Conformational Ensembles

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5 papers in the last four weeks, against 2 the four weeks before. 0.0% of all new papers.

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Latest papers 37

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Fold'EM: Direct atomic structure inference from Cryo-EM particles
Oct 1, 2026Advaith Maddipatla, Märt-Erik Mäeots, Marco Pegoraro +5Cryo-Electron Microscopy Conformational Ensembles
Institute of Science and Technology Austria · University of Zurich · Frankfurt Institute for Advanced Studies +2
Robust Biomolecular Complex Design Across Protein Conformational Landscapes
Sep 27, 2026Qingyuan Zeng, Zongqi Xu, Anglin Liu +7Conformational Ensembles Molecular Design
The Hong Kong University of Science and Technology (Guangzhou) · Southwest Minzu University · Guangzhou University of Chinese Medicine
When Riemann flows with Wasserstein: Generative Modeling of Probability Distributions on Manifolds
Sep 22, 2026Doron Haviv, Edward De Brouwer, Rishabh Anand +4Riemannian Flow Matching Data Manifold
Genentech Inc., South San Francisco, CA. · Yale University, New Haven, CT.
METALICA: METAdynamics and repLICA exchange for enhanced diffusion sampling
Sep 15, 2026Alireza Omidi, Jiajun He, Jörg Gsponer +1Markov Chain Monte Carlo Diffusion Sampling
University of British Columbia · University of Cambridge
Ensemble-Conditioned Molecular Design
Sep 14, 2026Ross Irwin, Alessandro Tibo, Jon Paul Janet +1Molecular Design Molecular Generation
Molecular AI Discovery Sciences, R&D AstraZeneca Gothenburg, Sweden · Department of Computer Science and Engineering Chalmers University of Technology and University of Gothenburg Gothenburg, Sweden
Hessian-based molecular conformation augmentation for a scalable and efficient strategy of machine learning interatomic potentials
Sep 4, 2026Bumju Kwak, Jeonghee JoInteratomic Potentials Conformational Ensembles
Independent researcher, Seoul, Republic of Korea
RAVEN: Frozen Random Graph Reservoirs with Physics-Informed Interaction Fingerprints for Protein-Ligand Binding Affinity Prediction
Aug 10, 2026Qingyang Zou, Jiaye Huang, Hangbo Xie +3Protein Structure Prediction Conformational Ensembles
School of Science, China Pharmaceutical University, Nanjing, 210009, China · School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
Temperature-Driven Sequential Modeling for the Prediction of Annual Power Conversion Efficiency Profiles of Organic Photovoltaic Materials: Douala Case Study
Aug 9, 2026Steve Cabrel Teguia Kouam, Rockefeller Rockefeller, Raoult Dabou Teukam +4Photovoltaic Conformational Ensembles
Department of Physics, Faculty of Science, University of Douala, Douala, PO. Box 24157, Littoral, Cameroon. · Division of Applied Mathematics, Faculty of Science, Stellenbosch University, Stellenbosch, South Africa. · Department of Engineering, University of Quebec in Abitibi-T´emiscamingue, Quebec, Canada. +1
Neonatal Hypoxic-ischaemic Encephalopathy Classification from the EEG and HRV Signals Using a Conformer based Masked Autoencoder
Jul 26, 2026Shuwen Yu, William P Marnane, Geraldine B. Boylan +1Electroencephalography Autoencoder Architectures
Department of Electrical & Electronic Engineering, School of Engineering and Architecture, University College Cork, Cork, Ireland · INFANT Research Centre, University College Cork, Cork, Ireland · Pediatrics and Child Health, University College Cork, Cork, Ireland
Chamaileon: Cross-Context Binder Design with Contextualized Modeling and Mixed Sampling
Jul 26, 2026Hengyuan Cao, Shizhuo Cheng, Mingxuan Liu +5Protein Design Conformational Ensembles
Zhejiang University, Hangzhou, China · Fudan University, Shanghai, China · Shanghai Institute for Advanced Study Zhejiang University, Shanghai, China +1
EnsembleEGNN: Set-Based Graph Learning for Thermodynamic Ensembles of Cyclic Peptides
Jul 23, 2026Aaron L. Feller, Kris Deibler, Maxim SecorConformational Ensembles Graph Neural Networks
Interdisciplinary Life Sciences, University of Texas at Austin, Austin, TX. · Molecular AI, Novo Nordisk, Lexington, MA.
Neural spectroscopy of AlphaFold2 reveals encoded protein conformational landscapes
