Evolutionary couplings from protein and RNA sequence alignments
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Updated
Jul 6, 2024 - Jupyter Notebook
Evolutionary couplings from protein and RNA sequence alignments
PSP is a python toolkit for predicting atomic-level structural models for a range of polymer geometries.
Predict the whole sequence and 3D structure of masked protein sequences with ESM by @evolutionaryscale
Your open-source alternative to AlphaFold3🚀
Python bindings for the `buildcell` program for Ab Initio Random Structure Searching (AIRSS)
Recommendation-based Basin-Hopping for cation ordering optimization
Visualize the inner workings of RNA bioinformatics algorithms for structure prediction, interaction prediction and sequence alignment.
deep learning based prediction of structures and functional groups from MS/MS spectra
A pipeline for AlphaFold2-Multimer on a SLURM compute cluster with visualization in ChimeraX.
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.
[ACL 2023] SPEECH: Structured Prediction with Energy-Based Event-Centric Hyperspheres
Searching proteins against a database of embeddings
Protein Secondary Structure predictor using Convolutional Neural Networks
[EMNLP 2022] Generative Knowledge Graph Construction: A Review
[ACL'23 main] DICE: Data-Efficient Clinical Event Extraction with Generative Models
nucleic acid folding
spdkit: Structure Predication Development Kit
Official code repository for EquiFold: Protein Structure Prediction with a Novel Coarse-Grained Structure Representation
Deep neural models for core NLP tasks (Pytorch version)
Data and code for the manuscript "Assessing the utility of CASP14 models for Molecular Replacement: https://doi.org/10.22541/au.162412334.48194370/v1
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