Repositories list

• MELDNMRParser

  Public
  Reader/writer for NEF files

  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 26, 2026May 26, 2026

• geemeld

  Public
  Python

  •11 fork•00 stars•00 issues•00 pull requests•Updated May 26, 2026May 26, 2026

• mddba-web

  Public
  MDDBAmerica Website

  HTML

  •

  MIT License

  •11 fork•00 stars•00 issues•00 pull requests•Updated May 15, 2026May 15, 2026

• NEF_MELD

  Public
  Using NOESY NMR data to fold and generate NMR accurate ensembles of proteins from sequence

  11 fork•00 stars•00 issues•00 pull requests•Updated May 12, 2026May 12, 2026

• Thompson_sampling

  Public
  Thompson sampling for enhanced exploration of peptide libraries

  Python

  •11 fork•22 stars•00 issues•00 pull requests•Updated May 9, 2026May 9, 2026

• AF3-CBA-pipeline

  Public
  AlphaFold 3 Competitive Binding Assay for High-Throughput Screening of Protein Candidates

  00 forks•00 stars•00 issues•00 pull requests•Updated Apr 1, 2026Apr 1, 2026

• MDDB-Automator

  Public
  This repository provides automation tools for MDDB to streamline data analysis, transfer, and upload workflows.

  Shell

  •11 fork•00 stars•00 issues•00 pull requests•Updated Mar 2, 2026Mar 2, 2026

• MDDB_Tutorials

  Public
  This repository contains the tutorials about MDDB.

  11 fork•00 stars•00 issues•00 pull requests•Updated Feb 24, 2026Feb 24, 2026

• Biomolecular-Design-with-AI-Perez-Lab

  Public
  This repo contains all the information needed to get started in Dr. Perez's lab, including sections on AutoDock, Chimera, BindCraft, AMBER, RFDiffusion, Protein…

  11 fork•00 stars•00 issues•00 pull requests•Updated Dec 31, 2025Dec 31, 2025

• meld-grappa

  Public
  Integrating Machine Learning Force Field Grappa to MELD

  Python

  •

  Other

  •3535 forks•11 star•00 issues•00 pull requests•Updated Dec 12, 2025Dec 12, 2025

• peptFF-benchmark

  Public
  Jupyter Notebook

  •00 forks•44 stars•00 issues•00 pull requests•Updated Dec 11, 2025Dec 11, 2025

• MDZip

  Public
  This Git repository contains MDZip, a program that leverages the power of autoencoders with residual connections to compress molecular dynamics trajectories whi…

  Jupyter Notebook

  •22 forks•33 stars•00 issues•00 pull requests•Updated Nov 12, 2025Nov 12, 2025

• FoldBindDataset

  Public
  Benchmark dataset of protein and protein peptide complexes.

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Nov 9, 2025Nov 9, 2025

• Competitive_binding

  Public
  Jupyter Notebook

  •00 forks•33 stars•00 issues•00 pull requests•Updated Oct 31, 2025Oct 31, 2025

• AlphaFolding

  Public
  Jupyter Notebook

  •

  MIT License

  •00 forks•44 stars•00 issues•00 pull requests•Updated Oct 28, 2025Oct 28, 2025

• ml-simplefold

  Public
  Python

  •

  MIT License

  •9494 forks•00 stars•00 issues•00 pull requests•Updated Oct 24, 2025Oct 24, 2025

• boltz_noesy

  Public
  Integration of NOESY restraints to Boltz-1 biomolecular interaction model

  Python

  •

  MIT License

  •873873 forks•00 stars•00 issues•00 pull requests•Updated Oct 6, 2025Oct 6, 2025

• MELD_essentials

  Public
  This repository contains helpful utilities and tools when working with MELD

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 29, 2025Aug 29, 2025

• Miniprotein_Design

  Public
  Shell

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 6, 2025Aug 6, 2025

• DIM

  Public
  Predict pucker conformations in a DNA with arbitrary length

  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 10, 2025Jun 10, 2025

• kinetic_fit

  Public
  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 21, 2025May 21, 2025

• peptide-binding-predictor

  Public
  A machine learning pipeline for predicting peptide binding from amino acid sequences using a convolutional neural network. Includes tools for handling sequences…

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 8, 2025May 8, 2025

• CHM4910

  Public
  CURE class Tutorials

  Shell

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 14, 2025Mar 14, 2025

• MELD_tutorials

  Public
  Python

  •00 forks•33 stars•00 issues•00 pull requests•Updated Nov 13, 2024Nov 13, 2024

• MELD-ADAPT

  Public
  Python

  •11 fork•00 stars•00 issues•00 pull requests•Updated Oct 23, 2024Oct 23, 2024

• BioML

  Public
  Shell

  •00 forks•00 stars•00 issues•00 pull requests•Updated Oct 7, 2024Oct 7, 2024

• AF-CBA-pipeline

  Public
  3 stage filtering pipeline for finding binding epitopes

  Python

  •

  MIT License

  •22 forks•66 stars•00 issues•00 pull requests•Updated Aug 2, 2024Aug 2, 2024

• ChemReality

  Public
  Students as Molecular Modelers

  Shell

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 14, 2024Jun 14, 2024

• Tutorials

  Public
  PDNALab's tutorials about writing, running, compiling softwares and more.

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 4, 2024Apr 4, 2024

• extended-ensemble

  Public
  Jupyter Notebook

  •

  GNU General Public License v3.0

  •22 forks•22 stars•00 issues•00 pull requests•Updated Mar 3, 2023Mar 3, 2023