Resources

Github

• MobleyLab Repositories
• BLUES: OpenMM Package for applying Non-equilibrium candidate Monte Carlo moves (NCMC) in molecular dynamics (MD) simulations to help sample between different ligand binding modes.
• Benchmark Sets: Benchmark sets for binding free energy calculations: Perpetual review paper, discussion, datasets, and standards
• FreeSolv: Experimental and calculated small molecule hydration free energies database
• Hydroxynator: Adjusts topology files with GAFF to have GAFF-DC charges.
• Lomap: Alchemical mutation scoring map
• Solvation Toolkit: Tools for setting up arbitrary (currently non-water) solute-solvent mixtures for simulation in GROMACS or AMBER formats.
• OpenForceField: Contains the SMIRNOFF force field and other tools from the Open Force Field Initiative related to creating and parameterizing force fields .

Reference Materials

Tutorial and Teaching Material

• Alchemistry.org: A website we help maintain with background information, tutorials, and other material on free energy calculations. Still a work in progress.
• Drug Computing course materials: Training materials relating to python, scientific computing, and common computational tools used in the lab and more broadly relating to drug discovery. Also repository for UCI’s PharmSci 175/275 course materials.
• Basic Simulation Training: A GitHub repository containing material introducing molecular dynamics simulations and giving some fundamentals/instruction in basic knowledge.

Books we like

• Leach’s Molecular Modelling: Principles and Applications. This is probably still the best relatively introductory overview of molecular modeling and simulations.
• Frenkel and Smit’s Understanding Molecular Simulation. A good companion to Leach — where Leach can lack technical detail, this book has it.
• Dill and Bromberg, Molecular Driving Forces: Statistical Thermodynamics in Biology, Chemistry, Physics, and Nanoscience. Statistical thermodynamics from a toy model point of view.
• Zuckerman’s Statistical Physics of Biomolecules
• Schlick’s Molecular Modeling and Simulation. Another good book on molecular simulations, and more recent than Leach.
• “Drug Design: Structure and Ligand-Based Approaches.” Disclosure — we wrote a chapter of this book.

For Prospective Lab Members

• Lab facilities and computing – We have a local computer cluster, part of the Green Planet cluster at UCI. Our portion of this is currently under expansion. We also have a number of GPU machines, and typically have time on larger supercomputing facilities as well.
• Software – We typically run simulations using OpenMM or GROMACS with force fields in the AMBER family. We have licenses to various software packages including AMBER, PyMol, and OpenEye toolkits.
• Why I chose UCI – a brief video by grad student Victoria Lim on how she chose UCI.

Info elsewhere

• For CVs and bios of Dr. Mobley and group members, see the People page.
• On occasion, positions in the lab are available, both at the undergraduate, graduate, and postdoctoral level. See the People page.

Test systems

• We compiled an extensive experimental dataset of hydration free energies which is relatively popular (DOI). The Supporting Info connected with the paper has the dataset, but we also have the mol2 files with partial charges and the parameter and coordinate files.
• On the same dataset, we also did a large number of hydration free energy calculations in implicit solvent (DOI) using molecular simulations. The test set is available, as is the set of stored AMBER trajectories for the molecules.