Jul 17, 2026Kaustav MehtaConformational Ensembles Protein
Independent researcher, India
Neural Non-Equilibrium Hamiltonian Monte Carlo for Corrected Boltzmann Sampling
Jul 17, 2026Moxian QianMarkovian Sampling Monte Carlo
Helmholtz Institute Mainz Johannes Gutenberg University Mainz Institute of Molecular Biology (IMB) Mainz, Germany
From Monolingual to Multilingual: Evaluating Mamba for ASR in South African Languages
Jul 1, 2026Jesujoba O. Alabi, Julian Herreilers, Badr M. Abdullah +1Multilingual Automatic Speech Recognition Automatic Speech Recognition
Saarland University, Germany · Saigen, South Africa
CryoACE: An Atom-centric Framework for Accurate and Automated Model Building in Cryo-EM
Jun 30, 2026Minzhang Li, Mingrui Li, Weichen Qin +5Cryo-Electron Microscopy Conformational Ensembles
School of Information Science and Technology, ShanghaiTech University, Shanghai, China · Cellverse Co, Ltd., Shanghai, China.
Unsupervised Thermodynamics of Molecular Diffusion Models: Action-Operator Semantics and Auditable Free-Energy Readout
Jun 28, 2026Wenjie XiDiffusion Dynamics Thermodynamics
Department of Physics and HK Institute of Quantum Science & Technology, The University of Hong Kong, Pokfulam Road, Hong Kong, China
Curvature-Informed Potential Energy Surface for Protein-Ligand Binding Affinity Prediction
Jun 12, 2026Peng-Fei Sun, Chuan-Xian Ren, Hong YanConformational Ensembles Molecular Property Prediction
School of Mathematics, Sun Yat-Sen University, Guangzhou, Guangdong 510275, China · Department of Electrical Engineering, City University of Hong Kong, Hong Kong
Flexible Kernels for Protein Property Prediction
Jun 9, 2026Martin Jankowiak, Yerdos Ordabayev, Rudraksh Tuwani +4Protein Structure Prediction Protein Design
Generate Biomedicines, Somerville, MA, USA
Few-step Cofolding with All-Atom Flow Maps
Jun 7, 2026Gianluca Scarpellini, Ron Shprints, Peter Holderrieth +7Conformational Ensembles Flow Map
1Genesis Molecular AI · Massachusetts Institute of Technology · Carnegie Mellon University +2
AlloGen: Conformation-Selective Binder Generation with Differential State Scoring
Jun 3, 2026Hanqun Cao, Zachary Quinn, Aastha Pal +4Conformational Ensembles
Department of Computer Science and Engineering, The Chinese University of Hong Kong · Department of Bioengineering, University of Pennsylvania · Department of Computer and Information Science, University of Pennsylvania
Conditioned free-energy density of proteins using unbalanced solutions to constraint satisfaction problems
May 31, 2026Pratik Worah, Subhash Khot, Srinivasa VaradhanConformational Ensembles Free Energy Principle
Geometric Flow Matching for Molecular Conformation Generation via Manifold Decomposition
May 25, 2026Yunqing Liu, Yi Zhou, Wenqi FanConformational Ensembles Riemannian Flow Matching
The Hong Kong Polytechnic University Hong Kong, China
Generative Pseudo-Force Fields for Molecular Generation
May 18, 2026Stefaan Simon Pierre Hessmann, Khaled Kahouli, Stefan Gugler +4Molecular Generation Conformational Ensembles
Machine Learning Group, Technische Universität Berlin, Berlin, Germany · BIFOLD – Berlin Institute for the Foundations of Learning and Data, Berlin, Germany · Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany +6
ENSEMBITS: an alphabet of protein conformational ensembles
May 13, 2026Kaiwen Shi, Carlos OliverConformational Ensembles Protein
Department of Computer Science, Vanderbilt University · Center for AI in Protein Dynamics, Vanderbilt University · Department of Molecular Physiology and Biophysics, Vanderbilt University
Modeling Atomic Conformational Ensembles of Proteins via Test-Time Supervision of Boltz-2 on Cryo-EM Density Maps
May 11, 2026Jay Shenoy, Miro Astore, Axel Levy +3Cryo-Electron Microscopy Conformational Ensembles
Department of Computer Science Stanford University, Flatiron Institute, & SLAC National Lab Stanford, CA 94305, USA · Center for Computational Biology & Center for Computational Mathematics Flatiron Institute New York, NY 10010, USA · Department of Electrical Engineering Stanford University & SLAC National Lab Stanford, CA 94305, USA +2
FlashMol: High-Quality Molecule Generation in as Few as Four Steps
