Learning structural motif representations for efficient protein structure search
暂无分享,去创建一个
Jian Peng | Yang Liu | Jian Peng | Yang Liu | Qing Ye | Liwei Wang | Qing Ye | Liwei Wang
[1] Adam Godzik,et al. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences , 2006, Bioinform..
[2] James Philbin,et al. FaceNet: A unified embedding for face recognition and clustering , 2015, 2015 IEEE Conference on Computer Vision and Pattern Recognition (CVPR).
[3] T. N. Bhat,et al. The Protein Data Bank , 2000, Nucleic Acids Res..
[4] Martin J. Wainwright,et al. Noisy matrix decomposition via convex relaxation: Optimal rates in high dimensions , 2011, ICML.
[5] Geoffrey E. Hinton,et al. ImageNet classification with deep convolutional neural networks , 2012, Commun. ACM.
[6] D. O’Leary,et al. Secondary structure spatial conformation footprint: a novel method for fast protein structure comparison and classification , 2006, BMC Structural Biology.
[7] C Venclovas,et al. Processing and analysis of CASP3 protein structure predictions , 1999, Proteins.
[8] Lenore Cowen,et al. Matt: Local Flexibility Aids Protein Multiple Structure Alignment , 2008, PLoS Comput. Biol..
[9] P E Bourne,et al. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. , 1998, Protein engineering.
[10] Yoram Singer,et al. Adaptive Subgradient Methods for Online Learning and Stochastic Optimization , 2011, J. Mach. Learn. Res..
[11] Jianzhu Ma,et al. Protein structure alignment beyond spatial proximity , 2013, Scientific Reports.
[12] Geoffrey E. Hinton,et al. Visualizing Data using t-SNE , 2008 .
[13] Ning Ma,et al. BLAST+: architecture and applications , 2009, BMC Bioinformatics.
[14] John Salvatier,et al. Theano: A Python framework for fast computation of mathematical expressions , 2016, ArXiv.
[15] Inbal Budowski-Tal,et al. FragBag, an accurate representation of protein structure, retrieves structural neighbors from the entire PDB quickly and accurately , 2010, Proceedings of the National Academy of Sciences.
[16] M. Karplus,et al. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .
[17] ChengXiang Zhai,et al. Text Data Management and Analysis: A Practical Introduction to Information Retrieval and Text Mining , 2016 .
[18] J. Skolnick,et al. TM-align: a protein structure alignment algorithm based on the TM-score , 2005, Nucleic acids research.
[19] P. Røgen,et al. Automatic classification of protein structure by using Gauss integrals , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[20] Yin Li,et al. Learning Deep Structure-Preserving Image-Text Embeddings , 2015, 2016 IEEE Conference on Computer Vision and Pattern Recognition (CVPR).
[21] Arne Elofsson,et al. MaxSub: an automated measure for the assessment of protein structure prediction quality , 2000, Bioinform..
[22] Marco Biasini,et al. lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests , 2013, Bioinform..
[23] Adam Zemla,et al. LGA: a method for finding 3D similarities in protein structures , 2003, Nucleic Acids Res..
[24] Adam Godzik,et al. Flexible structure alignment by chaining aligned fragment pairs allowing twists , 2003, ECCB.
[25] Yang Zhang,et al. Scoring function for automated assessment of protein structure template quality , 2004, Proteins.
[26] Peter A. Kollman,et al. AMBER: Assisted model building with energy refinement. A general program for modeling molecules and their interactions , 1981 .
[27] Jason Weston,et al. Mismatch String Kernels for SVM Protein Classification , 2002, NIPS.
[28] Steven E. Brenner,et al. SCOPe: Structural Classification of Proteins—extended, integrating SCOP and ASTRAL data and classification of new structures , 2013, Nucleic Acids Res..
[29] Martin J. Wainwright,et al. Randomized smoothing for (parallel) stochastic optimization , 2012, 2012 IEEE 51st IEEE Conference on Decision and Control (CDC).
[30] Nitish Srivastava,et al. Dropout: a simple way to prevent neural networks from overfitting , 2014, J. Mach. Learn. Res..
[31] David A. Lee,et al. CATH: comprehensive structural and functional annotations for genome sequences , 2014, Nucleic Acids Res..