no code implementations • 13 Dec 2024 • Peng Tao, Kazuyuki Aihara, Luonan Chen
To address this issue, inspired by possibly chaotic dynamics of real brain learning, we introduce a chaotic training algorithm, i. e. chaotic graph backpropagation (CGBP), which introduces a local loss function in GNN that makes the training process not only chaotic but also highly efficient.
no code implementations • 23 Jul 2024 • Rommie Amaro, Johan Åqvist, Ivet Bahar, Federica Battistini, Adam Bellaiche, Daniel Beltran, Philip C. Biggin, Massimiliano Bonomi, Gregory R. Bowman, Richard Bryce, Giovanni Bussi, Paolo Carloni, David Case, Andrea Cavalli, Chie-En A. Chang, Thomas E. Cheatham III, Margaret S. Cheung, Cris Chipot, Lillian T. Chong, Preeti Choudhary, Gerardo Andres Cisneros, Cecilia Clementi, Rosana Collepardo-Guevara, Peter Coveney, Roberto Covino, T. Daniel Crawford, Matteo Dal Peraro, Bert de Groot, Lucie Delemotte, Marco De Vivo, Jonathan Essex, Franca Fraternali, Jiali Gao, Josep Lluís Gelpí, Francesco Luigi Gervasio, Fernando Danilo Gonzalez-Nilo, Helmut Grubmüller, Marina Guenza, Horacio V. Guzman, Sarah Harris, Teresa Head-Gordon, Rigoberto Hernandez, Adam Hospital, Niu Huang, Xuhui Huang, Gerhard Hummer, Javier Iglesias-Fernández, Jan H. Jensen, Shantenu Jha, Wanting Jiao, William L. Jorgensen, Shina Caroline Lynn Kamerlin, Syma Khalid, Charles Laughton, Michael Levitt, Vittorio Limongelli, Erik Lindahl, Kresten Lindorff-Larsen, Sharon Loverde, Magnus Lundborg, Yun Lyna Luo, Francisco Javier Luque, Charlotte I. Lynch, Alexander MacKerell, Alessandra Magistrato, Siewert J. Marrink, Hugh Martin, J. Andrew McCammon, Kenneth Merz, Vicent Moliner, Adrian Mulholland, Sohail Murad, Athi N. Naganathan, Shikha Nangia, Frank Noe, Agnes Noy, Julianna Oláh, Megan O'Mara, Mary Jo Ondrechen, José N. Onuchic, Alexey Onufriev, Silvia Osuna, Anna R. Panchenko, Sergio Pantano, Carol Parish, Michele Parrinello, Alberto Perez, Tomas Perez-Acle, Juan R. Perilla, B. Montgomery Pettitt, Adriana Pietropalo, Jean-Philip Piquemal, Adolfo Poma, Matej Praprotnik, Maria J. Ramos, Pengyu Ren, Nathalie Reuter, Adrian Roitberg, Edina Rosta, Carme Rovira, Benoit Roux, Ursula Röthlisberger, Karissa Y. Sanbonmatsu, Tamar Schlick, Alexey K. Shaytan, Carlos Simmerling, Jeremy C. Smith, Yuji Sugita, Katarzyna Świderek, Makoto Taiji, Peng Tao, D. Peter Tieleman, Irina G. Tikhonova, Julian Tirado-Rives, Inaki Tunón, Marc W. Van Der Kamp, David van der Spoel, Sameer Velankar, Gregory A. Voth, Rebecca Wade, Ariel Warshel, Valerie Vaissier Welborn, Stacey Wetmore, Travis J. Wheeler, Chung F. Wong, Lee-Wei Yang, Martin Zacharias, Modesto Orozco
This letter illustrates the opinion of the molecular dynamics (MD) community on the need to adopt a new FAIR paradigm for the use of molecular simulations.
1 code implementation • 2 Feb 2023 • Hao Tian, Sian Xiao, Xi Jiang, Peng Tao
One of the major challenges in allosteric drug research is the identification of allosteric sites.
1 code implementation • 27 Apr 2022 • Hao Tian, Xi Jiang, Sian Xiao, Hunter La Force, Eric C. Larson, Peng Tao
Based on this characteristic, we proposed a new adaptive sampling method, latent space assisted adaptive sampling for protein trajectories (LAST), to accelerate the exploration of protein conformational space.
1 code implementation • 26 Apr 2022 • Peng Tao, Xiaohu Hao, Jie Cheng, Luonan Chen
Making an accurate prediction of an unknown system only from a short-term time series is difficult due to the lack of sufficient information, especially in a multi-step-ahead manner.
1 code implementation • 15 Apr 2022 • Hao Tian, Rajas Ketkar, Peng Tao
The absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties are important in drug discovery as they define efficacy and safety.
Ranked #2 on
TDC ADMET Benchmarking Group
on tdcommons
1 code implementation • 22 Apr 2020 • Hao Tian, Peng Tao
Molecular dynamics (MD) simulations have been widely applied to study macromolecules including proteins.
no code implementations • 6 Feb 2020 • Qianwei Zhou, Peng Tao, Xiaoxin Li, Sheng-Yong Chen, Fan Zhang, Haigen Hu
Shape illustration images (SIIs) are common and important in describing the cross-sections of industrial products.