May 7, 2026Xinyuan Wei, Zian Li, Shaoheng Yan +2Molecular Generation Conformational Ensembles
Institute for Artificial Intelligence, Peking University · Yuanpei College, Peking University · School of Intelligence Science and Technology, Peking University +2
Flow Sampling: Learning to Sample from Unnormalized Densities via Denoising Conditional Processes
May 5, 2026Aaron Havens, Brian Karrer, Neta ShaulDiffusion Sampling Riemannian Manifolds
FAIR at Meta · Weizmann Institute of Science
Free Energy Surface Sampling via Reduced Flow Matching
May 1, 2026Zichen Liu, Tiejun LiFree Energy Principle Conformational Ensembles
Center for Data Science, Peking University · LMAM and School of Mathematical Sciences, Peking University · Center for Machine Learning Research, Peking University
Learning Structure, Energy, and Dynamics: A Survey of Artificial Intelligence for Protein Dynamics
Apr 28, 2026Haocheng Tang, Liang Shi, Ya-Shi Zhang +3Protein Structure Prediction Conformational Ensembles
Mila – Quebec AI Institute · University of Pittsburgh · Work conducted during an internship at Mila +4
ConforNets: Latents-Based Conformational Control in OpenFold3
Apr 20, 2026Minji Lee, Colin Kalicki, Minkyu Jeon +3Conformational Ensembles Video Latents
Department of Computer Science, Columbia University, NY, USA · Department of Systems Biology, Columbia University, NY, USA · Department of Computer Science, Princeton University, Princeton, NJ, USA
Unraveling the Mechanism of Drug Binding to SARS-CoV-2 RNA Pseudoknot with Thermodynamics-Driven Machine Learning
Apr 16, 2026Mariia Ivonina, Jakub RydzewskiMessenger Rna Conformational Ensembles
Platform of Inter/Transdisciplinary Energy Research, Kyushu University, 744, Motooka, Nishi-ku, Fukuoka 819-0395, Japan · Current address: RIKEN Center for Interdisciplinary Theoretical and Mathematical Sciences (iTHEMS), RIKEN, Wako 351-0198, Japan · Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziądzka 5, 87-100 Toruń, Poland
Inference-time optimization for experiment-grounded protein ensemble generation
Feb 27, 2026Advaith Maddipatla, Anar Rzayev, Marco Pegoraro +5Conformational Ensembles Inference-Time
Institute of Science and Technology, Austria · University of Zurich, Switzerland · Tel Hai – University of Kiryat Shmona in the Galilee, Israel +4
Categorize Early, Integrate Late: Divergent Processing Strategies in Automatic Speech Recognition
Jan 11, 2026Nathan Roll, Pranav Bhalerao, Martijn Bartelds +7Automatic Speech Recognition Inductive Bias
Stanford University
Diverse Normal Prototypes-Guided Contrastive Reconstruction for Medical Anomaly Detection
Aug 27, 2025Luhu Li, Bin Liu, Bowen Lin +3Encoders Conformational Ensembles
School of Mathematics, Shandong University, Jinan 250100, China · Department of Interventional Medicine and Minimally Invasive Oncology, The Second Qilu Hospital of Shandong University, Jinan 250033, China · Department of Neurosurgery, The Second Qilu Hospital of Shandong University,2026 Jinan 250033, China
FastCSP: Accelerated Molecular Crystal Structure Prediction with Universal Model for Atoms
Aug 4, 2025Vahe Gharakhanyan, Yi Yang, Luis Barroso-Luque +24Crystal Structure Prediction Conformational Ensembles
Fundamental AI Research at Meta · Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, PA, USA · Department of Chemistry, University of California Riverside, Riverside, CA, USA +3
PETIMOT: A Novel Framework for Inferring Protein Motions from Sparse Data Using SE(3)-Equivariant Graph Neural Networks
Mar 19, 2025Valentin Lombard, Julien Nguyen Van, Sergei Grudinin +1Protein Structure Prediction Conformational Ensembles
aDepartment of Computational, Quantitative, and Synthetic Biology (CQSB), UMR 7238 IBPS, Sorbonne Universit´e, CNRS Paris, 75005, France · cUniv. Grenoble Alpes, CNRS, Grenoble INP, LJK 38000 Grenoble, France. · bInstitut universitaire de France (IUF)
ProtScape: A molecular structure and energy-aware representation for protein conformation generation
Oct 27, 2024Siddharth Viswanath, Xingzhi Sun, Lucas Lee +9Conformational Ensembles Protein
Department of Computer Science, Yale University · Department of Genetics, Yale University · Program in Computing, Boise State University +2

