Pinned Repositories
afes-openmm-atom-1
OpenMM-based framework for absolute and relative binding free energy calculations with the Alchemical Transfer Method
AsiteDesign
AutoMD
Easy to get started with molecular dynamics simulation.
backup-slack
A script for backing up your message history from Slack
BAT.py
The Binding Affinity Tool (BAT.py) is a fully automated tool for absolute binding free energy calculations on protein-ligand systems, compatible with the AMBER and OpenMM simulation packages.
BLaDE
BLaDE is a Basic Lambda Dynamics Engine for molecular dynamics based alchemical free energy calculations using multisite lambda dynamics on graphical processor units.
cappable-seq
Compare-annotations
A script for comparing old vs new versions of genome annotations
Convert-NAMD-coordinates-and-Amber-Parameters-to-Desmond-CMS
Use these files to convert Amber parameter file + NAMD simulation output file > desmond .cms file
CreateRemdDirs
Automatically generate input for running M-REMD simulations (and more) in Amber.
AkosNy's Repositories
AkosNy/afes-openmm-atom-1
OpenMM-based framework for absolute and relative binding free energy calculations with the Alchemical Transfer Method
AkosNy/AsiteDesign
AkosNy/AutoMD
Easy to get started with molecular dynamics simulation.
AkosNy/BAT.py
The Binding Affinity Tool (BAT.py) is a fully automated tool for absolute binding free energy calculations on protein-ligand systems, compatible with the AMBER and OpenMM simulation packages.
AkosNy/BLaDE
BLaDE is a Basic Lambda Dynamics Engine for molecular dynamics based alchemical free energy calculations using multisite lambda dynamics on graphical processor units.
AkosNy/cappable-seq
AkosNy/Compare-annotations
A script for comparing old vs new versions of genome annotations
AkosNy/Convert-NAMD-coordinates-and-Amber-Parameters-to-Desmond-CMS
Use these files to convert Amber parameter file + NAMD simulation output file > desmond .cms file
AkosNy/CreateRemdDirs
Automatically generate input for running M-REMD simulations (and more) in Amber.
AkosNy/DIMPLE
Coyote-Maestas Final Version
AkosNy/evolved_synthetic_auxotrophs
AkosNy/DESRES-ff
Force Fields
AkosNy/fep-restraints
Tools to add restraints to FEP runs (currently only AB-FEP). Includes a workflow to determine reference structures and restraint widths from plain MD simulations.
AkosNy/Force-Fields
Force Fields
AkosNy/IQmol3
IQmol version 3
AkosNy/MDFit
Automated molecular dynamics simulations workflow for high-throughput assessment of protein-ligand dynamics
AkosNy/Mutation_Maker
Application for mutagenic primer design. Facilitates development of biocatalysts (Green Chemistry) and new therapeutic proteins.
AkosNy/openmm_sdm_workflow
Example of the use of the single-decoupling method setup workflow
AkosNy/OSCAR
AkosNy/Pseudocycle_small_molecule_binder
Small_molecule_binder_design_use_pseudocycles
AkosNy/pssm_promoter_tool
AkosNy/puffin
deep learning-inspired explainable sequence model for transcription initiation
AkosNy/puffin_manuscript
AkosNy/qmhub
A QM/MM interface
AkosNy/reeds
This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration free energies or ligand binding free energies.
AkosNy/Schrodinger-Script
Some scripts to run Schrödinger jobs on HPC or localhost.
AkosNy/schrodinger_utils
Various integrations to the Schrodinger ecosystem. With major interest on analysis tools for Molecular Dynamics simulations run with Desmond.
AkosNy/Snowprint
Snowprint is a bioinformatic tool to predict the DNA-binding sequence of transcription factors. As opposed to DNAse footprinting, it requires no experimentation.
AkosNy/Thermoters
Structure and Evolution of Constitutive Bacterial Promoters
AkosNy/viparr-ffpublic
Public domain forcefields for viparr