Postdoc Gregory Ross awarded Postdoctoral MolSSI Fellowship

Congratulations to postdoc Gregory Ross for being awarded an inaugural MolSSI Postdoctoral Software Science Fellowship! Greg's project focuses on building a toolbox of self-tuning Monte Carlo methods for use alongside molecular dynamics based Markov chain Monte Carlo (MCMC) sampling to greatly enhance the efficiency of molecular simulations and facilitate the construction of new sampling algorithms. Read on for a more detailed description of his project.


An automatic sampling toolbox for molecular simulation

Gregory Ross, DPhil
In the biomolecular simulation community, molecular dynamics (MD) is the most popular method for sampling molecular configurations. MD is well suited to capturing global, concerted movements, but it struggles to sample configurations that are separated by large energetic barriers. As a result, configurations taken from MD simulations tend to be from the same local region. An equivalent problem is encountered in Bayesian inference when drawing samples from a high-dimensional, multimodal posterior distribution. MD-related techniques are a small subset of a large class of Markov chain Monte Carlo (MCMC) techniques, and practitioners in both the biomolecular simulation and Bayesian inference communities have, in principle, a great deal of choice on which sampling method to use. However, it is difficult to know which MCMC method will the most efficient at generating uncorrelated samples for a particular system. In my project, I will develop a toolbox for MCMC that is agnostic with regard to what is being sampled, whether a protein conformation or posterior distribution. I will focus on using adaptive MCMC methods to help select the sampling technique that works best for a given problem. The general idea is to write a library of MCMC tools and a software interface that allows for the construction of MCMC “blocks” which can be mixed together and easily applied. The goal is to simplify sampling from difficult distributions and, ultimately, to widen the range of phenomena currently accessible by molecular simulation.

Congratulations to TPCB graduate student Mehtap Isik on being awarded the 2017-2018 Doris J. Hutchison Fellowship

Congratulations to TPCB graduate student Mehtap Isik, who is the 2017-2018 recipient of the Doris J. Hutchison Fellowship from the Sloan Kettering Division of the Weill Cornell Graduate School of Medical Sciences. Her project focuses on the development of model protein:ligand systems for advancing the field of predictive quantitative computational modeling for drug discovery using robotic wetlab experiments and advanced GPU computing, and is described in this proposal she submitted to the fellowship competition.

Nature Chemical Biology paper about LDHA alternative substrate utilization at low pH is out!

At low pH, such as under anoxic conditions relevant to diseases like cancer, some metabolic enzymes like LDHA can shift their substrate preferences and cause the accumulation of metabolites that lock the cell into pathogenic states. The mystery of how and why these enzymes start to prefer alternative substrates has lingered.

In a paper from the Thompson laboratory at MSKCC just published in Nature Chemical Biology, graduate student Ariën S. ("Bas") Rustenburg in the lab, together with collaborators from the Gunner lab at CCNY, used modeling to show how protonation state effects explain why substrates like alpha-ketoglutarate that position a carboxylate tail proximal to LDHA's Q100 greatly increase turnover rates at low pH.

L-2-Hydroxyglutarate production arises from noncanonical enzyme function at acidic pH.
Andrew M. Intlekofer, Bo Huang, Hui Liu, Hardik Shah, Carlos Carmona-Fontaine, Ariën S. Rustenburg, Salah Salah, M R Gunner, John D. Chodera, Justin R. Cross, and Craig B. Thompson.
Nature Chemical Biology, in press. [DOI] [GitHub]

New Nature Chemical Biology paper on Aurora A kinase, a potential melanoma target

In collaboration with the Nicholas Levinson lab at the University of Minnesota, we have just published a paper in Nature Chemical Biology using experiment and simulation to probe the mechanism of allosteric activation of Aurora A kinase (AurA). AurA is found to be hyperphosphorylated in approximately 10% of melanoma patients due to mutations that deactivate the protein phosphatase PP6, leading to defects in chromosome segregation and genomic stability. 

