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Protein Structure Prediction

Papers archive 2025-07-28

archive papers tagged: 188 · with a code link: 67 · where Syntology ran a sample: 19 (17 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 (19 of 188 tagged: 17 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 188 of 188, 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.

• HelixFold-Multimer: Elevating Protein Complex Structure Prediction to New Heights
  16 Apr 2024 0 repositories listed
• AlphaCrystal-II: Distance matrix based crystal structure prediction using deep learning
  7 Apr 2024 0 repositories listed
• The curious case of A31P, a topology-switching mutant of the Repressor of Primer protein : A molecular dynamics study of its folding and misfolding
  1 Apr 2024 0 repositories listed
• Convergence of Continuous Normalizing Flows for Learning Probability Distributions
  31 Mar 2024 0 repositories listed
• AlphaFold2 for protein structure prediction: Best practices and critical analyses
  19 Mar 2024 0 repositories listed
• Deep Reinforcement Learning for Modelling Protein Complexes
  11 Mar 2024 0 repositories listed
• Advances of Deep Learning in Protein Science: A Comprehensive Survey
  8 Mar 2024 0 repositories listed
• SGNet: Folding Symmetrical Protein Complex with Deep Learning
  7 Mar 2024 0 repositories listed
• Understanding Biology in the Age of Artificial Intelligence
  6 Mar 2024 0 repositories listed
• A Protein Structure Prediction Approach Leveraging Transformer and CNN Integration
  29 Feb 2024 0 repositories listed
• Linker-Tuning: Optimizing Continuous Prompts for Heterodimeric Protein Prediction
  2 Dec 2023 0 repositories listed
• AI in Pharma for Personalized Sequential Decision-Making: Methods, Applications and Opportunities
  30 Nov 2023 0 repositories listed
• FoldExplorer: Fast and Accurate Protein Structure Search with Sequence-Enhanced Graph Embedding
  30 Nov 2023 0 repositories listed
• Direct Preference-Based Evolutionary Multi-Objective Optimization with Dueling Bandit
  23 Nov 2023 0 repositories listed
• CrysFormer: Protein Structure Prediction via 3d Patterson Maps and Partial Structure Attention
  5 Oct 2023 0 repositories listed
• Deep Learning in Computational Biology: Advancements, Challenges, and Future Outlook
  2 Oct 2023 0 repositories listed
• A Comprehensive Review of Generative AI in Healthcare
  1 Oct 2023 0 repositories listed
• FFF: Fragments-Guided Flexible Fitting for Building Complete Protein Structures
  7 Aug 2023 0 repositories listed
• Artificial intelligence-aided protein engineering: from topological data analysis to deep protein language models
  27 Jul 2023 0 repositories listed
• Data Resources for Structural Bioinformatics
  5 Jul 2023 0 repositories listed
• Function Prediction
  5 Jul 2023 0 repositories listed
• Introduction to Protein Folding
  5 Jul 2023 0 repositories listed
• Introduction to Protein Structure
  5 Jul 2023 0 repositories listed
• Molecular Dynamics
  5 Jul 2023 0 repositories listed
• Monte Carlo for Protein Structures
  5 Jul 2023 0 repositories listed
• Structural Property Prediction
  5 Jul 2023 0 repositories listed
• Structure Alignment
  5 Jul 2023 0 repositories listed
• Thermodynamics of Protein Folding
  5 Jul 2023 0 repositories listed
• Internal-Coordinate Density Modelling of Protein Structure: Covariance Matters
  27 Feb 2023 0 repositories listed
• Beating the Best: Improving on AlphaFold2 at Protein Structure Prediction
  18 Jan 2023 0 repositories listed
• FFF: Fragment-Guided Flexible Fitting for Building Complete Protein Structures
  1 Jan 2023 0 repositories listed
• On How AI Needs to Change to Advance the Science of Drug Discovery
  23 Dec 2022 0 repositories listed
• Protein Structure Prediction until CASP15
  15 Dec 2022 0 repositories listed
• E3Bind: An End-to-End Equivariant Network for Protein-Ligand Docking
  12 Oct 2022 0 repositories listed
• Direct Generation of Protein Conformational Ensembles via Machine Learning
  19 Jun 2022 0 repositories listed
• What is an equivariant neural network?
  15 May 2022 0 repositories listed
• Capturing the geometry, function, and evolution of enzymes with 3D templates
  5 Mar 2022 0 repositories listed
• Numeric Lyndon-based feature embedding of sequencing reads for machine learning approaches
  28 Feb 2022 0 repositories listed
• Proteome-scale Deployment of Protein Structure Prediction Workflows on the Summit Supercomputer
  25 Jan 2022 0 repositories listed
• Structure determination
  5 Aug 2021 0 repositories listed
• 6DCNN with roto-translational convolution filters for volumetric data processing
  26 Jul 2021 0 repositories listed
• An Automated Global Method for Extraction of Distance Distributions from Electron Spin Resonance Pulsed Dipolar Signals
  18 Jun 2021 0 repositories listed
• Protein sequence-to-structure learning: Is this the end(-to-end revolution)?
  16 May 2021 0 repositories listed
• EBM-Fold: Fully-Differentiable Protein Folding Powered by Energy-based Models
  11 May 2021 0 repositories listed
• tFold-TR: Combining Deep Learning Enhanced Hybrid Potential Energy for Template-Based Modeling Structure Refinement
  10 May 2021 0 repositories listed
• Functional Protein Structure Annotation Using a Deep Convolutional Generative Adversarial Network
  18 Apr 2021 0 repositories listed
• "Weak AI" is Likely to Never Become "Strong AI", So What is its Greatest Value for us?
  29 Mar 2021 0 repositories listed
• NMRPy: a novel NMR scripting system to implement artificial intelligence and advanced applications
  27 Mar 2021 0 repositories listed
• Deep Learning applications for COVID-19
  11 Jan 2021 0 repositories listed
• On the performance of deep learning for numerical optimization: an application to protein structure prediction
  17 Dec 2020 0 repositories listed
• DeepFoldit -- A Deep Reinforcement Learning Neural Network Folding Proteins
  28 Oct 2020 0 repositories listed
• Decoy Selection for Protein Structure Prediction Via Extreme Gradient Boosting and Ranking
  3 Oct 2020 0 repositories listed
• An Investigation in Optimal Encoding of Protein Primary Sequence for Structure Prediction by Artificial Neural Networks
  2 Aug 2020 0 repositories listed
• The prospects of quantum computing in computational molecular biology
  26 May 2020 0 repositories listed
• Mass spectrometry for semi-experimental protein structure determination and modeling
  29 Feb 2020 0 repositories listed
• Predicting the real-valued distances between residue pairs for proteins
  18 Dec 2019 0 repositories listed
• A new hybrid genetic algorithm for protein structure prediction on the 2D triangular lattice
  8 Jul 2019 0 repositories listed
• Seq-SetNet: Exploring Sequence Sets for Inferring Structures
  6 Jun 2019 0 repositories listed
• AmoebaContact and GDFold: a new pipeline for rapid prediction of protein structures
  28 May 2019 0 repositories listed
• FoldingZero: Protein Folding from Scratch in Hydrophobic-Polar Model
  3 Dec 2018 0 repositories listed
• Dihedral angle prediction using generative adversarial networks
  29 Mar 2018 0 repositories listed
• Preface to Introduction to Protein Structural Bioinformatics
  29 Jan 2018 0 repositories listed
• Real-value and confidence prediction of protein backbone dihedral angles through a hybrid method of clustering and deep learning
  19 Dec 2017 0 repositories listed
• Finding optimal finite biological sequences over finite alphabets: the OptiFin toolbox
  25 Jun 2017 0 repositories listed
• Deep Learning for Computational Chemistry
  17 Jan 2017 0 repositories listed
• Protein Secondary Structure Prediction Using Deep Multi-scale Convolutional Neural Networks and Next-Step Conditioning
  4 Nov 2016 0 repositories listed
• DeepQA: Improving the estimation of single protein model quality with deep belief networks
  15 Jul 2016 0 repositories listed
• Folding and Stabilization of Native-Sequence-Reversed Proteins
  16 Jun 2016 0 repositories listed
• Simultaneous identification of specifically interacting paralogs and inter-protein contacts by Direct-Coupling Analysis
  12 May 2016 0 repositories listed
• 3D RNA and functional interactions from evolutionary couplings
  21 Apr 2016 0 repositories listed
• Protein single-model quality assessment by feature-based probability density functions
  22 Mar 2016 0 repositories listed
• Guided macro-mutation in a graded energy based genetic algorithm for protein structure prediction
  7 Mar 2016 0 repositories listed
• Evaluation of Protein Structural Models Using Random Forests
  13 Feb 2016 0 repositories listed
• Variational Inference for Sparse and Undirected Models
  11 Feb 2016 0 repositories listed
• Liquid-theory analogy of direct-coupling analysis of multiple-sequence alignment and its implications for protein structure prediction
  10 Nov 2015 0 repositories listed
• Protein Structure Prediction by Protein Alignments
  19 Oct 2015 0 repositories listed
• Improving protein threading accuracy via combining local and global potential using TreeCRF model
  11 Sep 2015 0 repositories listed
• TOPO: Improving remote homologue recognition via identifying common protein structure framework
  12 Jul 2015 0 repositories listed
• Sparse, guided feature connections in an Abstract Deep Network
  16 Dec 2014 0 repositories listed
• GreMuTRRR: A Novel Genetic Algorithm to Solve Distance Geometry Problem for Protein Structures
  16 Nov 2014 0 repositories listed
• AIS-INMACA: A Novel Integrated MACA Based Clonal Classifier for Protein Coding and Promoter Region Prediction
  24 Mar 2014 0 repositories listed
• HMACA: Towards Proposing a Cellular Automata Based Tool for Protein Coding, Promoter Region Identification and Protein Structure Prediction
  21 Jan 2014 0 repositories listed
• PSMACA: An Automated Protein Structure Prediction Using MACA (Multiple Attractor Cellular Automata)
  13 Jan 2014 0 repositories listed
• Mixing Energy Models in Genetic Algorithms for On-Lattice Protein Structure Prediction
  15 Nov 2013 0 repositories listed
• A Hybrid Local Search for Simplified Protein Structure Prediction
  31 Oct 2013 0 repositories listed
• A Hybrid Monte Carlo Ant Colony Optimization Approach for Protein Structure Prediction in the HP Model
  30 Sep 2013 0 repositories listed
• Deep Spatio-Temporal Architectures and Learning for Protein Structure Prediction
  1 Dec 2012 0 repositories listed
• Conditional Neural Fields
  1 Dec 2009 0 repositories listed