Mobley Lab at UC Irvine
Binding free energies, molecular interactions, solvation thermodynamics, and statistical mechanics of biomolecules
University of California, Irvine
Pinned Repositories
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.
benchmarksets
Benchmark sets for binding free energy calculations: Perpetual review paper, discussion, datasets, and standards
blues
Applications of nonequilibrium candidate Monte Carlo (NCMC) to ligand binding mode sampling
drug-computing
Educational materials for, and related to, UC Irvine's Drug Discovery Computing Techniques course (PharmSci 175/275), currently taught by David Mobley.
FreeSolv
Experimental and calculated small molecule hydration free energies
GuthrieSolv
Experimental small molecule hydration free energy dataset
Lomap
Alchemical mutation scoring map
SolvationToolkit
In-house tools for setting up arbitrary solute-solvent mixtures for simulation in GROMACS, Amber, OpenMM or other codes
Training
Lab policies, training, style guides, etc.
Mobley Lab at UC Irvine's Repositories
MobleyLab/drug-computing
Educational materials for, and related to, UC Irvine's Drug Discovery Computing Techniques course (PharmSci 175/275), currently taught by David Mobley.
MobleyLab/alchemical-analysis
An open tool implementing some recommended practices for analyzing alchemical free energy calculations
MobleyLab/FreeSolv
Experimental and calculated small molecule hydration free energies
MobleyLab/benchmarksets
Benchmark sets for binding free energy calculations: Perpetual review paper, discussion, datasets, and standards
MobleyLab/Lomap
Alchemical mutation scoring map
MobleyLab/Training
Lab policies, training, style guides, etc.
MobleyLab/blues
Applications of nonequilibrium candidate Monte Carlo (NCMC) to ligand binding mode sampling
MobleyLab/GuthrieSolv
Experimental small molecule hydration free energy dataset
MobleyLab/SeparatedTopologies
Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).
MobleyLab/chemper
Repository for Chemical Perception Sampling Tools
MobleyLab/HiMap
High Information Mapper (HiMap), successor of the Lead Optimization Mapper (LOMAP)
MobleyLab/benchmarkff
Compare optimized geometries and energies from various force fields with respect to a QM reference.
MobleyLab/DEL_analysis
Code to analyze the data from DNA-encoded libraries (DELs)
MobleyLab/mobleylab.org
Lab website
MobleyLab/qm-theory-benchmark
MobleyLab/DEL_BB_design
Computational enumeration of DNA-encoded libraries with various building block filtering and selection strategies
MobleyLab/openff-spellbook
Handy functionality for working with OpenFF data
MobleyLab/waterNES
Workflows to calculate relative free energies using non-equilibrium switching for buried water molecules
MobleyLab/slow-rotations
Continuation of Travis' Slow Rotations project
MobleyLab/wbointerpolation
Analysis scripts for the development of wiberg bond order interpolated parameters in the Open Force Field.
MobleyLab/fitting-exp
MobleyLab/gmx_fileprep
Scripts for local gromacs input file preparation
MobleyLab/gromacs-binding-scripts
Scripts relating to setup of binding studies for the GROMACS simulation package
MobleyLab/PME-RF-benchmark
Supporting information for a paper benchmarking PME vs RF performance for relative free energies
MobleyLab/T4_MSM
Code and files for analyzing the discrete conformational states of T4 L99A
MobleyLab/binding_dG_water
MobleyLab/ConformerDependentCharges
MobleyLab/GCNCMC_GCMC
MobleyLab/sampl7-physical-property-challenge-manuscript
Provided are figures, tables, and supplementary documents for the "Evaluation of logP, pKa, and logD predictions from the SAMPL7 blind challenge" paper.
MobleyLab/water_benchmark_paper
Supporting information for paper on benchmarking enhanced sampling techniques for water sampling