structure-prediction

There are 1 repository under structure-prediction topic.

XuezheMax / NeuroNLP2
Deep neural models for core NLP tasks (Pytorch version)
natural-language-processing machine-learning deep-learning deep-neural-networks sequence-labeling structure-prediction syntactic-parsing core-nlp dependency-parsing pytorch named-entity-recognition
Language:Python 440
Urinx / alphafold_pytorch
An implementation of the DeepMind's AlphaFold based on PyTorch for research
alphafold protein-structure-prediction contact-prediction deep-learning pytorch-implementation casp13 structure-prediction
Language:Python 384
debbiemarkslab / EVcouplings
Evolutionary couplings from protein and RNA sequence alignments
structure-prediction 3d-structure protein protein-complexes
Language:Jupyter Notebook 212
Genentech / equifold
Official code repository for EquiFold: Protein Structure Prediction with a Novel Coarse-Grained Structure Representation
machine-learning structure-prediction proteins structural-biology
Language:Python 116
LucaAngioloni / ProteinSecondaryStructure-CNN
Protein Secondary Structure predictor using Convolutional Neural Networks
chain cnn cullpdb deep-learning keras machine-learning pdb protein-prediction protein-structure structure-prediction
Language:Python 108
zjunlp / Generative_KG_Construction_Papers
[EMNLP 2022] Generative Knowledge Graph Construction: A Review
genkgc knowledge-graph generative awesome-list paper-list natural-language-processing nlp generation information-extraction structure-prediction review survey named-entity-recognition relation-extraction relational-triple-extraction event-extraction natural-language-generation information-extration chatgpt paper
96
Lattice-Automation / seqfold
nucleic acid folding
dna rna folding rna-structure-prediction dna-structure-prediction structure-prediction rna-folding dna-folding
Language:Python 74
BackofenLab / RNA-Playground
Visualize the inner workings of RNA bioinformatics algorithms for structure prediction, interaction prediction and sequence alignment.
rna bioinformatics nussinov teaching alignment structure-prediction algorithm
Language:JavaScript 34
Ramprasad-Group / PSP
PSP is a python toolkit for predicting atomic-level structural models for a range of polymer geometries.
polymer structure-prediction initial-geometries smiles-strings lammps-input vasp-poscar autonomous-model-generator amorphous-model crystal-model infinite-polymer-chain loop-oligomer oligomer
Language:Jupyter Notebook 24
OkkeVanEck / prospr
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.
protein structure-prediction protein-folding toolbox cpp python package protein-structure-prediction datasets high-performance-computing computational-science bioinformatics
Language:C++ 18
zhubonan / airsspy
Python bindings for the `buildcell` program for Ab Initio Random Structure Searching (AIRSS)
airss materials-science structure-prediction
Language:Python 14
zjunlp / SPEECH
[ACL 2023] SPEECH: Structured Prediction with Energy-Based Event-Centric Hyperspheres
energy-model event-extraction information-extraction machine-learning pytorch speech structure-prediction physics acl2023 natural-language-processing ie nlp
Language:Python 12
xkianteb / leaqi
Active Imitation Learing with Noisy Guidance
structure-prediction learning-to-search imitation-learning reinforcement-learning natural-language-processing
Language:Python 10
StanIsAdmin / PyProt
A set of libraries for aligning, profiling, and predicting the structure of proteins
protein alignment amino-acids substitutions score-matrix profiling structure-prediction
Language:Python 9
OneAngstrom / DeepTrajectory
A deep learning method that identifies improved protein conformational states in trajectory data from refinement simulations
deep-learning temporal-learning structure-prediction casp protein-refinement tensorflow
Language:Python 8
dillondaudert / pssp_lstm
Recurrent neural network implementations for protein secondary structure prediction and language models
protein secondary structure prediction lstm rnn deep-learning tensorflow python3 jupyter-notebook recurrent-neural-networks structure-prediction amino-acid-sequence deep-neural-networks paper language-models unsupervised-learning pretrained-models
Language:Python 7
derekmma / DICE
[ACL'23 main] DICE: Data-Efficient Clinical Event Extraction with Generative Models
clinical-data clinical-information-extraction clinical-research event-extraction generative-model information-extraction pytorch structure-prediction
6
volvox292 / mass2smiles
deep learning based prediction of structures and functional groups from MS/MS spectra
deep-learning mass-spectrometry smiles-strings structure-prediction
Language:Jupyter Notebook 4
evalkov / alphafold
A pipeline for AlphaFold2-Multimer on a SLURM compute cluster with visualization in ChimeraX.
protein-protein-complexes protein-protein-interaction protein-structure structure-prediction
Language:Shell 3
zhubonan / res2desc
Computing descriptors for AIRSS style SHELX files.
airss materials-science structure-prediction
Language:Python 3
Singularitty / Genetic-Algorithm-Structure-Prediction
An implementation of a genetic algorithm in Python for predicting equilibrium crystal structures for a given potential. The potential implemented here is the Daoud-Cotton model, but this can be easily changed.
genetic-algorithm structure-prediction physics-2d statistical-physics crystal-structure
Language:Python 2
clacri / CASP14_MR_evaluation
Data and code for the manuscript "Assessing the utility of CASP14 models for Molecular Replacement: https://doi.org/10.22541/au.162412334.48194370/v1
casp likelihood molecular-replacement model-refinement structure-prediction
Language:Jupyter Notebook 1
ybyygu / spdkit
spdkit: Structure Predication Development Kit
chemistry structure-prediction molecule
Language:Rust 1
spdkit / spdkit
spdkit: Structure Predication Development Kit
structure-prediction computational-chemistry
Language:Rust 0
biovino1 / SearchEmb
Searching proteins against a database of embeddings
homology-search protein-language-model structure-prediction
Language:Python