Reverse Dependencies of ProDy

The following projects have a declared dependency on ProDy:

• alphafold2-pytorch — AlphaFold2 - Pytorch
• caretta — Fast multiple protein structure alignment
• clumps-ptm — CLUMPS-PTM driver gene discovery using 3D protein structure (Getz Lab).
• compassdock — A comprehensive accurate assessment approach for deep learning based molecular docking
• correlationPlus — A Python package to calculate, visualize and analyze correlations of proteins.
• ddpm-proteins — Denoising Diffusion Probabilistic Models - for Proteins - Pytorch
• fpocketr — Find, characterize, and visualize drug-like pockets in RNA structures.
• frag-pele — FragPELE, a new tool for in silico hit-to-lead drug design, capable of growing a frag_pelement into a core while exploring the protein-ligand conformational space
• geometricus — Fast, structure-based, alignment-free protein embedding
• libprot — A library of utilities for working with proteins
• MSM-PELE — Monte Carlo Protein Energy Landscape Exploration (PELE) coupled with Markov State Model (MSM) analysis with the aim to calculate absolute free energies
• nerrds — NERRDS uses backbone chemical shifts to generate an ensemble
• posebench — Comprehensive benchmarking of protein-ligand structure generation methods
• prody-rhapsody — Python program, based on ProDy, for pathogenicity prediction of human missense variants.
• proflex — A package for proflex creation and manipulation
• ProteinStructureVisualizer — A tool for 3D visualization of monomeric protein structures from PDB files
• PySteMoDA — PySteMoDA
• sblu — Library for munging data files from ClusPro/FTMap/etc.