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The regulation of various cellular processes heavily relies on the protein complexes within a living cell, necessitating a comprehensive understanding of their three-dimensional structures to elucidate the underlying mechanisms.
The reflection of x-rays by crystals
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Molecular structure of nucleic acids: a structure for deoxyribose nucleic acid
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The dependence of cell-free protein synthesis in e. coli upon naturally occurring or synthetic polyribonucleotides
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Haddock: a protein- protein docking approach based on biochemical or biophysical information
Cyril Dominguez, Rolf Boelens, and Alexandre MJJ Bonvin · 2003
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Zdock: an initial-stage protein-docking algorithm
Rong Chen, Li Li, and Zhiping Weng · 2003
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Protein structure prediction via combinatorial assembly of sub-structural units
Yuval Inbar, Hadar Benyamini, Ruth Nussinov, and Haim J Wolfson · 2003
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Prediction of multimolecular assemblies by multiple docking
Yuval Inbar, Hadar Benyamini, Ruth Nussinov, and Haim J Wolfson · 2005
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Integrating statistical pair potentials into protein complex prediction
Julian Mintseris, Brian Pierce, Kevin Wiehe, Robert Anderson, Rong Chen, and Zhiping Weng · 2007
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The rosettadock server for local protein–protein docking
Sergey Lyskov and Jeffrey J Gray · 2008
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Protein-protein docking using region-based 3d zernike descriptors
Vishwesh Venkatraman, Yifeng D Yang, Lee Sael, and Daisuke Kihara · 2009
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Cell signaling by receptor tyrosine kinases
Mark A Lemmon and Joseph Schlessinger · 2010
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Ultra-fast fft protein docking on graphics processors
David W Ritchie and Vishwesh Venkatraman · 2010
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Protein nmr using paramagnetic ions
Gottfried Otting · 2010
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The haddock web server for data-driven biomolecular docking
Sjoerd J De Vries, Marc Van Dijk, and Alexandre MJJ Bonvin · 2010
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An integrated suite of fast docking algorithms
Efrat Mashiach, Dina Schneidman-Duhovny, Aviyah Peri, Yoli Shavit, Ruth Nussinov, and Haim J Wolfson · 2010
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Survey of public domain software for docking simulations and virtual screening
Jacek Biesiada, Aleksey Porollo, Prakash Velayutham, Michal Kouril, and Jaroslaw Meller · 2011
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Multi-lzerd: multiple protein docking for asymmetric complexes
Juan Esquivel-Rodríguez, Yifeng David Yang, and Daisuke Kihara · 2012
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Multi-lzerd: multiple protein docking for asymmetric complexes
Juan Esquivel-Rodríguez, Yifeng David Yang, and Daisuke Kihara · 2012
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Flexible docking and refinement with a coarse-grained protein model using attract
Sjoerd de Vries and Martin Zacharias · 2013
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Swarmdock: a server for flexible protein–protein docking
Mieczyslaw Torchala, Iain H Moal, Raphael AG Chaleil, Juan Fernandez-Recio, and Paul A Bates · 2013
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Swarmdock: a server for flexible protein–protein docking
Mieczyslaw Torchala, Iain H Moal, Raphael AG Chaleil, Juan Fernandez-Recio, and Paul A Bates · 2013
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Protein-protein docking: From interaction to interactome
Ilya A Vakser · 2014
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Robust absolute rotation estimation via low-rank and sparse matrix decomposition
Federica Arrigoni, Luca Magri, Beatrice Rossi, Pasqualina Fragneto, and Andrea Fusiello · 2014
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Spherical polar fourier assembly of protein complexes with arbitrary point group symmetry
Bottom-up structural proteomics: cryoem of protein complexes enriched from the cellular milieu
Chi-Min Ho, Xiaorun Li, Mason Lai, Thomas C Terwilliger, Josh R Beck, James Wohlschlegel, Daniel E Goldberg, Anthony WP Fitzpatrick, and Z Hong Zhou · 2020
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The hdock server for integrated protein–protein docking
Yumeng Yan, Huanyu Tao, Jiahua He, and Sheng-You Huang · 2020
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Learning multiview 3d point cloud registration
Zan Gojcic, Caifa Zhou, Jan D Wegner, Leonidas J Guibas, and Tolga Birdal · 2020
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Learning from protein structure with geometric vector perceptrons
Bowen Jing, Stephan Eismann, Patricia Suriana, Raphael JL Townshend, and Ron Dror · 2020
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Lzerd webserver for pairwise and multiple protein–protein docking
Charles Christoffer, Siyang Chen, Vijay Bharadwaj, Tunde Aderinwale, Vidhur Kumar, Matin Hormati, and Daisuke Kihara · 2021
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David W Ritchie and Sergei Grudinin · 2016
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Progress in protein crystallography
Zbigniew Dauter and Alexander Wlodawer · 2016
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Spectral synchronization of multiple views in se (3)
Federica Arrigoni, Beatrice Rossi, and Andrea Fusiello · 2016
Cited alongside, same era.
