Alternatives and similar repositories for mdml

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

• tiwarylab / af2rave
  Boltzmann-ranked alternative protein conformations from reduced-MSA AlphaFold2
  ☆59Updated 2 weeks ago
• patrickbryant1 / RareFold
  Structure prediction and design of proteins with noncanonical amino acids
  ☆108Updated last week
• tiwarylab / alphafold2rave
  ☆69Updated last year
• tiwarylab / GrASP
  Graph Attention Site Prediction (GrASP): Identifying Druggable Binding Sites Using Graph Neural Networks with Attention
  ☆54Updated 4 months ago
• iambic-therapeutics / np-bench
  A benchmark for 3D biomolecular structure prediction models
  ☆66Updated 5 months ago
• KULL-Centre / CALVADOS
  ☆74Updated last week
• iriziotis / Uniprot-PDB-mapper
  Quick mapping of Uniprot sequences to PDB structures
  ☆34Updated 6 months ago
• huhlim / cg2all
  Convert coarse-grained protein structure to all-atom model
  ☆46Updated 4 months ago
• PeptoneLtd / proteinmpnn_ddg
  Novel estimator for the change in stability upon point mutation in monomeric and multimeric proteins.
  ☆56Updated 5 months ago
• wallnerlab / AFsample2
  Modelling protein conformational landscape with Alphafold
  ☆53Updated 2 months ago
• vsomnath / flexdock
  Composing Unbalanced Flows for Flexible Docking and Relaxation (ICLR 2025)
  ☆50Updated 4 months ago
• GMdSilva / gms_natcomms_1705932980_data
  Data sharing for High-throughput Prediction of Changes in Protein Conformational Distributions with Subsampled AlphaFold2
  ☆39Updated last year
• haddocking / arctic3d
  Automatic Retrieval and ClusTering of Interfaces in Complexes from 3D structural information
  ☆32Updated 3 weeks ago
• ShenLab / SeqDance
  code for SeqDance/ESMDance, biophysics-informed protein language models
  ☆41Updated 6 months ago
• microsoft / bioemu-benchmarks
  Benchmarking code accompanying the release of `bioemu`
  ☆46Updated 3 months ago
• kamerlinlab / KIF
  KIF - Key Interactions Finder. A python package to identify the key molecular interactions that regulate any conformational change.
  ☆31Updated last month
• fmaschietto / mdigest
  ☆34Updated last year
• molecularmodelinglab / plantain
  Fast and accurate molecular docking with an AI pose scoring function
  ☆42Updated last year
• matteoferla / rdkit_to_params
  Create or modify Rosetta params files (topology files) from scratch, RDKit mols or another params file
  ☆35Updated 3 months ago
• plinder-org / runs-n-poses
  A benchmark dataset for protein-ligand co-folding prediction
  ☆35Updated 2 months ago
• patrickbryant1 / Cfold
  Structure prediction of alternative protein conformations
  ☆80Updated 8 months ago
• pstansfeld / MemProtMD
  ☆45Updated 5 months ago
• aethertier / secstructartist
  A python module to plot secondary structure schemes
  ☆25Updated 2 years ago
• ci-lab-cz / streamd
  Fully automated high-throughput MD pipeline
  ☆81Updated last month
• BrooksResearchGroup-UM / pyCHARMM-Workshop
  pyCHARMM tutorial, documentation and examples. This repository contains materials originally from the pyCHARMM Workshop run at the Univer…
  ☆71Updated 3 weeks ago
• novonordisk-research / pepfunn
  Python package for the analysis of natural and modified peptides using a set of modules to study their sequences
  ☆40Updated 2 weeks ago
• log-md / logmd
  ☆65Updated 6 months ago
• miqueleg / protonation-optimizer
  Histidine Protonation State Optimizer for setting up MD simulations based on semi-empirical QM resonance
  ☆20Updated 3 weeks ago
• giacomo-janson / sam2
  Deep generative modeling of protein structural ensembles
  ☆28Updated last month
• pritampanda15 / PandaMap
  Ligand-Protein Interaction Mapping
  ☆62Updated 5 months ago