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Search results for jupyter notebook protein
jupyter-notebook
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protein
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89 search results found
Educational
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1,112
Prottrans
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938
ProtTrans is providing state of the art pretrained language models for proteins. ProtTrans was trained on thousands of GPUs from Summit and hundreds of Google TPUs using Transformers Models.
Graphein
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932
Protein Graph Library
Deeppurpose
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826
A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinformatics)
Modeling Examples
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487
Gurobi modeling examples
Pyrosetta.notebooks
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399
Jupyter Notebooks for learning the PyRosetta platform for biomolecular structure prediction and design
Foldingdiff
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393
Diffusion models of protein structure; trigonometry and attention are all you need!
Jupyter_dock
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215
Jupyter Dock is a set of Jupyter Notebooks for performing molecular docking protocols interactively, as well as visualizing, converting file formats and analyzing the results.
Evcouplings
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177
Evolutionary couplings from protein and RNA sequence alignments
Icn3d
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135
web-based protein structure viewer and analysis tool interactively or in batch mode
Bnt162b2
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134
Markdown version of Reverse Engineering the source code of the BioNTech/Pfizer SARS-CoV-2 Vaccine
Flexs
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112
Fitness landscape exploration sandbox for biological sequence design.
Proteinfer
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110
Deep networks for protein functional inference
Covid 19 Community
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103
Community effort to build a Neo4j Knowledge Graph (KG) that links heterogeneous data about COVID-19
Lasagne4bio
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88
2019 Ncov
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68
Efforts towards proposing a potentially highly active molecule against a target protein of the 2019 Novel Coronavirus
Mmtf Pyspark
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64
Methods for the parallel and distributed analysis and mining of the Protein Data Bank using MMTF and Apache Spark.
Flip
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61
A collection of tasks to probe the effectiveness of protein sequence representations in modeling aspects of protein design
Hsm
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58
Code associated with "Biophysical prediction of protein-peptide interactions and signaling networks using machine learning."
Factored Attention
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50
This repository contains code for reproducing results in our paper Interpreting Potts and Transformer Protein Models Through the Lens of Simplified Attention
D Script
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49
A structure-aware interpretable deep learning model for sequence-based prediction of protein-protein interactions
Protein Design Tutorials
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49
Tutorials, cheat sheets, and other resources for computational methods for protein design.
Protein Atlas Fastai
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46
Code for training a Resnet model for the Human Protein Atlas Image Classification competition
Bionlp
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45
Repository for student projects within biomedical text mining from Lund University
Trdesign
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44
trRosetta for protein design
Vae_protein_function
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44
Protein function prediction using a variational autoencoder
Protein Localization
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43
Using Transformer protein embeddings with a linear attention mechanism to make SOTA de-novo predictions for the subcellular location of proteins 🔬
Drugmechdb
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41
A database of paths that represent the mechanism of action from a drug to a disease in an indication.
Md Ifp
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40
MD trajectory analysis using protein-ligand Interaction Fingerprints
Machine Learning With Ontologies
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39
Amazon Sagemaker Protein Classification
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35
Implementation of Protein Classification based on subcellular localization using ProtBert(Rostlab/prot_bert_bfd_localization) model from Hugging Face library, based on BERT model trained on large corpus of protein sequences.
Flu Sequence Predictor
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34
An experimental deep learning & genotype network-based system for predicting new influenza protein sequences.
Subcellular_localization
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30
Mmtf Genomics
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25
Methods for mapping genomic data onto 3D protein structure.
Protein Transformer
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25
Predicting protein structure through sequence modeling
Pdnet
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25
PDNET: A fully open-source framework for deep learning protein real-valued distances
Sgt
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23
Sequence Graph Transform
Sequencework
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22
programs and scripts, mainly python, for analyses related to nucleic or protein sequences
Geometricus
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22
A structure-based, alignment-free embedding approach for proteins. Can be used as input to machine learning algorithms.
Crisprdisco
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21
CRISPR discovery pipeline
Omicsintegrator2
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20
Prize-Collecting Steiner Forests for Interactomes
Pytorch Rgn
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19
Recurrent Geometric Network in Pytorch
Alphaspace2
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16
Protein surface topographical mapping tool
Emap2sec
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15
Emap2sec is a computational tool to identify protein secondary structures
Protease Gcnn Pytorch
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15
Rfscorevs
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15
RF-Score-VS - Random forest based protein-ligand scoring function for Virtual Screening
Emap2secplus
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15
Emap2sec+: Detecting Protein and DNA/RNA Structures in Cryo-EM Maps of Intermediate Resolution Using Deep Learning
Coronavirus Knowledge Graph
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14
OBSOLETE: Prototype Neo4j Knowledge Graph for Coronavirus outbreaks (new version: https://github.com/sbl-sdsc/coronavirus-knowledge-
Lm Gvp
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13
LM-GVP: A Generalizable Deep Learning Framework for Protein Property Prediction from Sequence and Structure
Smartas
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13
📓Notebook of Climente-González et al. (2017), The Functional Impact of Alternative Splicing in Cancer.
Sbm Openmm
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13
Python library to run structure based model (SBM) simulations using the OpenMM toolkit
Nanotext
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13
Proteins as words, genomes as documents.