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Fold'EM: Direct atomic structure inference from Cryo-EM particles

Advaith Maddipatla, Märt-Erik Mäeots, Marco Pegoraro, Nikolaus Dräger+4

Institute of Science and Technology Austria · University of Zurich · Frankfurt Institute for Advanced Studies+2

Cryo-Electron Microscopy Conformational Ensembles Atoms

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Single-particle cryo-electron microscopy (cryo-EM) has become a widely adopted technique for biomolecular structure determination. The conventional cryo-EM computational pipeline first combines many particle images to reconstruct an electrostatic potential (ESP) map and then fits an atomic model to the recovered map. Density reconstruction has high sample complexity, requiring large numbers of particle images and making structure determination high-cost and low-throughput, particularly for heterogeneous samples. Downstream atomic model building, in turn, becomes increasingly difficult as the resolution of the reconstructed map deteriorates. Protein structure prediction models provide strong sequence-derived priors on atomic structure, and experiment-guided approaches can use these priors to recover structures consistent with experimental measurements. Yet, in cryo-EM, such priors are typically integrated only after density reconstruction during atomic model fitting. We introduce Fold'EM, an inference-time framework that combines priors from protein generative models directly with cryo-EM particle images to determine atomic models from a small number of single particle images, bypassing both intermediate density reconstruction and downstream model building against the reconstructed map. Across synthetic and experimental cryo-EM datasets, Fold'EM recovers accurate atomic structures both with known particle orientations and in an ab-initio setting where orientations are inferred jointly with structure. In heterogeneous datasets, Fold'EM further resolves distinct conformational states from mixed particle populations without separately reconstructing a density map and building an atomic model for each state. We believe these results open new avenues for structure determination in the low-sample regime and for characterizing low-population conformational states directly from cryo-EM particles.

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