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Protein Folding

Papers archive 2025-07-28

archive papers tagged: 185 · with a code link: 51 · where Syntology ran a sample: 7 (5 with a run with no instrument failure, 2 where every run was a failure of Syntology's instrument) Syntology

Show: all tagged papersonly where code ran (7 of 185 tagged: 5 with a run with no instrument failure, 2 where every run was a failure of Syntology's instrument)

Page 2 of 2: papers 101 to 185 of 185, in archive order: by repositories listed in the archive (most first), then newest first, not by stars (the archive holds no stars, so PwC's “Social” and “Latest” sorts cannot be reproduced). Papers that list no repository come after every paper that lists one.

Papers without a page here are shown as plain text. A Syntology line reads “N ran (of which C constructed an object rather than computing a result; K with no instrument failure: H honoured, V violated, P with no contract checked; I where Syntology's instrument failed) · U unverified”; the figure “where Syntology's instrument failed” counts failures of Syntology's instrument, not of the code. When the archive marks a repository official for the paper, the line starts with that repository's state (the archive's flag, not a verdict on who wrote the code); hover it for the repositories the samples that ran came from. Abstracts are on each paper's page.

• On the Robustness of AlphaFold: A COVID-19 Case Study
  10 Jan 2023 0 repositories listed
• Deep learning applied to computational mechanics: A comprehensive review, state of the art, and the classics
  18 Dec 2022 0 repositories listed
• Economic impacts of AI-augmented R&D
  15 Dec 2022 0 repositories listed
• Invariance-Aware Randomized Smoothing Certificates
  25 Nov 2022 0 repositories listed
• Friends in need: how chaperonins recognize and remodel proteins that require folding assistance
  16 Nov 2022 0 repositories listed
• Variational Quantum Algorithms for Chemical Simulation and Drug Discovery
  15 Nov 2022 0 repositories listed
• Rethinking the protein folding problem from a new perspective
  10 Oct 2022 0 repositories listed
• Generalization Properties of Retrieval-based Models
  6 Oct 2022 0 repositories listed
• Geometric Signatures of Switching Behavior in Mechanobiology
  7 Sep 2022 0 repositories listed
• GANs and Closures: Micro-Macro Consistency in Multiscale Modeling
  23 Aug 2022 0 repositories listed
• Protein Folding: From Classical Issues to a New Perspective
  5 Aug 2022 0 repositories listed
• Selectivity of Protein Interactions Stimulated by Terahertz Signals
  4 Jul 2022 0 repositories listed
• Molecular information theory meets protein folding
  29 Jun 2022 0 repositories listed
• Learning Geometrically Disentangled Representations of Protein Folding Simulations
  20 May 2022 0 repositories listed
• Chetaev Instability Framework for Kinetostatic Compliance-Based Protein Unfolding
  15 May 2022 0 repositories listed
• First-passage times in complex energy landscapes: a case study with nonmuscle myosin II assembly
  7 Apr 2022 0 repositories listed
• A 23 MW data centre is all you need
  31 Mar 2022 0 repositories listed
• Disentangled Spatiotemporal Graph Generative Models
  28 Feb 2022 0 repositories listed
• From evolution to folding of repeat proteins
  24 Feb 2022 0 repositories listed
• Collective Variable for Metadynamics Derived from AlphaFold Output
  17 Feb 2022 0 repositories listed
• Prompt-Guided Injection of Conformation to Pre-trained Protein Model
  7 Feb 2022 0 repositories listed
• GraphVAMPNet, using graph neural networks and variational approach to markov processes for dynamical modeling of biomolecules
  12 Jan 2022 0 repositories listed
• RoMA: a Method for Neural Network Robustness Measurement and Assessment
  21 Oct 2021 0 repositories listed
• Protein Folding Neural Networks Are Not Robust
  9 Sep 2021 0 repositories listed
• Variational embedding of protein folding simulations using gaussian mixture variational autoencoders
  27 Aug 2021 0 repositories listed
• Exploring generative atomic models in cryo-EM reconstruction
  3 Jul 2021 0 repositories listed
• Embedding Principle of Loss Landscape of Deep Neural Networks
  30 May 2021 0 repositories listed
• Protein folding simulations in the hydrophobic-polar model using a hybrid cuckoo search algorithm
  22 May 2021 0 repositories listed
• EBM-Fold: Fully-Differentiable Protein Folding Powered by Energy-based Models
  11 May 2021 0 repositories listed
• Predictive landscapes hidden beneath biological cellular automata
  5 May 2021 0 repositories listed
• Quadratic Optimization-Based Nonlinear Control for Protein Conformation Prediction
  27 Apr 2021 0 repositories listed
• Coupling streaming AI and HPC ensembles to achieve 100-1000x faster biomolecular simulations
  10 Apr 2021 0 repositories listed
• Mimetic Neural Networks: A unified framework for Protein Design and Folding
  7 Feb 2021 0 repositories listed
• Analyzing the Performance of Graph Neural Networks with Pipe Parallelism
  20 Dec 2020 0 repositories listed
• Exact Reduction of Huge Action Spaces in General Reinforcement Learning
  18 Dec 2020 0 repositories listed
• The finite size effects and the two-state paradigm of protein folding
  26 Oct 2020 0 repositories listed
• The role of hydrophobic interactions in folding of β-sheets
  16 Sep 2020 0 repositories listed