The cluspro web server for protein–protein docking
Dima Kozakov, David R Hall, Bing Xia, Kathryn A Porter, Dzmitry Padhorny, Christine Yueh, Dmitri Beglov, and Sandor Vajda · 2017
Cited alongside, same era.
Pseudocontact shifts in biomolecular nmr using paramagnetic metal tags
Christoph Nitsche, Gottfried Otting, et al · 2017
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Structural analysis of protein complexes by cryo electron microscopy
Tiago RD Costa, Athanasios Ignatiou, and Elena V Orlova · 2017
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Protein-protein and peptide-protein docking and refinement using attract in capri
Christina EM Schindler, Isaure Chauvot de Beauchêne, Sjoerd J de Vries, and Martin Zacharias · 2017
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Highly accurate protein structure prediction with alphafold
John Jumper, Richard Evans, Alexander Pritzel, Tim Green, Michael Figurnov, Olaf Ronneberger, Kathryn Tunyasuvunakool, Russ Bates, Augustin Žídek, Anna Potapenko, et al · 2021
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Accurate prediction of protein structures and interactions using a three-track neural network
Minkyung Baek, Frank DiMaio, Ivan Anishchenko, Justas Dauparas, Sergey Ovchinnikov, Gyu Rie Lee, Jue Wang, Qian Cong, Lisa N Kinch, R Dustin Schaeffer, et al · 2021
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Can alphafold2 predict protein-peptide complex structures accurately?
Junsu Ko and Juyong Lee · 2021
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Deeptracer for fast de novo cryo-em protein structure modeling and special studies on cov-related complexes
Jonas Pfab, Nhut Minh Phan, and Dong Si · 2021
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Fpdock: Protein–protein docking using flower pollination algorithm
Sharon Sunny and PB Jayaraj · 2021
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Lzerd webserver for pairwise and multiple protein–protein docking
Charles Christoffer, Siyang Chen, Vijay Bharadwaj, Tunde Aderinwale, Vidhur Kumar, Matin Hormati, and Daisuke Kihara · 2021
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Benchmarking of structure refinement methods for protein complex models
Jacob Verburgt and Daisuke Kihara · 2021
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Deep regression on manifolds: a 3d rotation case study
Romain Brégier · 2021
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Rl-mlzerd: Multimeric protein docking using reinforcement learning
Tunde Aderinwale, Charles Christoffer, and Daisuke Kihara · 2022
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Nature Methods
Method of the year 2021: Protein structure prediction · 2022
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Harnessing protein folding neural networks for peptide–protein docking
Tomer Tsaban, Julia K Varga, Orly Avraham, Ziv Ben-Aharon, Alisa Khramushin, and Ora Schueler-Furman · 2022
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Improved prediction of protein-protein interactions using alphafold2
Patrick Bryant, Gabriele Pozzati, and Arne Elofsson · 2022
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Independent SE(3)-equivariant models for end-to-end rigid protein docking
Octavian-Eugen Ganea, Xinyuan Huang, Charlotte Bunne, Yatao Bian, Regina Barzilay, Tommi S. Jaakkola, and Andreas Krause · 2022
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