Pinned Repositories
2018SpringProblems
Homework for 2018 Spring semester
2020-10-cp2k_qmmm_intro
Course materials for "Practical Introduction to QM/MM using CP2K for biomolecular modelling" (https://www.archer2.ac.uk/training/courses/201013-cp2k)
DOCK6_Screening_Protocols
DOCK6_Screening_Protocols: Version 6.9 developed and managed by the Rizzo Lab of Stony Brook University
gnina
A deep learning framework for molecular docking
LigParGen_PyPI
https://pypi.org/project/LigParGen/#files
Q6
Q6 Repository -- EVB, FEP and LIE simulator.
rdkit
The official sources for the RDKit library
setupFEP
Python module to generate .prm files and set up FEP for Q
teachopencadd
TeachOpenCADD: a teaching platform for computer-aided drug design (CADD) using open source packages and data
xy21hb's Repositories
xy21hb/QSARtuna
QSARtuna: QSAR model building with the optuna framework
xy21hb/AToM-OpenMM
OpenMM-based framework for absolute and relative binding free energy calculations with the Alchemical Transfer Method
xy21hb/AutoMolDesigner
The official open-source repository for AutoMolDesigner, an easy-to-use Python application dedicated to automated molecular design.
xy21hb/ThermoNet
ThermoNet is a computational method for quantitative prediction of the impact of single-point mutations on protein thermodynamic stability. The core algorithm of ThermoNet is an ensemble of deep 3D convolutional neural networks.
xy21hb/ResGen
3D_Molecular_Generation
xy21hb/3D-SMGE
A Pipeline for Molecules Generate and Evaluate based on Scaffolds
xy21hb/SeparatedTopologies
Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).
xy21hb/DFRscore
Scoring Synthesizability of Candidates for Virtual Screening
xy21hb/perses
Experiments with expanded ensembles to explore chemical space
xy21hb/RMG-Py
Python version of the amazing Reaction Mechanism Generator (RMG).
xy21hb/Synt-On
Open-source tool for synthons-based library design.
xy21hb/freud
Powerful, efficient particle trajectory analysis in scientific Python.
xy21hb/awesome-gpt4
A curated list of prompts, tools, and resources regarding the GPT-4 language model.
xy21hb/proteinchat
xy21hb/drugchat
DrugChat: Towards Enabling ChatGPT-Like Capabilities on Drug Molecule Graphs
xy21hb/ConPLex_dev
xy21hb/Tora3D
this is official implement of Tora3D
xy21hb/Uni-Mol
Official Repository for the Uni-Mol Series Methods
xy21hb/waterkit
Tool to predict water molecules placement and energy in ligand binding sites
xy21hb/solvation-analysis
A comprehensive suite of tools for analyzing liquid solvation structure.
xy21hb/papers_for_protein_design_using_DL
List of papers about Proteins Design using Deep Learning
xy21hb/Tree-Invent
Tree-Invent: A novel molecular generative model constrained with topological tree
xy21hb/CProMG
xy21hb/HiMap
High Information Mapper (HiMap), successor of the Lead Optimization Mapper (LOMAP)
xy21hb/Machine-learning-for-proteins
Listing of papers about machine learning for proteins.
xy21hb/Survey_AI_Drug_Discovery
xy21hb/autofep
xy21hb/FEgrow
An Open-Source Molecular Builder and Free Energy Preparation Workflow
xy21hb/DRlinker
xy21hb/DrugTax
Categorize small ligands according to chemical properties. Derive simple and explainable features. Only requires SMILEs as inputs.