Making Protein folding accessible to all!
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Jul 3, 2025 - Jupyter Notebook
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structure-prediction
Here are 43 public repositories matching this topic...
Deep neural models for core NLP tasks (Pytorch version)
machine-learning natural-language-processing deep-neural-networks deep-learning pytorch named-entity-recognition sequence-labeling dependency-parsing structure-prediction core-nlp syntactic-parsing
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Feb 1, 2022 - Python
An implementation of the DeepMind's AlphaFold based on PyTorch for research
deep-learning contact-prediction structure-prediction protein-structure-prediction pytorch-implementation alphafold casp13
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Jan 23, 2021 - Python
Evolutionary couplings from protein and RNA sequence alignments
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Mar 2, 2025 - Jupyter Notebook
Comprehensive benchmarking of protein-ligand structure prediction methods. (ICML 2024 AI4Science)
benchmark machine-learning deep-learning computational-biology computational-chemistry structure-prediction molecular-docking
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Mar 24, 2025 - Jupyter Notebook
Official code repository for EquiFold: Protein Structure Prediction with a Novel Coarse-Grained Structure Representation
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Jan 8, 2023 - Python
Protein Secondary Structure predictor using Convolutional Neural Networks
machine-learning deep-learning pdb chain protein-structure keras cnn structure-prediction protein-prediction cullpdb
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Jul 15, 2023 - Python
[EMNLP 2022] Generative Knowledge Graph Construction: A Review
nlp review natural-language-processing paper information-extraction survey knowledge-graph named-entity-recognition generation awesome-list event-extraction generative natural-language-generation structure-prediction relation-extraction paper-list relational-triple-extraction information-extration genkgc chatgpt
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Jul 11, 2023
A geometric flow matching model for generative protein-ligand docking and affinity prediction. (ISMB 2025)
machine-learning deep-learning computational-biology computational-chemistry generative-model structure-prediction molecular-docking
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Apr 7, 2025 - Python
nucleic acid folding
dna rna folding rna-structure-prediction structure-prediction rna-folding dna-structure-prediction dna-folding
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Aug 3, 2024 - Python
This repository includes the slides and the practicals for the course of Structural Bioinformatics of the MBB/QB degrees at the University of Milano, originally inspired by https://github.com/pb3lab/ibm3202
structural-biology molecular-dynamics docking teaching-materials structure-prediction structural-bioinformatics
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Apr 3, 2025 - Jupyter Notebook
PSP is a python toolkit for predicting atomic-level structural models for a range of polymer geometries.
polymer structure-prediction vasp-poscar smiles-strings lammps-input oligomer initial-geometries autonomous-model-generator amorphous-model crystal-model infinite-polymer-chain loop-oligomer
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Jul 5, 2024 - Jupyter Notebook
Visualize the inner workings of RNA bioinformatics algorithms for structure prediction, interaction prediction and sequence alignment.
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Feb 28, 2024 - JavaScript
Python bindings for the `buildcell` program for Ab Initio Random Structure Searching (AIRSS)
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May 31, 2024 - Python
RNA secondary structure prediction tool
bioinformatics biology structural-biology structure prediction alignment rna-structure rna biological-data-analysis prediction-algorithm secondary-structure 2d rna-structure-prediction structure-prediction secondary-structure-prediction bioinformatics-tool rna-secondary-structure rna-secondary-structure-prediction single-sequence pseudoknot
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May 15, 2025 - Jupyter Notebook
Prospr is a universal toolbox for protein structure prediction within the HP-model. The Python package is based on a C++ core, which gives Prospr its high performance. The C++ core is made available as a separate zip file to facilitate high-performance computing applications. The package comes with many prediction algorithms and datasets to use.
python package bioinformatics cpp toolbox protein high-performance-computing datasets computational-science structure-prediction protein-folding protein-structure-prediction
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Jun 25, 2025 - C++
RNAGenesis: A Generalist Foundation Model for Functional RNA Therapeutics
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Jul 2, 2025 - Jupyter Notebook
[ACL 2023] SPEECH: Structured Prediction with Energy-Based Event-Centric Hyperspheres
nlp machine-learning natural-language-processing physics speech pytorch information-extraction ie event-extraction structure-prediction energy-model acl2023
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Dec 22, 2023 - Python
deep learning based prediction of structures and functional groups from MS/MS spectra
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Jan 31, 2025 - Jupyter Notebook
POC Nextflow pipeline to run the Chai-1, SOTA model for biomolecular structure prediction
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Jan 16, 2025 - Nextflow
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