AurA kinase plays two distinct roles in mitosis, with a centrosomal pool of kinase activated by phosphorylation similarly to other kinases, but a separate pool controlled by a more exotic mechanism of binding to the spindle-associated protein Tpx2. Using an aggregate of several microseconds of data generated on Folding@home to study wild-type AurA and some engineered mutants, we helped the Levinson lab puzzle out a key role of highly stable waters localized in the active site that mediate allosteric communication in the Tpx2-mediated activation of AurA.

Soreen Cyphers, Emily F Ruff, Julie M Behr, John D Chodera, and Nicholas M Levinson.
A water-mediated allosteric network governs activation of Aurora kinase A
Nature Chemical Biology, in press. [DOI] [GitHub]

We have made all the explicit-solvent Folding@home simulation data and analysis scripts used in this paper available for download:

The trajectory data itself is too large to share via GitHub, so we make it available via the Open Science Framework.

OpenMM 7.1 beta released

Christmas comes early! We've released a beta of OpenMM 7.1, packed with speed improvements and new features, including:

  • Optimized clang builds of both Anaconda packages and ZIP installers, offering anywhere from a 30% to 50x boost for some applications that use the CPU platform.
  • Custom Forces can now compute energy derivatives with respect to global parameters! Lambda dynamics can now be implemented via a CustomIntegrator.
  • Gay-Berne ellipsoid potential!
  • Bonded forces can now use periodic boundary conditions.

To get the updated OpenMM conda package, use the beta channel:

conda install -c omnia/label/beta openmm==7.1.0

If you have already been using the dev channel 7.1.0 nightly builds, force a downgrade first:

# Force downgrade to 7.0.1
conda install --yes -c omnia openmm==7.0.1
# Clear local cache
conda clean -plti --yes
# Install the beta
conda install --yes -c omnia/label/beta openmm==7.1.0

See the OpenMM SimTK page for more information on the beta release. Feel free to give feedback there, or on the OpenMM GitHub issue tracker.

Nightly dev builds are now called 7.2.0. You can always get the latest version with:

conda install --yes -c omnia/label/dev openmm

Help us reach one million folders on Folding@home!

Our lab is a core member of the Folding@home Consortium, a research network of 11 laboratories around the world that use Folding@home to study the molecular mechanisms underlying cancer and other diseases and identify new routes toward therapies. Together, we are aiming to recruit one million volunteers donating compute cycles to help us! 

Please join us, especially if you have a GPU: Folding@home can harness the power of your GPU
It costs nothing (other than your electrical bill) and provides a way to donate your idle computer cycles to biomedical research.

Download Folding@home now


Other useful links:

Fourth Alchemical Free Energy Calculations in Drug Design meeting at Vertex

The fourth Alchemical Free Energy Calculations in Drug Discovery workshop is already underway, held once again at the beautiful Vertex facility in Boston. We're livetweeting the meeting for those who can't make it, and have set up a new Slack team to keep the conversation going after the meeting. There's even a job postings page to keep track of the abundant new jobs in computational chemistry and alchemical free energy calculations in industry and academia this field has created. We're thrilled to see so much activity, how far the field is come, and certainly how far the field has left to go.

Slides from my talk can be found here in PDF format.

ICMS Edinburgh Workshop on multiscale methods for stochastic dynamical systems in biology


The International Centre for Mathematical Sciences (ICMS) held a fantastic workshop over the last week here in Edinburgh, covering multiscale methods for stochastic dynamical systems in biology.  It's phenomenal that there are organizations that are strongly committed to supporting the exciting interface between mathematics and the biological sciences, and the enthusiastic discussions at this meeting were a reflection of the enormous potential that work at this interface holds for both fields. These workshops also attempt to engage the public to communicate the importance of this interdisciplinary work through a public lecture series, with Sarah A. Harris delivering a talk on the interface of physics and biology.

PDF slides from my talk are available online, and the talks were all recorded to be posted online shortly.