Ppi Typed Relation Extractor
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12
Relation extraction for protein to protein interactions to extraction strongly typed PPI relations.. My research topic.. So work in progress
Proteinsolver
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12
Graph neural network capable of generating novel amino acid sequences that fold into proteins with predetermined topologies.
Deepseq
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12
Code for paper titled, "Beyond Homology Transfer: Deep Learning for Automated Annotation of Proteins". Preprint available at: http://www.biorxiv.org/content/early/2017/07/25/16
Nerfax
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12
An efficient method for the conversion from internal to Cartesian coordinates that utilizes the platform-agnostic JAX Python library.
Cspred
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12
UCBShift is a program for predicting chemical shifts for backbone atoms and β-carbon of a protein in solution. It utilizes a machine learning module that makes predictions from features extracted from the 3D structures of the proteins.
Mmtf Proteomics
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11
Methods for mapping proteomics data on 3D protein structure.
Prolif
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11
Protein-Ligand Interaction Fingerprints
Mupipr
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11
Kaggle Protein Image Classification
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10
This is the solution for Kaggle human protein classification competition.
Gsp_2019
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9
Code for reproducing results from the paper "RNA velocity and protein acceleration from single-cell multiomics experiments."
Fragalysis Api
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9
A python API for fragalysis (fragalysis.diamond.ac.uk)
Huri_paper
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9
Code for the analyses in the human reference interactome paper.
Pyrosettabook
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9
Ijcai2016
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9
This repository is for the replication of our published paper "Protein Secondary Structure Prediction Using Cascaded Convolutional and Recurrent Neural Networks" on IJCAI2016. Please consult and consider citing the following papers:
Dognet
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8
A Deep Architecture for Synapse Detection in Multiplexed Fluorescence Images
Public_notebooks
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8
Repository of Jupyter Notebooks created by the Bio2Byte group
Perchlorate Metagenome 2018
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8
Scripts used in the publication Tyler P. Barnum, Israel A. Figueroa, Charlotte I. Carlström, Lauren N. Lucas, Anna L. Engelbrektson, and John D. Coates. (2018) Genome-resolved metagenomics identifies genetic mobility, metabolic interactions, and unexpected diversity in perchlorate-reducing communities.
Hpa Competition Solutions
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8
Team original solutions for the Human Protein Atlas image classification competition
Protein Folding
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8
Protein structure prediction using optimization methods from the field of machine learning
Phage Host Prediction
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7
Published in PLOS ONE. We show that using embeddings of receptor-binding proteins presents improvements over handcrafted genomic and protein sequence features for phage-host interaction prediction — with the highest performance obtained using the transformer-based protein language model ProtT5
Protein_solubility
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7
Modellernotebooks
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7
Running Modeller for Protein Modelling using Python and Jupyter Notebooks
Protein Reconstruction
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7
Learning to recover orientations from projections in single-particle cryo-EM
Awe
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7
Accelerated Weighted Ensemble (AWE) provides a Python library for adaptive sampling of molecular dynamics.
Deepripe
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6
Exmachina
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6
Sequence aligner for accurate template-based protein structure prediction
Cu Tsp
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6
Implementation of Accurate Protein Structure Prediction by Embeddings and Deep Learning Representations
Human Protein Atlas Image Classification
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6
Proposing a neural network architecture capable of classifying protein organelle localization labels, the proposed model was able to reach an accuracy of 95 percent for test data and training data. The proposed model deals with the input of the proposed neural network as three-dimensional (each dimension represents colors (red filter, blue filter, yellow filter, green filter)), and thus the input to the neural network (samples, 2, 90, 90, 3) represents the number 2 In the proposed structure (RGB
Pyemma_ipython
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6
PyEMMA Jupyter Notebooks
Milieu
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6
Mutual Interactors: A graph-based machine learning model with applications in molecular phenotype prediction
Skipgnn
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6
SkipGNN: Predicting Molecular Interactions with Skip-Graph Networks
Gmx_performance_on_hpc
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6
Gromacs performance benchmarking on different HPC platforms
Deep Learning For Drug Protein Interactions
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5
A Python implementation for training a neural network for predicting drug-protein interactions using Keras and Tensorflow
Unsupervised Supervised Protein Genes Diseases Organisms Extraction
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5
Extract Proteins, Genes, and Diseases from text
Smlmvis
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5
Superresolution visualization of 3D protein localization data from a range of microscopes
Protein Dihedral Angles Prediction
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5
A hybrid approach to protein structure (dihedral / torsional angles) prediction using techniques from Mohammed AlQuraishi's work on End-to-end differentiable learning of protein structure and Gao et al. on RaptorX.
Reactome2py
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5
python client for reactome content, analysis, and human functional protein interactions (FI) services api calls.
Envision2017
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5
We present Envision, an accurate predictor of protein variant molecular effect, trained using large-scale experimental mutagenesis data. All data and software in this study are freely available. The training data set and all code used to train the models and generate the figures presented in this manuscript are available here. Envision predictions, along with feature annotations, are available at https://envision.gs.washington.edu/.
Proteinmotifrbm
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5
Learning Protein Constitutive Motifs from Sequence Data: RBM toolbox
Vapur
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5
Search Engine to Find Related Protein - Compound Pairs in COVID-19 Literature
Mybiotools
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5
Python scripts for biologists
Gempro
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5
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