ndonyapour
Senior Computational Scientist
Axle Research and Technologies6116 Executive Blvd #400, Rockville, MD 20852
Pinned Repositories
ClassicalGSG
A new logP predictor method using GSG and NNs
flexibletopology
ML-based molecular representation models using PyTorch
AutoDock-Vina
AutoDock Vina
BFEE2_NAMD
Binding free energy simulations with BFEE2
BFEE2_OpenMM
Free energy calculations by running OpenMM simulations with BFEE2 protocol
funnel_metadynamics
Funnel Metadynamics MD Simulations
geometricCVs_OpenMM
Geometric CVs are implemented as OpenMM force plugin
mm-workflows
Molecular modeling workflows and extensions for workflow inference compiler
MolGAN
Tensorflow implementation of MolGAN: An implicit generative model for small molecular graphs
workflow-inference-compiler
A domain specific language for creating scientific pipelines
ndonyapour's Repositories
ndonyapour/geometricCVs_OpenMM
Geometric CVs are implemented as OpenMM force plugin
ndonyapour/funnel_metadynamics
Funnel Metadynamics MD Simulations
ndonyapour/BFEE2_NAMD
Binding free energy simulations with BFEE2
ndonyapour/BFEE2_OpenMM
Free energy calculations by running OpenMM simulations with BFEE2 protocol
ndonyapour/MolGAN
Tensorflow implementation of MolGAN: An implicit generative model for small molecular graphs
ndonyapour/AutoDock-Vina
AutoDock Vina
ndonyapour/BFEE2
binding free energy estimator 2
ndonyapour/bindpredict
A method to predict the protein category a molecule can bind
ndonyapour/mm-workflows
Molecular modeling workflows and extensions for workflow inference compiler
ndonyapour/wepy
Weighted Ensemble simulation framework in Python
ndonyapour/workflow-inference-compiler
A domain specific language for creating scientific pipelines
ndonyapour/biobb_adapters
Biobb_adapters is the Biobb module collection to use the building blocks with several workflow managers.
ndonyapour/biobb_amber
Biobb_amber is a BioBB category for AMBER MD package.
ndonyapour/biobb_analysis
Biobb_analysis is the Biobb module collection to perform analysis of molecular dynamics simulations.
ndonyapour/biobb_vs
Biobb_vs is the Biobb module collection to perform virtual screening studies.
ndonyapour/ClassicalGSG
A new logP predictor method using GSG and NNs
ndonyapour/cwl-utils
Python utilities for CWL
ndonyapour/cwltool
Common Workflow Language reference implementation
ndonyapour/flexibletopology
ML-based molecular representation models using PyTorch
ndonyapour/mm-tools
ndonyapour/pdbfixer
PDBFixer fixes problems in PDB files
ndonyapour/timeseriesplots
Tools for analyzing and plotting timeseries data in realtime
ndonyapour/toil
A scalable, efficient, cross-platform (Linux/macOS) and easy-to-use workflow engine in pure Python.
ndonyapour/TorchBFEE2
Implementing BFEE2 CVs with PyTorch