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S=k.logW · Molecular Stimulation

Written by John D. Chodera. We recently submitted an R01 grant proposal. To the NIH focused on removing a major limitation to the accuracy of alchemical free energy calculations: Incorporating fully consistent treatments of protonation states and tautomers for both ligands and proteins, especially in key systems like kinase:inhibitor binding. This post reviews some of the theory and describes the algorithm we’ve come up with to make this efficient. Click here to read the full post. Written by Gregory Ross.

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S=k.logW · Molecular Stimulation | klogw.org Reviews

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Written by John D. Chodera. We recently submitted an R01 grant proposal. To the NIH focused on removing a major limitation to the accuracy of alchemical free energy calculations: Incorporating fully consistent treatments of protonation states and tautomers for both ligands and proteins, especially in key systems like kinase:inhibitor binding. This post reviews some of the theory and describes the algorithm we’ve come up with to make this efficient. Click here to read the full post. Written by Gregory Ross.

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1 s=klogw

2 molecular stimulation

3 chodera lab

4 jchodera

5 github project

6 dynamic protomer sampling

7 steven floor

8 and bas rustenburg

9 older

10 newer

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S=k.logW · Molecular Stimulation | klogw.org Reviews

https://klogw.org

Written by John D. Chodera. We recently submitted an R01 grant proposal. To the NIH focused on removing a major limitation to the accuracy of alchemical free energy calculations: Incorporating fully consistent treatments of protonation states and tautomers for both ligands and proteins, especially in key systems like kinase:inhibitor binding. This post reviews some of the theory and describes the algorithm we’ve come up with to make this efficient. Click here to read the full post. Written by Gregory Ross.

INTERNAL PAGES

klogw.org

1

Fitting the Correlation Function · S=k.logW

http://klogw.org/2016/08/15/fitting-the-correlation-function

Fitting the Correlation Function. Written by Chaya D. Stern. The theoretical correlation function can be expressed as a sum of exponential . The correlation function can also be computed from Markov State Models that were parameterized with many Molecular Dynamics trajectories as described in this. Paper, thus providing a way to directly connect simulations with experiments. Dynamic protomer sampling 20 Dec 2016. Response to NIH RFI on Interim Research Products 09 Dec 2016.

2

Nonequilibrium candidate Monte Carlo · S=k.logW

http://klogw.org/2016/09/07/ncmc

Nonequilibrium candidate Monte Carlo. Written by Josh Fass. In a recent Computational Statistics Club meeting, we covered the topic of Nonequilibrium candidate Monte Carlo (NCMC). What’s new in NCMC? What are concrete examples of NCMC algorithms / design choices? Example from paper: WCA dimer. Distribution of the bond length, if it were in isolation. This allows us to construct an instantaneous Monte Carlo move that extends / compacts the dimer, in effect tunneling through the 5kT barrier to a distan...

3

S=k.logW · Molecular Stimulation

http://klogw.org/page2

How to write a Methods section. Written by John D. Chodera. Please feel free to provide feedback or suggestions as to how we can improve these resources and suggestions! Click here to read the full post. We have a blog! Written by John D. Chodera. Various members of the Chodera lab. Will contribute from time to time as we have interesting results to share, useful literature roundups, or new ideas for algorithms. As always, we appreciate your feedback! You can find us at http:/ choderalab.org.

4

Integrated likelihood methods for eliminating nuisance parameters · S=k.logW

http://klogw.org/2016/09/28/eliminating-nuisance-parameters

Integrated likelihood methods for eliminating nuisance parameters. Written by Gregory Ross. The process of inferring conclusions from experimental observations often requires the construction and evaluation of a likelihood function, which gives the probability, or probability density, of the observed data given a particular statistical model. Berger et al. present a number of scenarios where an integrated likelihood function forms a more robust basis for inference than the frequentist candidates....Imagi...

5

About · S=k.logW

http://klogw.org/about

You can find more from the Chodera lab at:. John Chodera’s twitter feed. The Chodera lab GitHub page. This site uses the Hyde. The static site generator. It was based on Poole. And designed and developed by @mdo. To provide a clear and concise foundational setup for any Jekyll site. It does so by furnishing a full vanilla Jekyll install with example layouts, pages, posts, and styles. Equation support is provided via MathJax.

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choderalab.org

Jobs — Chodera lab // MSKCC

http://www.choderalab.org/jobs

Chodera lab / MSKCC. Chodera lab / MSKCC. Chodera lab / MSKCC. Changing drug discovery one ratio of partition functions at a time. Chodera lab / MSKCC. We are always looking for talented individuals to work with us. 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? Then come join us! Learn...

choderalab.org

Resources — Chodera lab // MSKCC

http://www.choderalab.org/resources

Chodera lab / MSKCC. Chodera lab / MSKCC. Chodera lab / MSKCC. Changing drug discovery one ratio of partition functions at a time. Is a clean, professional-looking template that's easy to set up. It is prized by small and mid-sized businesses for its numerous customization options and professional layouts. Chodera lab / MSKCC. Our laboratory is equipped with a variety of computational and experimental resources for the quantitative study of protein-ligand association. 2x Intel Xeon E5-2665 2.4GHz. Liquid...

