Research
Energy-Based Models for Atomic-Resolution Protein Conformations
April 25, 2020
Abstract
We propose an energy-based model (EBM) of protein conformations that operates at atomic scale. The model is trained solely on crystallized protein data. By contrast, existing approaches for scoring conformations use energy functions that incorporate knowledge of physical principles and features that are the complex product of several decades of research and tuning. To evaluate the model, we benchmark on the rotamer recovery task, the problem of predicting the conformation of a side chain from its context within a protein structure, which has been used to evaluate energy functions for protein design. The model achieves performance close to that of the Rosetta energy function, a state-of-the-art method widely used in protein structure prediction and design. An investigation of the model’s outputs and hidden representations finds that it captures physicochemical properties relevant to protein energy.
AUTHORS
Written by
Yilun Du
Joshua Meier
Jerry Ma
Rob Fergus
Alexander Rives
Publisher
International Conference on Learning Representations (ICLR)
Recent Publications
April 16, 2026
AIRA₂: Overcoming Bottlenecks in AI Research Agents
Karen Hambardzumyan, Nicolas Baldwin, Edan Toledo, Rishi Hazra, Michael Kuchnik, Bassel Al Omari, Thomas Simon Foster, Anton Protopopov, Jean-Christophe Gagnon-Audet, Ishita Mediratta, Kelvin Niu, Michael Shvartsman, Alisia Lupidi, Alexis Audran-Reiss, Parth Pathak, Tatiana Shavrina, Despoina Magka, Hela Momand, Derek Dunfield, Nicola Cancedda, Pontus Stenetorp, Carole-Jean Wu, Jakob Foerster, Yoram Bachrach, Martin Josifoski
April 16, 2026
March 17, 2026
NLP
Omnilingual MT: Machine Translation for 1,600 Languages
Omnilingual MT Team, Belen Alastruey, Niyati Bafna, Andrea Caciolai, Kevin Heffernan, Artyom Kozhevnikov, Christophe Ropers, Eduardo Sánchez, Charles-Eric Saint-James, Ioannis Tsiamas, Chierh CHENG, Joe Chuang, Paul-Ambroise Duquenne, Mark Duppenthaler, Nate Ekberg, Cynthia Gao, Pere Lluís Huguet Cabot, João Maria Janeiro, Jean Maillard, Gabriel Mejia Gonzalez, Holger Schwenk, Edan Toledo, Arina Turkatenko, Albert Ventayol-Boada, Rashel Moritz, Alexandre Mourachko, Surya Parimi, Mary Williamson, Shireen Yates, David Dale, Marta R. Costa-jussa
March 17, 2026
March 17, 2026
Speech & Audio
Omnilingual SONAR: Cross-Lingual and Cross-Modal Sentence Embeddings Bridging Massively Multilingual Text and Speech
Omnilingual SONAR Team, João Maria Janeiro, Pere Lluís Huguet Cabot, Ioannis Tsiamas, Yen Meng, Vivek Iyer, Guillem Ramirez, Loic Barrault, Belen Alastruey, Yu-An Chung, Marta R. Costa-jussa, David Dale, Kevin Heffernan, Jaehyeong Jo, Artyom Kozhevnikov, Alexandre Mourachko, Christophe Ropers, Holger Schwenk, Paul-Ambroise Duquenne
March 17, 2026
February 27, 2026
Human & Machine Intelligence
Unified Vision–Language Modeling via Concept Space Alignment
Yifu Qiu, Paul-Ambroise Duquenne, Holger Schwenk
February 27, 2026
October 31, 2019
NLP
Facebook AI's WAT19 Myanmar-English Translation Task Submission
Peng-Jen Chen, Jiajun Shen, Matt Le, Vishrav Chaudhary, Ahmed El-Kishky, Guillaume Wenzek, Myle Ott, Marc’Aurelio Ranzato
October 31, 2019
October 27, 2019
Order-Aware Generative Modeling Using the 3D-Craft Dataset | Facebook AI Research
Zhuoyuan Chen, Demi Guo, Tong Xiao, Saining Xie, Xinlei Chen, Haonan Yu, Jonathan Gray, Kavya Srinet, Haoqi Fan, Jerry Ma, Charles R. Qi, Shubham Tulsiani, Arthur Szlam, Larry Zitnick
October 27, 2019
April 25, 2020
Energy-Based Models for Atomic-Resolution Protein Conformations | Facebook AI Research
Yilun Du, Joshua Meier, Jerry Ma, Rob Fergus, Alexander Rives
April 25, 2020
June 11, 2019
Computer Vision
ELF OpenGo: An Analysis and Open Reimplementation of AlphaZero | Facebook AI Research
Yuandong Tian, Jerry Ma, Qucheng Gong, Shubho Sengupta, Zhuoyuan Chen, James Pinkerton, Larry Zitnick
June 11, 2019
Help Us Pioneer The Future of AI
We share our open source frameworks, tools, libraries, and models for everything from research exploration to large-scale production deployment.
Our approach
Latest news
Foundational models
Meta © 2026