panernie
Fei Pan is currently currently studying for a Ph.D. at the Chinese Academy of Agricultural Sciences (CAAS). His research interests include natural product pharm
ChinaBeijing
Pinned Repositories
AHTPeptideFusion
alphafold
Open source code for AlphaFold.
apbs-pdb2pqr
APBS - software for biomolecular electrostatics and solvation
Boltzmann-Machine-DCA
Implementation of direct coupling analysis (DCA) for proteins using a Boltzmann machine algorithm.
casanovo
De Novo Mass Spectrometry Peptide Sequencing with a Transformer Model
chemshell-QMMM-protein-setup
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.)
ControlNet
Let us control diffusion models!
DDGScan
Scripts and facilities for in-silico mutagenesis with FoldX, Rosetta and ABAUCS1/2
Peptide_docking_with_AF2_and_RosettAfold
Code and data used in https://doi.org/10.1101/2021.08.01.454656
PyAutoFEP_Gromacs_FEP
panernie's Repositories
panernie/AHTPeptideFusion
panernie/Boltzmann-Machine-DCA
Implementation of direct coupling analysis (DCA) for proteins using a Boltzmann machine algorithm.
panernie/Peptide_docking_with_AF2_and_RosettAfold
Code and data used in https://doi.org/10.1101/2021.08.01.454656
panernie/PyAutoFEP_Gromacs_FEP
panernie/alphafold
Open source code for AlphaFold.
panernie/apbs-pdb2pqr
APBS - software for biomolecular electrostatics and solvation
panernie/chemshell-QMMM-protein-setup
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.)
panernie/ControlNet
Let us control diffusion models!
panernie/DDGScan
Scripts and facilities for in-silico mutagenesis with FoldX, Rosetta and ABAUCS1/2
panernie/DuIvy
some scripts for analysis of MD and CADD. And some tutorials.
panernie/esm
Evolutionary Scale Modeling (esm): Pretrained language models for proteins
panernie/gitskills
panernie/gmx_MMPBSA
gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.
panernie/gromacs_ff
Trusted force field files for gromacs
panernie/Learngit
panernie/Oligomerization-State_and_Contact-Map
panernie/ParaTemp
A package for molecular dynamics analysis and parallel tempering in GROMACS
panernie/Pymol-script-repo
Collected scripts for Pymol
panernie/pytorch-book
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》)
panernie/Swarm-CG
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
panernie/tensorflow-yolov3
🔥 TensorFlow Code for technical report: "YOLOv3: An Incremental Improvement"
panernie/TTClust
clusterize molecular dynamic trajectories (amber, gromacs, charmm, namd, pdb...)
panernie/watvina
implicit or explicit water model based docking with Autodock vina engine. supporting pharmacophore /position constrained docking
panernie/chat2api
A service that can convert ChatGPT on the web to OpenAI API format.
panernie/esm-AxP-GDL
panernie/PACMAN-charge
panernie/pyensembl
Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl