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The Boltzmann distribution of a protein provides a roadmap to all of its functional states.
Protein structure comparison by alignment of distance matrices
Liisa Holm and Chris Sander · 1993
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The third igg-binding domain from streptococcal protein g. an analysis by x-ray crystallography of the structure alone and in a complex with fab
Jeremy P. Derrick and Dale B. Wigley · 1994
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Atomic-level characterization of the structural dynamics of proteins
David E. Shaw, Paul Maragakis, Kresten Lindorff-Larsen, Stafano Piana, Ron O. Dror, Michael P. Eastwood, Joseph A. Bank, John M. Jumper, John K. Salmon, and Willy Wriggers · 2010
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Simple few-state models reveal hidden complexity in protein folding
Kyle A. Beauchamp, Robert McGibbon, Yu-Shan Lin, and Vijay S. Pande · 2012
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Amber 14, 2014
D. A. Case, V. Babin, J. T. Berryman, R. M. Betz, Q. Cai, D.S. Cerutti, T.E. Cheatham III, T.A. Darden, R. E. Duke, H. Gohlke, A. W. Goetz, S. Gusarov, N. Homeyer, P. Janowski, J. Kaus, I. Kolossváry, A. Kovalenko, T. S. Lee, S. LeGrand, T. Luchko, R. Luo, B. Madej, K. M. Merz, F. Paesani, D. R. Roe, A. Roitberg, C. Sagui, R. Salomon-Ferrer, G. Seabra, C. L. Simmerling, W. Smith, J. Swails, R. C. Walker, J. Wang, R. M. Wolf, X. Wu, and P. A. Kollman · 2014
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Variational inference with normalizing flows
Danilo Rezende and Shakir Mohamed · 2015
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Internal coordinate molecular dynamics: A foundation for multiscale dynamics
Nagarajan Vaidehi and Abhinandan Jain · 2015
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Effective sample size for importance sampling based on discrepancy measures
Luca Martino, Víctor Elvira, and Francisco Louzada · 2016
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Density estimation using real nvp
Laurent Dinh, Jascha Sohl-Dickstein, and Samy Bengio · 2017
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Gans trained by a two time-scale update rule converge to a local nash equilibrium
Martin Heusel, Hubert Ramsauer, Thomas Unterthiner, Bernhard Nessler, and Sepp Hochreiter · 2017
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Searching for activation functions, 2017
Prajit Ramachandran, Barret Zoph, and Quoc V. Le · 2017
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Principal component analysis on a torus: Theory and application to protein dynamics
Florian Sittel, Thomas Filk, and Gerhard Stock · 2017
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Umap: Uniform manifold approximation and projection
Leland McInnes, John Healy, Nathaniel Saul, and Lukas Grossberger · 2018
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Peter Shaw, Jakob Uszkoreit, and Ashish Vaswani · 2018
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Tensor field networks: Rotation- and translation-equivariant neural networks for 3d point clouds, 2018
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Relaxing bijectivity constraints with continuously indexed normalising flows, 2019
Rob Cornish, Anthony L. Caterini, George Deligiannidis, and Arnaud Doucet · 2019
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Neural spline flows
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Protein tertiary structure modeling driven by deep learning and contact distance prediction in casp13
Jie Hou, Tianqi Wu, Renzhi Cao, and Jianlin Cheng · 2019
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Transformers without tears: Improving the normalization of self-attention
Toan Q. Nguyen and Julian Salazar · 2019
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Boltzmann generators: Sampling equilibrium states of many-body systems with deep learning
Frank Noé, Simon Olsson, Jonas Köhler, and Hao Wu · 2019
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Protein structure prediction using multiple deep neural networks in the 13th critical assessment of protein structure prediction (casp13)
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, Karen Simonyan, Steve Crossan, Pushmeet Kohli, David T. Jones, David Silver, Koray Kavukcuoglu, and Demis Hassabis · 2019
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Temperature steerable flows and boltzmann generators
Manuel Dibak, Leon Klein, Andreas Krämer, and Frank Noé · 2022
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Transformer quality in linear time, 2022
Weizhe Hua, Zihang Dai, Hanxiao Liu, and Quoc V. Le · 2022
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Topological data analysis gives two folding paths in hp35(nle-nle), double mutant of villin headpiece subdomain
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Skipping the replica exchange ladder with normalizing flows
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Torsional diffusion for molecular conformer generation
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Flow-matching – efficient coarse-graining molecular dynamics without forces
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Analysis of distance-based protein structure prediction by deep learning in casp13
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A unified approach to protein domain parsing with inter-residue distance matrix
Kun Zhu, Hong Su, Zhenling Peng, and Jianyi Yang · 2019
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Using dali for protein structure comparison
Liisa Holm · 2020
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Exploring the limits of transfer learning with a unified text-to-text transformer, 2020
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Normalizing flows on tori and spheres
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Stochastic normalizing flows
Hao Wu, Jonas Köhler, and Frank Noé · 2020
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Densely connected normalizing flows, 2021
Matej Grcić, Ivan Grubišić, and Siniša Šegvić · 2021
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Jonas Köhler, Yaoyi Chen, Andreas Krämer, Cecilia Clementi, and Frank Noé · 2022
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Accurate sampling of macromolecular conformations using adaptive deep learning and coarse-grained representation
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Flow annealed importance sampling bootstrap
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From data to noise to data for mixing physics across temperatures with generative artificial intelligence
Yihang Wang, Lukas Herron, and Pratyush Tiwary · 2022
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Normalizing flows for atomic solids
Peter Wirnsberger, George Papamakarios, Borja Ibarz, Sébastien Racanière, Andrew J. Ballard, Alexander Pritzel, and Charles Blundell · 2022
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Protein structure generation via folding diffusion
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Simulate time-integrated coarse-grained molecular dynamics with multi-scale graph networks
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Learning correlations between internal coordinates to improve 3d cartesian coordinates for proteins
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Mega: Moving average equipped gated attention, 2023
Xuezhe Ma, Chunting Zhou, Xiang Kong, Junxian He, Liangke Gui, Graham Neubig, Jonathan May, and Luke Zettlemoyer · 2023
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Se(3) equivariant augmented coupling flows, 2023
Laurence I. Midgley, Vincent Stimper, Javier Antorán, Emile Mathieu, Bernhard Schölkopf, and José Miguel Hernández-Lobato · 2023
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