Alternatives and similar repositories for BeEM

Users that are interested in BeEM are comparing it to the libraries listed below

• meilerlab / HyperMPNN
  HyperMPNN ‒ A general strategy to design thermostable proteins learned from hyperthermophiles
  ☆70Updated 7 months ago
• psipred / Merizo
  Fast and accurate protein domain segmentation using Invariant Point Attention
  ☆46Updated 8 months ago
• patrickbryant1 / AFProfile
  Improved protein complex prediction with AlphaFold-multimer by denoising the MSA profile
  ☆72Updated last year
• brianjimenez / pydock_tutorial
  PyDock Tutorial
  ☆35Updated 7 years ago
• jsunn-y / ALDE
  Active Learning-Assisted Directed Evolution for Protein Engineering
  ☆78Updated 3 months ago
• Kuhlman-Lab / alphafold3
  Kuhlman Lab Installation of AlphaFold3
  ☆39Updated 4 months ago
• ievapudz / TemStaPro
  TemStaPro - a program for protein thermostability prediction using sequence representations from a protein language model.
  ☆72Updated last year
• hefeda / PGP
  ☆41Updated 5 months ago
• Kuhlman-Lab / ThermoMPNN-D
  Extension of ThermoMPNN for double mutant predictions
  ☆53Updated 4 months ago
• KULL-Centre / _2022_ML-ddG-Blaabjerg
  ☆56Updated 5 months ago
• GMdSilva / gms_natcomms_1705932980_data
  Data sharing for High-throughput Prediction of Changes in Protein Conformational Distributions with Subsampled AlphaFold2
  ☆43Updated last year
• JinyuanSun / DDGScan
  DDGScan: an integrated parallel workflow for the in silico point mutation scan of protein
  ☆50Updated last year
• minmarg / gtalign_alpha
  GTalign, high-performance protein structure alignment, superposition and search
  ☆54Updated 5 months ago
• idlutz / protein-backbone-MCTS
  ☆52Updated last year
• mabr3112 / riff_diff_protflow
  ProtFlow Implementation of the RiffDiff pipeline to design enzymes from theozymes.
  ☆80Updated 2 months ago
• JinyuanSun / PymolFold
  Protein folding in Pymol
  ☆138Updated 2 months ago
• seanrjohnson / protein_gibbs_sampler
  Gibbs sampling for generating protein sequences
  ☆58Updated last year
• Wublab / Pythia
  Structure-based self-supervised learning enables ultrafast prediction of stability changes upon mutations
  ☆95Updated 2 months ago
• data2code / afpdb
  Efficient manipulation of protein structures in Python
  ☆63Updated 4 months ago
• chloechsu / combining-evolutionary-and-assay-labelled-data
  ☆76Updated 4 years ago
• Kuhlman-Lab / evopro
  ☆94Updated 3 months ago
• SLx64 / af3cli
  A command-line interface and Python library for generating AlphaFold3 input files.
  ☆38Updated last month
• rochoa85 / PepFun
  Bioinformatics and Cheminformatics protocols for peptide analysis
  ☆45Updated 3 years ago
• marcellszi / rna3db
  A dataset for training and benchmarking deep learning models for RNA structure prediction
  ☆62Updated 3 weeks ago
• duerrsimon / folding_tools
  A collection of *fold* tools
  ☆24Updated 3 years ago
• samgoldman97 / enzyme-datasets
  Enzyme datasets used to benchmark enzyme-substrate promiscuity models
  ☆40Updated 4 years ago
• ShintaroMinami / PyDSSP
  A simplified implementation of DSSP algorithm for PyTorch and NumPy
  ☆97Updated 8 months ago
• drhicks / Kejia_peptide_binders
  code for IDR binding paper 2025
  ☆67Updated 11 months ago
• luo-group / MODIFY
  ML-optimized library design with improved fitness and diversity for protein engineering
  ☆36Updated 3 months ago
• DunbrackLab / IPSAE
  Scoring function for interprotein interactions in AlphaFold2 and AlphaFold3
  ☆198Updated last month