• Protein Folding/Unfolding Phenomenon is originated by Synchronization/Desynchronization of Instantaneously Induced Oscillating Dipoles. A Hypothesis
  4 Sep 2020 0 repositories listed
• Unsupervised and Supervised Structure Learning for Protein Contact Prediction
  31 Aug 2020 0 repositories listed
• GPU accelerated enumeration and exploration of HP model genotype-phenotype maps for protein folding
  1 Aug 2020 0 repositories listed
• Characterizing SARS-CoV-2 mutations in the United States
  24 Jul 2020 0 repositories listed
• First-Passage Time Distributions in Two-State Protein Folding Kinetics: Exploring the Native-Like States vs Overcoming the Free Energy Barrier
  27 May 2020 0 repositories listed
• Effect of protein structure on evolution of cotranslational folding
  7 Apr 2020 0 repositories listed
• Neighborhood Information-based Probabilistic Algorithm for Network Disintegration
  8 Mar 2020 0 repositories listed
• Adaptive Markov State Model estimation using short reseeding trajectories
  12 Dec 2019 0 repositories listed
• Machine learning for protein folding and dynamics
  22 Nov 2019 0 repositories listed
• A Tale of Two Desolvation Potentials: An Investigation of Protein Behavior Under High Hydrostatic Pressure
  15 Nov 2019 0 repositories listed
• Using Residual Dipolar Couplings from Two Alignment Media to Detect Structural Homology
  6 Nov 2019 0 repositories listed
• Machine Learning and Big Scientific Data
  12 Oct 2019 0 repositories listed
• A topological study of protein folding kinetics
  28 Sep 2019 0 repositories listed
• Weighted persistent homology for osmolyte molecular aggregation and hydrogen-bonding network analysis
  14 Jul 2019 0 repositories listed
• Learning Protein Structure with a Differentiable Simulator
  1 May 2019 0 repositories listed
• Two-phase protein folding optimization on a three-dimensional AB off-lattice model
  4 Mar 2019 0 repositories listed
• Forming native shortcut networks to simulate protein folding
  17 Feb 2019 0 repositories listed
• FoldingZero: Protein Folding from Scratch in Hydrophobic-Polar Model
  3 Dec 2018 0 repositories listed
• CoHSI III: Long proteins and implications for protein evolution
  19 Oct 2018 0 repositories listed
• On the scale-free nature of RNA secondary structure networks
  30 Jun 2018 0 repositories listed
• A method for partitioning the information contained in a protein sequence between its structure and function
  23 May 2018 0 repositories listed
• Doing the impossible: Why neural networks can be trained at all
  13 May 2018 0 repositories listed
• Rare-Event Sampling of Epigenetic Landscapes and Phenotype Transitions
  29 Dec 2017 0 repositories listed
• Folding with a protein's native shortcut network
  13 Dec 2017 0 repositories listed
• The impact of hydrodynamic interactions on protein folding rates depends on temperature
  12 Dec 2017 0 repositories listed
• Dimensionality reduction methods for molecular simulations
  29 Oct 2017 0 repositories listed
• Protein Folding Optimization using Differential Evolution Extended with Local Search and Component Reinitialization
  19 Oct 2017 0 repositories listed
• Evidence of evolutionary selection for co-translational folding
  10 Oct 2017 0 repositories listed
• A glass-box interactive machine learning approach for solving NP-hard problems with the human-in-the-loop
  3 Aug 2017 0 repositories listed
• Prediction of amino acid side chain conformation using a deep neural network
  26 Jul 2017 0 repositories listed
• Controllability analysis and control synthesis for the ribosome flow model
  17 May 2017 0 repositories listed
• Analysis and prediction of protein folding energy changes upon mutation by element specific persistent homology
  31 Mar 2017 0 repositories listed
• Intra-protein binding peptide fragments have specific and intrinsic sequence patterns
  26 Feb 2017 0 repositories listed
• Selection originating from protein stability/foldability: Relationships between protein folding free energy, sequence ensemble, and fitness
  30 Dec 2016 0 repositories listed
• Recursive Decomposition for Nonconvex Optimization
  8 Nov 2016 0 repositories listed
• Normalizing Flows on Riemannian Manifolds
  7 Nov 2016 0 repositories listed
• Cooperativity and modularity in protein folding
  30 Aug 2016 0 repositories listed
• Structure-based prediction of protein-folding transition paths
  27 Jul 2016 0 repositories listed
• Folding and Stabilization of Native-Sequence-Reversed Proteins
  16 Jun 2016 0 repositories listed
• A maximum-caliber approach to predicting perturbed folding kinetics due to mutations
  25 May 2016 0 repositories listed
• Folding of Protein L with implications for collapse in the denatured state ensemble
  29 Feb 2016 0 repositories listed
• Protein residue networks from a local search perspective
  30 Nov 2015 0 repositories listed
• Bloch spin waves and emergent structure in protein folding with HIV envelope glycoprotein as an example
  23 Nov 2015 0 repositories listed
• Chaos of Protein Folding
  31 Oct 2015 0 repositories listed
• The short-cut network within protein residue networks
  12 Aug 2015 0 repositories listed
• Solvent Effects in the Helix-Coil Transition Model can explain the Unusual Biophysics of Intrinsically Disordered Proteins
  14 Jul 2015 0 repositories listed
• Structural Learning for Template-free Protein Folding
  6 Nov 2013 0 repositories listed
• Deep Spatio-Temporal Architectures and Learning for Protein Structure Prediction
  1 Dec 2012 0 repositories listed