yongwangcph Goto Github PK

abpenabledgromacs

A hacked, hardwired GROMACS-4.5.5 that runs a few types of adaptively biased molecular dynamics

af2complex

Predicting direct protein-protein interactions with AlphaFold deep learning neural network models.

alphafold-multistate

alphafold-stepbystep

Run AlphaFold-Multimer step by step

alphafold_non_docker

AlphaFold2 non-docker setup

alphapickle

amber-maestro-lipid-tutorial

Tutorial to build AMBER compatable protein+lipid systems

azahar

A PyMOL plugin for construction, visualization and analysis of glycan molecules. https://www.ncbi.nlm.nih.gov/pubmed/27549814

ball

The Biochemical Algorithms Library

bat.py

A fully automated python tool for high-performance absolute binding free energy calculations

benchmarksets

Benchmark sets for binding free energy calculations: Perpetual review paper, discussion, datasets, and standards

binless-wham

Binless weighted histogram analysis

bioicons

A library of free open source icons for science illustrations in biology and chemistry

biologists-guide-to-computing

Book introducing practical computing concepts to biologists

bitcoin

Bitcoin integration/staging tree

blenderspike

A Blender add-on to bring animations from NEURON

cadnano2

PyQt5 port of cadnano2

calculate-bilayer-power-spectrum

ccmpred

Protein Residue-Residue Contacts from Correlated Mutations predicted quickly and accurately.

cg2all

Convert coarse-grained protein structure to all-atom model

cg2at

Conversion of coarsegrain to atomistic (complete rewrite of the original CG2AT)

cg2at2

chem-ga-2600

Notebooks for NYU Statistical Mechanics

cmapoptimizer

Monte Carlo simulated annealing to optimize the CMAP potentials in molecular mechanics force fields with reweighting calculation

cypacatalysis_input

dctmd

dissipation corrected targeted molecular dynamics

dna-hinge-simulations

Files associated with DNA hinge simulations

drdiff

Stochastic drift-diffusion (DrDiff) framework can evaluate free energy, drift and diffusion coefficients, transition path and first passage times using trajectory time traces.

ensembler

evodock

A Memetic Algorithm boosts accuracy and speed of all-atom protein-protein docking