almeida85

almeida85's Stars

• kyegomez/AlphaFold3

  Implementation of Alpha Fold 3 from the paper: "Accurate structure prediction of biomolecular interactions with AlphaFold3" in PyTorch

  Language:Python69925692

• pharmai/plip

  Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Adasme et al. (2021), https://doi.org/10.1093/nar/gkab294

  Language:Python45416109105

• westlake-repl/SaProt

  [ICLR'24 spotlight] Saprot: Protein Language Model with Structural Alphabet

  Language:Python32366532

• video2game/video2game

  Code release of Video2Game

  Language:JavaScript30111522

• maabuu/posebusters

  Plausibility checks for generated molecule poses.

  Language:Python21531913

• patrickbryant1/Umol

  Protein-ligand structure prediction

  Language:Jupyter Notebook18863417

• HeliXonProtein/binding-ddg-predictor

  open source repository

  Language:Python12371027

• aqlaboratory/genie2

  Protein structure diffusion model for unconditional protein generation and motif scaffolding

  Language:Python1138716

• Kortemme-Lab/flex_ddG_tutorial

  Language:Python7843229

• Wangchentong/Proteus

  Pytorch implementation for ICML 2024 paper Proteus: Exploring Protein Structure Generation for Enhanced Designability and Efficiency.

  Language:Python66324

• ELELAB/RosettaDDGPrediction

  Language:Python4555610

• sokrypton/af2bind

  Language:Jupyter Notebook41435

• CDDLeiden/PCMol

  Multi-target de novo molecular generator conditioned on AlphaFold's latent protein embeddings.

  Language:Python38522

• HySonLab/Protein_Redesign

  Complex-based Ligand-Binding Proteins Redesign by Equivariant Diffusion-based Generative Models

  Language:Python38435

• iamysk/AFsample2

  Modelling protein conformational landscape with Alphafold

  Language:Python33515

• bpmunson/polygon

  POLYGON VAE For de novo Polypharmacology

  Language:Python282108

• ETHmodlab/dragonfly_gen

  De novo drug design with deep interactome learning

  Language:Python23004

• GradinaruLab/APPRAISE

  Rank binders by structure modeling

  Language:Python154

• Hoecker-Lab/atligator

  Analysis and design of protein-protein or protein-peptide interactions based on atlas database.

  Language:Python13101

• hongliangduan/HighFold

  Language:Python12125

• ddingding/CoVES

  Protein scoring and sampling of 'Combinatorial Variant Effects from Structure' (CoVES)

  Language:Jupyter Notebook10102

• durrantlab/molmoda

  MolModa provides a secure, accessible environment where users can perform molecular docking entirely in their web browsers.

  Language:JavaScript9142

• APAJanssen/KinaseDocker2

  A PyMOL plugin with accompanying Docker image for kinase inhibitor binding and affinity prediction

  Language:Python8113

• BiolApps/VaccineDesigner

  R Shiny application "Vaccine Designer" aiming for the construction of vaccine sequences based on multi epitope design workflow.

  Language:R71

• KULL-Centre/PRISM

  Software development pipelines related to the PRISM project

  Language:Python74544

• GenScript-IBDPE/ProSTAGE

  6

• SimonCrouzet/g-plip

  Repository for G-PLIP (paper "Knowledge graph neural network for structure-free protein-ligand affinity prediction")

  Language:Python6321

• casperg92/opportunities_in_protein_design_review

  Language:Jupyter Notebook5

• Martini-Force-Field-Initiative/GoMartini

  New virtual-site implementation of GōMartini for the Martini 3 forcefield

  Language:C34130

• mmravic314/CHAMP2023

  Language:Python2