Deciphering interaction fingerprints from protein molecular surfaces
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[1] Charles R. Cantor,et al. Annual Review of Biophysics and Bioengineering , 1972 .
[2] F M Richards,et al. Areas, volumes, packing and protein structure. , 1977, Annual review of biophysics and bioengineering.
[3] R. Doolittle,et al. A simple method for displaying the hydropathic character of a protein. , 1982, Journal of molecular biology.
[4] T. Pollard,et al. Annual review of biophysics and biophysical chemistry , 1985 .
[5] K. Sharp,et al. Electrostatic interactions in macromolecules: theory and applications. , 1990, Annual review of biophysics and biophysical chemistry.
[6] Andrea J. van Doorn,et al. Surface shape and curvature scales , 1992, Image Vis. Comput..
[7] M. Sanner,et al. Reduced surface: an efficient way to compute molecular surfaces. , 1996, Biopolymers.
[8] Patrick J. F. Groenen,et al. Modern Multidimensional Scaling: Theory and Applications , 2003 .
[9] S. Jones,et al. Prediction of protein-protein interaction sites using patch analysis. , 1997, Journal of molecular biology.
[10] J. Richardson,et al. Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. , 1999, Journal of molecular biology.
[11] Nathan A. Baker,et al. Electrostatics of nanosystems: Application to microtubules and the ribosome , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[12] Ruth Nussinov,et al. Efficient Unbound Docking of Rigid Molecules , 2002, WABI.
[13] D. Baker,et al. An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes. , 2003, Journal of molecular biology.
[14] D. Baker,et al. Computational redesign of protein-protein interaction specificity , 2004, Nature Structural &Molecular Biology.
[15] J. Skolnick,et al. TM-align: a protein structure alignment algorithm based on the TM-score , 2005, Nucleic acids research.
[16] Rita Casadio,et al. Algorithms in Bioinformatics, 5th International Workshop, WABI 2005, Mallorca, Spain, October 3-6, 2005, Proceedings , 2005, WABI.
[17] Aleksey A. Porollo,et al. Prediction‐based fingerprints of protein–protein interactions , 2006, Proteins.
[18] Gerhard Klebe,et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations , 2007, Nucleic Acids Res..
[19] Hye-Kyung Kim,et al. Crystal structure of D-erythronate-4-phosphate dehydrogenase complexed with NAD. , 2007, Journal of molecular biology.
[20] Johannes C. Hermann,et al. Structure-based activity prediction for an enzyme of unknown function , 2007, Nature.
[21] Daisuke Kihara,et al. Protein-protein docking using region-based 3D Zernike descriptors , 2009, BMC Bioinformatics.
[22] Shuangye Yin,et al. Fast screening of protein surfaces using geometric invariant fingerprints , 2009, Proceedings of the National Academy of Sciences.
[23] Gaël Varoquaux,et al. Scikit-learn: Machine Learning in Python , 2011, J. Mach. Learn. Res..
[24] Timothy A. Whitehead,et al. Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin , 2011, Science.
[25] Jens Meiler,et al. ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. , 2011, Methods in enzymology.
[26] Bruce Randall Donald,et al. Algorithms in Structural Molecular Biology , 2011 .
[27] Daisuke Kihara,et al. Molecular surface representation using 3D Zernike descriptors for protein shape comparison and docking. , 2011, Current protein & peptide science.
[28] Zhengwei Zhu,et al. CD-HIT: accelerated for clustering the next-generation sequencing data , 2012, Bioinform..
[29] B. Honig,et al. Structure-based prediction of protein-protein interactions on a genome-wide scale , 2012, Nature.
[30] Geoffrey E. Hinton,et al. ImageNet classification with deep convolutional neural networks , 2012, Commun. ACM.
[31] D. Baker,et al. Computational Design of Self-Assembling Protein Nanomaterials with Atomic Level Accuracy , 2012, Science.
[32] David Baker,et al. Computational design of ligand-binding proteins with high affinity and selectivity , 2013, Nature.
[33] M. Fleming,et al. The Crystal Structure of Six-transmembrane Epithelial Antigen of the Prostate 4 (Steap4), a Ferri/Cuprireductase, Suggests a Novel Interdomain Flavin-binding Site* , 2013, The Journal of Biological Chemistry.
[34] Elisenda Feliu,et al. Understanding protein-protein interactions using local structural features. , 2013, Journal of molecular biology.
[35] David Baker,et al. Proof of principle for epitope-focused vaccine design , 2014, Nature.
[36] U. Sauer,et al. Coordination of microbial metabolism , 2014, Nature Reviews Microbiology.
[37] Yang Zhang,et al. The I-TASSER Suite: protein structure and function prediction , 2014, Nature Methods.
[38] Ozlem Keskin,et al. PRISM: a web server and repository for prediction of protein–protein interactions and modeling their 3D complexes , 2014, Nucleic Acids Res..
[39] David G. Lowe,et al. Scalable Nearest Neighbor Algorithms for High Dimensional Data , 2014, IEEE Transactions on Pattern Analysis and Machine Intelligence.
[40] Jiye Shi,et al. SAbDab: the structural antibody database , 2013, Nucleic Acids Res..
[41] Raphael A. G. Chaleil,et al. Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2. , 2015, Journal of molecular biology.
[42] Daisuke Kihara,et al. Large-scale binding ligand prediction by improved patch-based method Patch-Surfer2.0 , 2015, Bioinform..
[43] Jimmy Ba,et al. Adam: A Method for Stochastic Optimization , 2014, ICLR.
[44] Pierre Vandergheynst,et al. Geodesic Convolutional Neural Networks on Riemannian Manifolds , 2015, 2015 IEEE International Conference on Computer Vision Workshop (ICCVW).
[45] K. Zak,et al. Structure of the Complex of Human Programmed Death 1, PD-1, and Its Ligand PD-L1. , 2015, Structure.
[46] Jie Li,et al. PDB-wide collection of binding data: current status of the PDBbind database , 2015, Bioinform..
[47] Michael J E Sternberg,et al. The Phyre2 web portal for protein modeling, prediction and analysis , 2015, Nature Protocols.
[48] D. Baker,et al. The coming of age of de novo protein design , 2016, Nature.
[49] Jonathan Masci,et al. Palmprint recognition via discriminative index learning , 2016, 2016 23rd International Conference on Pattern Recognition (ICPR).
[50] Pierre Vandergheynst,et al. Geometric Deep Learning: Going beyond Euclidean data , 2016, IEEE Signal Process. Mag..
[51] Luis Perez,et al. The Effectiveness of Data Augmentation in Image Classification using Deep Learning , 2017, ArXiv.
[52] Jonathan Masci,et al. Geometric Deep Learning on Graphs and Manifolds Using Mixture Model CNNs , 2016, 2017 IEEE Conference on Computer Vision and Pattern Recognition (CVPR).
[53] Vladlen Koltun,et al. Open3D: A Modern Library for 3D Data Processing , 2018, ArXiv.
[54] Thomas C. Northey,et al. IntPred: a structure-based predictor of protein–protein interaction sites , 2017, Bioinform..
[55] Jeffrey W. Martin,et al. OSPREY 3.0: Open-Source Protein Redesign for You, with Powerful New Features , 2018, bioRxiv.
[56] U. Sauer,et al. A Map of Protein-Metabolite Interactions Reveals Principles of Chemical Communication , 2018, Cell.
[57] Carlo Ferrari,et al. Antibody interface prediction with 3D Zernike descriptors and SVM , 2018, Bioinform..