edumenezes77

edumenezes77's Stars

• Graylab/DL4Proteins-notebooks

  Colab Notebooks covering deep learning tools for biomolecular structure prediction and design

  Language:Jupyter Notebook29037

• hgbrian/pdb2png

  Create a PNG from a PDB file

  Language:Python53

• rcedgar/muscle

  Multiple sequence and structure alignment with top benchmark scores scalable to thousands of sequences. Generates replicate alignments, enabling assessment of downstream analyses such as trees and predicted structures.

  Language:C++22723

• AspirinCode/awesome-AI4MolConformation-MD

  List of molecules (small molecules, RNA, peptide, protein, enzymes, antibody, and PPIs) conformations and molecular dynamics (force fields) using generative artificial intelligence and deep learning

  13713

• mlabonne/llm-course

  Course to get into Large Language Models (LLMs) with roadmaps and Colab notebooks.

  Language:Jupyter Notebook41.1k4.4k

• westlake-repl/SaprotHub

  SaprotHub: Making Protein Modeling Accessible to All Biologists

  Language:Jupyter Notebook858

• tuplexyz/PD-1_Fab_Diffusion

  PD-1 Targeted Antibody Discovery Using AI Protein Diffusion

  Language:Shell81

• kalininalab/alphafold_non_docker

  AlphaFold2 non-docker setup

  Language:Shell350121

• evolutionaryscale/esm

  Language:Python1.6k179

• AlgoMole/MolFM

  Implementation for NeurIPS 2023 paper "Equivariant Flow Matching with Hybrid Probability Transport for 3D Molecule Generation"

  Language:Python311

• svalkiers/clusTCR

  CDR3 clustering module providing a new method for fast and accurate clustering of large data sets of CDR3 amino acid sequences, and offering functionalities for downstream analysis of clustering results.

  Language:Python509

• GMdSilva/gms_natcomms_1705932980_data

  Data sharing for High-throughput Prediction of Changes in Protein Conformational Distributions with Subsampled AlphaFold2

  Language:Jupyter Notebook385

• muhaochen/seq_ppi

  This is the repository for PIPR. This repository contains the source code and links to some datasets used in the ISMB/ECCB-2019 paper "Multifaceted Protein-Protein Interaction Prediction Based on Siamese Residual RCNN".

  Language:Python9026

• aqlaboratory/genie

  De Novo Protein Design by Equivariantly Diffusing Oriented Residue Clouds

  Language:Python17319

• DeepRank/deeprank2

  An open-source deep learning framework for data mining of protein-protein interfaces or single-residue variants.

  Language:Python4110

• DeepRank/pdb2sql

  Fast and versatile biomolecular structure PDB file parser using SQL queries

  Language:Python2412

• DeepRank/Deeprank-GNN

  Graph Network for protein-protein interface

  Language:Python11732

• zaixizhang/FLAG

  Implementation of ICLR23 paper "Molecule Generation for Target Protein Binding with Structural Motifs"

  Language:Python608

• LirongWu/awesome-protein-representation-learning

  Awesome Protein Representation Learning

  62872

• divelab/GraphBP

  Official implementation of "Generating 3D Molecules for Target Protein Binding" [ICML2022 Long Presentation]

  Language:Python10624

• AbSciBio/unlocking-de-novo-antibody-design

  11116

• kiharalab/GNN_pocket

  The project of pocket prediction based on GNN model

  Language:C12

• microsoft/evodiff

  Generation of protein sequences and evolutionary alignments via discrete diffusion models

  Language:Python54978

• yassermb/DLA-Ranker

  Deep Local Analysis evaluates protein docking conformations with Locally oriented Cubes

  Language:Python21

• drroe/AmberMdPrep

  Wrapper script for preparing explicitly solvated systems for molecular dynamics simulations with Amber.

  Language:Shell163

• Peldom/papers_for_protein_design_using_DL

  List of papers about Proteins Design using Deep Learning

  1.5k182

• A4Bio/DiffSDS

  Official implementation of the paper "DiffSDS: A Language Diffusion Model for Protein Backbone Inpainting under Geometric Conditions and Constraints".

  Language:Jupyter Notebook142

• generatebio/chroma

  A generative model for programmable protein design

  Language:Python70690

• blt2114/ProtDiff_SMCDiff

  Code implementation of "Diffusion probabilistic modeling of protein backbones in 3D for the motif-scaffolding problem" https://arxiv.org/abs/2206.04119

  Language:Python708

• jasonkyuyim/se3_diffusion

  Implementation for SE(3) diffusion model with application to protein backbone generation

  Language:Python34755