bio-otto Goto Github PK

dynophores

Dynamic pharmacophore modeling of molecular interactions

easygromacs

This is a simple GUI for protein simulations with Gromacs on Linux systems

efmc

Code to accompany "Practical Cheminformatics With Open Source Software"

emdee

EmDee: A Molecular Dynamics Laboratory

ensembler

example_md_scripts

Python / Molecular Dynamic Simulation Analysis Scripts

gamd-openmm

Gaussian Accelerated Molecular Dynamics (GaMD) is a computational method for both unconstrained enhanced sampling and free energy calculations of biomolecules. It works by adding a harmonic boost potential to smooth the potential energy surface and reduce system energy barriers. http://miao.compbio.ku.edu/GaMD/

gmx_performance_on_hpc

Gromacs performance benchmarking on different HPC platforms

gmx_protocols

Protocols for running MD simulations in Gromacs

gromacs-utilities

gromacs short scripts

gromacs_ff

Trusted force field files for gromacs

hbind

Calculates hydrogen-bond interaction tables for protein-small molecule complexes, based on protein PDB and protonated ligand MOL2 structure input. Raschka et al. (2018) J. Computer-Aided Molec. Design

ibenchmark

Benchmark interpretation of QSAR models

jupyter_dock

Jupyter Dock is a set of Jupyter Notebooks for performing molecular docking protocols interactively, as well as visualizing, converting file formats and analyzing the results.

lab-releated-stuffs

Ready-to-use tools that are always needed in the Lab

lacytools

A high-throughput data extraction package for LC-MS data.

ligand-optimiser

Python optimisation of atomistic ligand charges to maximize receptor binding affinity

lightdock

Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm

ligule

Python Scripts, CLI, and modules for analyzing protein-ligand trajectories

logic-node-editor

Simple Node Editor is just that. Very basic minimal code for implementing a node graph or editor using PySide2. All nodes are built from using QGraphicsItems.

mabdi2-model

Model equations to simulate monoclonal antibody production in a fed batch bioreactor

machine-learning-for-proteins

Listing of papers about machine learning for proteins.

making-it-rain

Cloud-based molecular simulations for everyone

matplotlib-pyside2-example

mbuild

A hierarchical, component based molecule builder

md-course

Material related to the course in Molecular Dynamics

mdacli

Command line interface for MDAnalysis

mdanalysis-talks

A repository for MDAnalysis talks

mdciao

mdciao: Analysis of Molecular Dynamics Simulations Using Residue Neighborhoods

mdorado