MobleyLab/gromacs-binding-scripts

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MobleyLab/gromacs-binding-scripts

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Scripts relating to setup of binding studies for the GROMACS simulation package

drug-computing

Educational materials for, and related to, UC Irvine's Drug Discovery Computing Techniques course (PharmSci 175/275), currently taught by David Mobley.

Jupyter Notebook

alchemical-analysis

An open tool implementing some recommended practices for analyzing alchemical free energy calculations

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.

FreeSolv

Experimental and calculated small molecule hydration free energies

benchmarksets

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

Lomap

Alchemical mutation scoring map

Training

Lab policies, training, style guides, etc.

blues

Applications of nonequilibrium candidate Monte Carlo (NCMC) to ligand binding mode sampling

SolvationToolkit

In-house tools for setting up arbitrary solute-solvent mixtures for simulation in GROMACS, Amber, OpenMM or other codes

GuthrieSolv

Experimental small molecule hydration free energy dataset

SeparatedTopologies

Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).

chemper

Repository for Chemical Perception Sampling Tools

HiMap

High Information Mapper (HiMap), successor of the Lead Optimization Mapper (LOMAP)

alchemical-setup

benchmarkff

Compare optimized geometries and energies from various force fields with respect to a QM reference.

DEL_analysis

Code to analyze the data from DNA-encoded libraries (DELs)

Jupyter Notebook

off-ffcompare

Compare molecular structures after energy minimization in various force fields.

Jupyter Notebook

D3R-2018-AutoDock-MMGBSA

binding affinity ranking using MM-GBSA and AutoDock score in D3R 2018

mobleylab.org

quanformer

quanformer: quantum mechanical analysis of molecular conformers

SMIRNOFF_paper_code

Code/tools relating to the initial SMIRNOFF format paper

Jupyter Notebook

qm-theory-benchmark

Jupyter Notebook

openff-spellbook

Handy functionality for working with OpenFF data

wbointerpolation

Analysis scripts for the development of wiberg bond order interpolated parameters in the Open Force Field.

Jupyter Notebook

thermoML_data

Jupyter Notebook

blues-water-hopping-paper

Contains files for blues-water-hopping paper

off_nitrogens

Exploring the planar or pyramidal nature of conjugated nitrogens

lysozyme_binding

Aggregator of binding data of small molecules to model binding sites in T4 lysozyme mutants, as popularized by Matthews, Shoichet and others.

orphans

Orphaned tools/scripts that might be useful but don't currently have a good home

slow-rotations

DEL_BB_design

Computational enumeration of DNA-encoded libraries with various building block filtering and selection strategies

Jupyter Notebook

fitting-exp

gmx_fileprep

Scripts for local gromacs input file preparation

yank-restraints

Benchmarking project testing different restraints schemes for free energy calculations with Yank

PME-RF-benchmark

Supporting information for a paper benchmarking PME vs RF performance for relative free energies

waterNES

Workflows to calculate relative free energies using non-equilibrium switching for buried water molecules

Hydroxynator

Adjusts topology files with GAFF to have GAFF-DC charges

buried-water-electrostatics

We examined the electrostatic potential at the locations of buried waters within proteins to see if this exhibited any asymmetric behavior (previous work we had done suggested perhaps it might) and found none. Here's the code to reproduce.