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ligpargen_2.3

LigParGen python package version 2.3 (beta)

ligpargentools

Scripts to set up condensed phase simulations using of LigParGen Server

ligpos

Position ligand back into its bound position

lintools

Python script that creates 2D protein-ligand interaction images

lipid14togromacs

liquidbenchmark

lstm_peptides

Long short-term memory recurrent neural networks for learning peptide and protein sequences to later design new, similar examples.

machine-learning-tutorials

machine learning and deep learning tutorials, articles and other resources

machinelearningtcgahnsc-binf

Supplementary materials and code for the BMC Bioinformatics journal article "Machine learning with the TCGA-HNSC dataset: Improving performance by addressing inconsistency, sparsity, and high-dimensionality" by authors Michael C. Rendleman, B.S.E.; John M. Buatti, MD; Terry A. Braun, Ph.D.; Brian J. Smith, Ph.D.; Bart Brown; Chibuzo Nwakama; Reinhard Beichel, Ph.D.; Thomas L. Casavant, Ph.D.

macro_analyzer

This is a public source for the files reported in "Automatization of Generic Shapes for Macrocycle Conformational Sampling"

making-it-rain

Cloud-based molecular simulations for everyone

mapd

Model-based Analysis of Protein Degradability

matplotlib-gallery

Examples of matplotlib codes and plots

mbuild

A hierarchical, component based molecule builder

mcdock

McDock: Simple Monte Carlo docking algorithm in C++

md-analysis-tools

scripts for analyzing molecular dynamics trajectories using VMD

md-nonparametric-clustering

Uncovering large-scale conformational change in molecular dynamics without prior knowledge using modern clustering techniques.

md_workflow

Molecular dynamics workflow directory structure

mdanalysis-workshop

MDAnalysis Tutorial at the 2015 CECAM Macromolecular simulation software workshop

mdanalysiscookbook

Examples and tutorials of using MDAnalysis

mdpow

Calculation of water/solvent partition coefficients with Gromacs.

medchem_moves

meetdock

Protein-Protein Docking software

megadock

An ultra-high-performance protein-protein docking for heterogeneous supercomputers

metabolicpathwayprediction

mhfp

Molecular MHFP fingerprints for cheminformatics applications

mldl-md-dynamics

A repository of update in molecular dynamics field by recent progress in machine learning and deep learning.

mmdevel

Molecular modeling scripts and things

mmtf-workshop-2018

Structural Bioinformatics Training Workshop & Hackathon 2018

modseminario

Contains the modified Seminario method program along with set of example files.