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@PDNALab

Perez Lab @ Chemistry UF

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  1. AF-CBA-pipeline AF-CBA-pipeline Public

    Forked from arupmondal835/AF-CBA-pipeline

    3 stage filtering pipeline for finding binding epitopes

    Python 6 1

  2. peptFF-benchmark peptFF-benchmark Public

    Jupyter Notebook 5

  3. AlphaFolding AlphaFolding Public

    Jupyter Notebook 4

  4. Competitive_binding Competitive_binding Public

    Jupyter Notebook 3

  5. QM_MM_Study_P53-MDM2_Binding QM_MM_Study_P53-MDM2_Binding Public

    Inputs for QM, MM and MELD. Structural outputs

    Python 3

  6. MDZip MDZip Public

    This Git repository contains MDZip, a program that leverages the power of autoencoders with residual connections to compress molecular dynamics trajectories while reconstructing global and local st…

    Jupyter Notebook 3 3

Repositories

Showing 10 of 40 repositories
  • MELDNMRParser Public

    Reader/writer for NEF files

    PDNALab/MELDNMRParser's past year of commit activity
    Python 0 MIT 0 0 0 Updated Sep 15, 2026
  • geemeld Public
    PDNALab/geemeld's past year of commit activity
    Python 0 1 0 0 Updated May 26, 2026
  • mddba-web Public Forked from ImeCMR/mddba-web

    MDDBAmerica Website

    PDNALab/mddba-web's past year of commit activity
    HTML 0 MIT 1 0 0 Updated May 15, 2026
  • NEF_MELD Public Forked from binodlk/NEF_MELD

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

    PDNALab/NEF_MELD's past year of commit activity
    0 1 0 0 Updated May 12, 2026
  • Thompson_sampling Public

    Thompson sampling for enhanced exploration of peptide libraries

    PDNALab/Thompson_sampling's past year of commit activity
    Python 2 1 0 0 Updated May 9, 2026
  • AF3-CBA-pipeline Public

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

    PDNALab/AF3-CBA-pipeline's past year of commit activity
    0 0 0 0 Updated Apr 1, 2026
  • MDDB-Automator Public

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

    PDNALab/MDDB-Automator's past year of commit activity
    Shell 0 1 0 0 Updated Mar 2, 2026
  • MDDB_Tutorials Public

    This repository contains the tutorials about MDDB.

    PDNALab/MDDB_Tutorials's past year of commit activity
    0 1 0 0 Updated Feb 24, 2026
  • Biomolecular-Design-with-AI-Perez-Lab Public Forked from alyssablood/Biomolecular-Design-with-AI-Perez-Lab

    This repo contains all the information needed to get started in Dr. Perez's lab, including sections on AutoDock, Chimera, BindCraft, AMBER, RFDiffusion, ProteinMPNN, and AlphaFold3.

    PDNALab/Biomolecular-Design-with-AI-Perez-Lab's past year of commit activity
    0 1 0 0 Updated Dec 31, 2025
  • meld-grappa Public Forked from maccallumlab/meld

    Integrating Machine Learning Force Field Grappa to MELD

    PDNALab/meld-grappa's past year of commit activity
    Python 1 35 0 0 Updated Dec 12, 2025
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