Name: Mobley Lab at UC Irvine
Type: Organization
Bio: Binding free energies, molecular interactions, solvation thermodynamics, and statistical mechanics of biomolecules
Location: University of California, Irvine
Blog: http://www.mobleylab.org
Mobley Lab at UC Irvine's Projects
An open tool implementing some recommended practices for analyzing alchemical free energy calculations
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.
Compare optimized geometries and energies from various force fields with respect to a QM reference.
Benchmark sets for binding free energy calculations: Perpetual review paper, discussion, datasets, and standards
Applications of nonequilibrium candidate Monte Carlo (NCMC) to ligand binding mode sampling
contains files for blues-flexible-ligand paper
Contains files for blues-water-hopping paper
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.
Repository for Chemical Perception Sampling Tools
Using chemper to generate a protein SMIRNOFF with minimal human interference
binding affinity ranking using MM-GBSA and AutoDock score in D3R 2018
This repositories contains all the relevant files and scripts we used in D3R Grand Challenge 2018.
Contains all the input and run scripts for affinity ranking prediction done for D3R 2018 in collaboration with Stefano Forli.
Code to analyze the data from DNA-encoded libraries (DELs)
Computational enumeration of DNA-encoded libraries with various building block filtering and selection strategies
Educational materials for, and related to, UC Irvine's Drug Discovery Computing Techniques course (PharmSci 175/275), currently taught by David Mobley.
Experimental and calculated small molecule hydration free energies
Scripts for local gromacs input file preparation
Scripts relating to setup of binding studies for the GROMACS simulation package
Experimental small molecule hydration free energy dataset
High Information Mapper (HiMap), successor of the Lead Optimization Mapper (LOMAP)
Adjusts topology files with GAFF to have GAFF-DC charges
Alchemical mutation scoring map
Aggregator of binding data of small molecules to model binding sites in T4 lysozyme mutants, as popularized by Matthews, Shoichet and others.
Lab website