hklem

TITAN

elecTric fIeld generaTion And maNipulation

basic_simulation_training

A document for the Living Journal of Computational Molecular Science (LiveCoMS) which describes basic training for molecular simulations (oriented towards molecular dynamics (MD)), providing some training itself and linking out to other helpful information elsewhere. The intent is that this provide information on the prerequisites which will be required for understanding/following many of the other "best practices" documents being prepared.

zotero-reading-list

Keep track of whether you've read items in Zotero

tupa

TUPÃ was developed to analyze electric field properties in molecular simulations

QMzyme

QM-based enzyme model generation and validation.

icons-for-chemists

camlc24.github.io

Website of the CAMLC24 workshop

robert

Automated machine learning protocols that start from CSV databases of descriptors or SMILES and produce publication-quality results in Chemistry studies with only one command line.

camlc24.github.io

Website of the CAMLC24 workshop

grant-template

A template for NIH style grants in Latex

camlc24.github.io

Website of the CAMLC24 workshop

enlighten2-pymol

PyMOL plugin for enlighten2

enlighten2

Protocols and tools to run (automated) atomistic simulations of enzyme-ligand systems

scikit-learn

scikit-learn: machine learning in Python

biosimspace

An interoperable Python framework for biomolecular simulation.

cclib

Parsers and algorithms for computational chemistry logfiles

IGPS_QM_cluster_models

software-development

A primer on software development best practices for computational chemistry

RINRUS

Residue Interaction Network ResidUe Selector (RINRUS) public release

theory-suite-wiki

This repository holds the source files and html files of a documentation webpage made by the members of the Patonlab and BioE-KimLab at CSU

enzyASM

A toolkit for enzyme active site modeling (ASM).

shapeGMMTorch

DISCO

DISCO - distributing computed outputs.

GoodVibes

Calculate quasi-harmonic free energies from Gaussian output files with temperature and other corrections

aqme

Automated Quantum Mechanical Environments (AQME) offers transparent and reproducible workflows available for Jupyter Notebooks and command lines, including: 1) RDKit- and CREST-based conformer generation, 2) QM input file creation, 3) post-processing of QM output files, 4) generation of xTB, DFT and RDKit descriptors. https://aqme.readthedocs.io

Pymol-script-repo

Collected scripts for Pymol

pyssian

Pyssian is an object oriented library for parsing Gaussian logfiles and input files which aims to facilitate the everyday scripting of computational chemists using Gaussian.

sdsc-summer-institute-2021

San Diego Supercomputer Center Summer Institute

GMM-Positions

Gaussian Mixture Model for particle positions using alignments

paton_group_workflows

Python Code, shell scripts, templates, submission scripts and compchem specific workflows for use in the Paton Lab