Selected recent presentations:
- “Machine Learning and pKa in SAMPL6”, Chodera lab seminar by Caitlin Bannan on YouTube.
- “Molecular Dynamics Simulations of Protein X-ray Crystallographic Diffuse Scattering”, American Crystallographic Association Annual Meeting, Covington, KY, July 2019 (DOI)
- “Infinite dilution activity coefficients… no, really, you should care!” OpenEye CUP Meeting, Santa Fe, NM, March 7, 2019. (DOI)
- “OpenFF: Fitting of valence parameters,” Open Force Field Workshop, San Diego, CA, Jan. 9, 2019. (DOI)
- “The Open Force Field Initiative: A brief update on our progress and plans,” OpenEye MiniCUP Meeting, San Diego, CA, Oct. 2, 2018. (DOI)
- “Automated Chemical Perception for Force Field Parameterization”, 256th ACS National Meeting, Boston, MA, August 2018. (DOI)
- “Learned chemical perception of force field typing rules using Monte Carlo sampling”, Inaugural Data Science Workshop, July 2018. (DOI)
- “BLUES: Binding modes of Ligands Using Enhanced Sampling”, Computational Chemistry Gordon Research Seminar, West Dover, VT, July 2018 (DOI, DOI).
- “The BLUES Report”, OpenEye CUP CVIII Meeting, Santa Fe, NM, March 2018. (Link)
- “Machine Learning and pKa Predictions in SAMPL6”, OpenEye CUP XVIII Meeting, Santa Fe, NM, March 2018. (DOI)
- “Automating chemical perception to improve force field parameterization”, 254th ACS National Meeting, Washington, DC, August 2017. (DOI)
- “Adapting free energy methods to predict binding modes of ligands”, CECAM workshop on “Beyond Kd’s: New computational methods to address challenges in drug discovery“, EPFL, Lausanne, Switzerland, June 7, 2017. (DOI)
- “Making alchemical free energy calculations practical for drug discovery”, Pfizer WebEx presentation, April, 2017. (DOI)
- “What happened when Ant let us put MD on Orion: Towards fragment binding occupancies using BLUES”, OpenEye CUP XVII Meeting, Santa Fe, NM, March 2017. (DOI)
- “Improving Force Field Parameterization with Bayesian Inference for Chemical Perception”, OpenEye CUP XVII Meeting, Santa Fe, NM, March 2017. (DOI)
- “Computing Partition Coefficients using Alchemical Free Energy Calculations”, 251st ACS National Meeting, San Diego, CA, March 2016. (DOI)
Older work which may still be helpful:
- “Finite size artifacts” (charge corrections for alchemical free energy calculations), Dec.15, 2015, Gabriel Rocklin, via Hangouts on Air. Available on YouTube.