mobleylab Goto Github PK

alchemical-analysis

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

alchemical-setup

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.

benchmarkff

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

benchmarksets

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

binding_dg_water

blues

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

blues-flexible-ligand

contains files for blues-flexible-ligand paper

blues-water-hopping-paper

Contains files for blues-water-hopping paper

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.

chemper

Repository for Chemical Perception Sampling Tools

chemper_si

Using chemper to generate a protein SMIRNOFF with minimal human interference

d3r-2018-autodock-mmgbsa

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

d3r_2018

This repositories contains all the relevant files and scripts we used in D3R Grand Challenge 2018.

d3r_autodock_collab_2018

Contains all the input and run scripts for affinity ranking prediction done for D3R 2018 in collaboration with Stefano Forli.

del_analysis

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

del_bb_design

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

drug-computing

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

fitting-exp

freesolv

Experimental and calculated small molecule hydration free energies

gcncmc_gcmc

gmx_fileprep

Scripts for local gromacs input file preparation

gromacs-binding-scripts

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

guthriesolv

Experimental small molecule hydration free energy dataset

himap

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

hydroxynator

Adjusts topology files with GAFF to have GAFF-DC charges

idac_code

lomap

Alchemical mutation scoring map

lysozyme_binding

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

mobleylab.org

Lab website