Bioinform..
[35] Zhen Li,et al. Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model , 2016, bioRxiv.
[36] David T. Jones,et al. High precision in protein contact prediction using fully convolutional neural networks and minimal sequence features , 2018, Bioinform..
[37] W. Taylor,et al. Global fold determination from a small number of distance restraints. , 1995, Journal of molecular biology.
[38] W. Taylor,et al. Estimating polypeptideα-carbon distances from multiple sequence alignments , 1995 .
[39] D. Baker,et al. Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information , 2014, eLife.
[40] Jinbo Xu,et al. Analysis of distance-based protein structure prediction by deep learning in CASP13 , 2019, bioRxiv.
[41] Ankur Taly,et al. Axiomatic Attribution for Deep Networks , 2017, ICML.
[42] Yang Zhang,et al. Scoring function for automated assessment of protein structure template quality , 2004, Proteins.
[43] A. Tramontano,et al. Critical assessment of methods of protein structure prediction (CASP)—round IX , 2011, Proteins.
[44] A. Biegert,et al. HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment , 2011, Nature Methods.
[45] Torsten Schwede,et al. Critical assessment of methods of protein structure prediction (CASP)—Round XIII , 2019, Proteins.
[46] Kuldip K. Paliwal,et al. Sixty-five years of the long march in protein secondary structure prediction: the final stretch? , 2016, Briefings Bioinform..
[47] Yang Zhang,et al. Template‐based and free modeling of I‐TASSER and QUARK pipelines using predicted contact maps in CASP12 , 2018, Proteins.
[48] Randy J Read,et al. Evaluation of template‐based modeling in CASP13 , 2019, Proteins.
[49] Andriy Kryshtafovych,et al. Assessment of contact predictions in CASP12: Co‐evolution and deep learning coming of age , 2017, Proteins.
[50] J. Skolnick,et al. TM-align: a protein structure alignment algorithm based on the TM-score , 2005, Nucleic acids research.
[51] J. Kirkwood. Statistical Mechanics of Fluid Mixtures , 1935 .
[52] Jorge Nocedal,et al. On the limited memory BFGS method for large scale optimization , 1989, Math. Program..
[53] Ilya A Vakser,et al. Docking of protein models , 2002, Protein science : a publication of the Protein Society.
[54] Massimiliano Pontil,et al. PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments , 2012, Bioinform..
[55] Markus Gruber,et al. CCMpred—fast and precise prediction of protein residue–residue contacts from correlated mutations , 2014, Bioinform..
[56] W. Kabsch,et al. Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features , 1983, Biopolymers.