akosny Goto Github PK
Name: Akos Nyerges
Type: User
Bio: https://www.linkedin.com/in/akosnyerges/
Location: Boston, US
Name: Akos Nyerges
Type: User
Bio: https://www.linkedin.com/in/akosnyerges/
Location: Boston, US
OpenMM-based framework for absolute and relative binding free energy calculations with the Alchemical Transfer Method
Easy to get started with molecular dynamics simulation.
A script for backing up your message history from Slack
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 is a Basic Lambda Dynamics Engine for molecular dynamics based alchemical free energy calculations using multisite lambda dynamics on graphical processor units.
A script for comparing old vs new versions of genome annotations
Use these files to convert Amber parameter file + NAMD simulation output file > desmond .cms file
Automatically generate input for running M-REMD simulations (and more) in Amber.
Force Fields
Coyote-Maestas Final Version
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.
Force Fields
IQmol version 3
A Generalised workflow for obtaining protein and peptide molecular structures, docking the peptide into the protein and running a molecular dynamic simulation over a large number of trajectories.
Automated molecular dynamics simulations workflow for high-throughput assessment of protein-ligand dynamics
Application for mutagenic primer design. Facilitates development of biocatalysts (Green Chemistry) and new therapeutic proteins.
Example of the use of the single-decoupling method setup workflow
Funding schemes and travel grant opportunities for postdocs
Small_molecule_binder_design_use_pseudocycles
deep learning-inspired explainable sequence model for transcription initiation
A QM/MM interface
Supporting code for Ostrov et al., Science, 2016
A declarative, efficient, and flexible JavaScript library for building user interfaces.
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google ❤️ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.