The Chodera lab teams up with Andrea Volkamer to explore the interface of machine learning and free energy calculations

 Professor Andrea Volkamer, Charité (Berlin) works at the frontier of structure-guided machine learning for drug discovery and kinase inhibition.

Professor Andrea Volkamer, Charité (Berlin) works at the frontier of structure-guided machine learning for drug discovery and kinase inhibition.

The Einstein Foundation and Stiftung Charité have awarded a BIH Einstein Visiting Fellowship to a new collaboration between the Chodera lab and Professor Andrea Volkamer of the Charité in Berlin to develop new approaches that meld structure-informed machine learning with free energy calculations to predict and design kinase polypharmacology. We will be hiring a postdoc and PhD student to be embedded within the Volkamer group within the exciting human health research environment at the Charité in Berlin. John Chodera will be making four extended visits to Berlin each year, and a significant travel budget will allow research personnel to make extended visits to both the Volkamer group at the Charité and the Chodera lab at the Memorial Sloan Kettering Cancer Center (MSKCC). [Job Postings]

 An example workflow for utilizing structure-informed machine learning and free energy calculations to predict kinase polypharmacology.

An example workflow for utilizing structure-informed machine learning and free energy calculations to predict kinase polypharmacology.

Seeking a joint Open Force Field Consortium / XtalPi Distinguished Postdoctoral Fellow

The Open Force Field Consortium (OpenFF, openforcefield.org) and XtalPi, Inc. (xtalpi.com) seeks a Distinguished Postdoctoral Fellow to perform cutting-edge research in a unique academic-industrial joint effort.

OpenFF is an academic collaboration (based at UC Irvine / UC Davis / UC San Diego / Univ. Colorado Boulder / Sloan Kettering Institute in New York) that seeks to develop next-generation molecular mechanics force fields and associated parameterization software and data infrastructure. XtalPi is a pharmaceutical technology company founded in 2014 that is introducing revolutionary advances in drug research and development, and has established strategic partnerships with several major pharmaceutical companies and recently completed a Series B funding round with Sequoia, Tencent, and Google.

The Postdoctoral Fellow will work with OpenFF and XtalPi to improve the accuracy of molecular mechanics force fields for predicting crystal structures and binding free energies. The work spans the disciplines of force field development/validation and Bayesian inference, and seeks to answer the fundamental scientific questions: 1) What regions of chemical space are critical failures for current force fields? 2) What are the fundamental limitations of (a) current functional forms and (b) parameterization methods?

The position spans a two-year project period that involves a gradual transition from the OpenFF side to the XtalPi side. In Year 1, the Fellow will be hosted for ~9 months in one of the academic groups (to be determined by the OpenFF PIs, XtalPi, and the Fellow) and ~3 months at XtalPi in Shenzhen, China or Boston, MA. In Year 2, the time division will be 3-6 months academic / 6-9 months XtalPi. The Fellow will be considered for full-time employment at XtalPi after Year 2.

For more information, see the full job posting.

Postdoc Sonya Hanson joins Nobel Laureate Joachim Frank's lab

Congratulations to Postdoctoral Fellow Dr. Sonya Hanson, who has joined the laboratory of Joachim Frank at Columbia University to learn the exciting new technique of cryo-EM spectroscopy coupled with manifold embedding to reveal the dynamic conformational landscapes of TRP channels, an important class of integrative sensing proteins Sonya extensively studied as a graduate student. Frank was recently awarded the Nobel Prize in Chemistry (along with Jacques Dubochet and Richard Henderson) for his seminal contributions to advancing the technology of cryo-electron microscopy to become a powerful technique for imaging the conformations of biomolecules. Sonya will maintain strong links with the laboratory and the Folding@home Consortium as she progresses toward an independent faculty position.

You can see more fantastic work from Dr. Hanson at her Google Scholar page, check out her recent paper on the heat activation of TRPV1 in PNAS, and find out more about her career trajectory at her website.

Chodera lab seeking awesome tech to help advance drug discovery science with robots and Python!

Are you someone with a life/physical sciences degree eager to help design new therapeutics for cancer and other diseases using robots and cutting-edge computing technology? Looking to do something amazing before heading to graduate school or industry? Enthusiastic about working alongside scientists that integrate computation and experiment to push the boundaries of rational drug design? Then come join us!

The Chodera lab is looking to hire a talented technician to help us maximize our ability to make the most of the unique technological resources at our disposal.

We're looking for someone with:

  • life or physical sciences BS/BA degree
  • strong organizational skills
  • most importantly, an unbounded enthusiasm for SCIENCE!

And one or more of the following:

  • biological wetlab experience
  • eagerness to learn about (or previous experience with) laboratory robotics and automation
  • coding skills (especially Python) a huge plus

In the Chodera lab, you will:

  • work in the basic science arm of a world-class cancer research institute
  • work alongside amazing postdoc and graduate students that integrate computation and experiment
  • become an integral part of several projects that push the boundaries of rational drug design
  • learn the ins and outs of our whole-wetlab automation system
  • help develop new robotic protocols
  • run assays and coordinate with instrument vendors for service
  • help organize wet and dry labs to keep everything running smoothly
  • delve into data analysis and lab infrastructure with Python
  • help blog about exciting science going on in the lab

Official application link: http://careers.mskcc.org/job/5331414/research-technician-computational-biology-new-york-ny/
Please send inquiries to apply@choderalab.org