choderalab.org

Ensembler: Enabling high-throughput molecular simulations at the superfamily scale — Chodera lab // MSKCC

http://www.choderalab.org/publications/2015/5/19/l1wso8cubio6hq0wua9lcmggmdqdrw

Chodera lab / MSKCC. Chodera lab / MSKCC. Chodera lab / MSKCC. Changing drug discovery one ratio of partition functions at a time. Chodera lab / MSKCC. June 23, 2016. Ensembler: Enabling high-throughput molecular simulations at the superfamily scale. June 23, 2016. Daniel L. Parton, Patrick B. Grinaway, Sonya M. Hanson, Kyle A. Beauchamp, and John D. Chodera. PLoS Comput. Biol. 12. E1004728, 2016. [ DOI. June 23, 2016. An open library of human kinase .

choderalab.org

Markov state models of biomolecular conformational dynamics — Chodera lab // MSKCC

http://www.choderalab.org/publications/2014/4/26/markov-state-models-of-biomolecular-conformational-dynamics

Chodera lab / MSKCC. Chodera lab / MSKCC. Chodera lab / MSKCC. Changing drug discovery one ratio of partition functions at a time. Chodera lab / MSKCC. April 26, 2014. Markov state models of biomolecular conformational dynamics. April 26, 2014. John D. Chodera. Curr Opin. Struct. Biol., 25. 135-144, 2014. [ DOI. A review of the exciting developments in the stochastic modeling of biomolecular dynamics over the last few years. April 26, 2014. Towards Automated Benchmarking of .

choderalab.org

Spectral rate theory for two-state kinetics — Chodera lab // MSKCC

http://www.choderalab.org/publications/2014/4/26/spectral-rate-theory-for-two-state-kinetics

Chodera lab / MSKCC. Chodera lab / MSKCC. Chodera lab / MSKCC. Changing drug discovery one ratio of partition functions at a time. Chodera lab / MSKCC. February 24, 2014. Spectral rate theory for two-state kinetics. February 24, 2014. Jan-Hendrik Prinz, John D. Chodera. Phys Rev. X 4:011020, 2014. [ DOI. February 24, 2014. Markov state models of biomolecular . Time step rescaling recovers .

choderalab.org

Time step rescaling recovers continuous-time dynamical properties for discrete-time Langevin integration of nonequilibrium systems — Chodera lab // MSKCC

http://www.choderalab.org/publications/2014/4/26/time-step-rescaling-recovers-continuous-time-dynamical-properties-for-discrete-time-langevin-integration-of-nonequilibrium-systems

Chodera lab / MSKCC. Chodera lab / MSKCC. Chodera lab / MSKCC. Changing drug discovery one ratio of partition functions at a time. Chodera lab / MSKCC. February 20, 2014. Time step rescaling recovers continuous-time dynamical properties for discrete-time Langevin integration of nonequilibrium systems. February 20, 2014. David A. Sivak, John D. Chodera. And Gavin E. Crooks. J Phys. Chem. B, 118. 6466-6474, 2014. William C. Swope Festschrift issue. [ DOI. February 20, 2014. Identifying ligand binding sites .

choderalab.org

News — Chodera lab // MSKCC

http://www.choderalab.org/news

Chodera lab / MSKCC. Chodera lab / MSKCC. Chodera lab / MSKCC. Changing drug discovery one ratio of partition functions at a time. Chodera lab / MSKCC. July 29, 2016. July 29, 2016. We've started a blog! This will be an outlet to discuss ideas for new molecular simulation algorithms, new analyses of existing ones, interesting results, literature we find exciting, or anything we come up with that may be of use to others! Let us know what you think. July 29, 2016. May 17, 2016. May 17, 2016. May 17, 2016.

choderalab.org

Kinase Inhibitor Dorm Room Poster! — Chodera lab // MSKCC

http://www.choderalab.org/news/2015/5/21/kinase-inhibitor-dorm-room-poster

Chodera lab / MSKCC. Chodera lab / MSKCC. Chodera lab / MSKCC. Changing drug discovery one ratio of partition functions at a time. Chodera lab / MSKCC. May 21, 2015. Kinase Inhibitor Dorm Room Poster! May 21, 2015. Postdoc Sonya Hanson and grad student Julie Behr have collected all 27 FDA approved small molecule kinase inhibitors into a poster suitable for your lab wall or undergrad student's dorm room! A bit more official information on the more recently approved molecules can be found here. May 21, 2015.

choderalab.org

Code — Chodera lab // MSKCC

http://www.choderalab.org/code

Chodera lab / MSKCC. Chodera lab / MSKCC. Chodera lab / MSKCC. Changing drug discovery one ratio of partition functions at a time. Chodera lab / MSKCC. See the Chodera lab. We contribute applications and tools to the Omnia suite. Of molecular modeling and simulation tools based on the OpenMM. GPU-accelerated molecular modeling package. An open, extensible platform for GPU-accelerated alchemical binding free energy calculations. Using the OpenMM toolkit.

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S=k.logW · Molecular Stimulation

Written by John D. Chodera. We recently submitted an R01 grant proposal. To the NIH focused on removing a major limitation to the accuracy of alchemical free energy calculations: Incorporating fully consistent treatments of protonation states and tautomers for both ligands and proteins, especially in key systems like kinase:inhibitor binding. This post reviews some of the theory and describes the algorithm we’ve come up with to make this efficient. Click here to read the full post. Written by Gregory Ross.

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