Fei Pan's Projects
Open source code for AlphaFold.
APBS - software for biomolecular electrostatics and solvation
Implementation of direct coupling analysis (DCA) for proteins using a Boltzmann machine algorithm.
De Novo Mass Spectrometry Peptide Sequencing with a Transformer Model
A service that can convert ChatGPT on the web to OpenAI API format.
MM and QM/MM setup for a metalloprotein using GROMACS, Chemshell and ORCA (Using the CHARMM forcefield (both in GROMACS and with Chemshell) and the ORCA code as QM code for Chemshell.)
Let us control diffusion models!
Scripts and facilities for in-silico mutagenesis with FoldX, Rosetta and ABAUCS1/2
some scripts for analysis of MD and CADD. And some tutorials.
Evolutionary Scale Modeling (esm): Pretrained language models for proteins
gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.
Trusted force field files for gromacs
User-friendly WebUI for LLMs (Formerly Ollama WebUI)
A package for molecular dynamics analysis and parallel tempering in GROMACS
Code and data used in https://doi.org/10.1101/2021.08.01.454656
Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl
Collected scripts for Pymol
PyTorch tutorials and fun projects including neural talk, neural style, poem writing, anime generation (《深度学习框架PyTorch:入门与实战》)
#1 Locally hosted web application that allows you to perform various operations on PDF files
Swarm-CG: Automatic Parametrization of Bonded Terms in MARTINI-based Coarse-Grained Models of Simple to Complex Molecules via Fuzzy Self-Tuning Particle Swarm Optimization
🔥 TensorFlow Code for technical report: "YOLOv3: An Incremental Improvement"
clusterize molecular dynamic trajectories (amber, gromacs, charmm, namd, pdb...)
implicit or explicit water model based docking with Autodock vina engine. supporting pharmacophore /position constrained docking