Tuesday, January 20, 2015

New manuscript: Predicting binding free energies in solution

Here is a new manuscript of mine that appeared on arXiv today.  It is a perspective paper, i.e. I mostly summarize what has already been published, and here is the abstract.

AbstractRecent predictions of absolute binding free energies of host-guest complexes in aqueous solution using electronic structure theory have been encouraging for some systems, while other systems remain problematic for others. In paper I summarize some of the many factors that could easily contribute 1-3 kcal/mol errors at 298 K: three-body dispersion effects, molecular symmetry, anharmonicity, spurious imaginary frequencies, insufficient conformational sampling, wrong or changing ionization states, errors in the solvation free energy of ions, and explicit solvent (and ion) effects that are not well-represented by continuum models. While the paper is primarily a synthesis of previously published work there are two new results: the adaptation of Legendre transformed free energies to electronic structure theory and a use of water clusters that maximizes error cancellation in binding free energies computed using explicit solvent molecules. While I focus on binding free energies in aqueous solution the approach also applies (with minor adjustments) to any free energy difference such as conformational free energy differences or activation free energies in any solvent.  

I am very interested in feedback on this paper and I'll wait a while with the submission to incorporate any suggestions.  There are several ways of providing feedback: comments below, comments on PubPeer (which allows for anonymous comments), and comments on Google docs using either the comment or editing tool.

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Saturday, January 17, 2015

What do I want in a learning management system?

I am in a university work group where we discuss recommendations for a new learning management system (LMS). The point of this blogpost is to help me get my thoughts together on this topic.

General philosophy.
1. I would like a barebones open source or easily customizable system where I seamlessly can plug and play different modules such as quizzes, discussion forums, etc.  There could be a default for each, but if I find better options I should be able to use them.

2. I think it is better to encourage the use freely available tools (Google Calendar, Google Docs, Sharelatex, Youtube, Wolfram-Alpha, Reddit, Quora, etc.) that the students will have access to after they graduate. I think the university should offer tutorials, etc. on using these tools directly to students.

3. I think the default for material on the course page should be "viewable by anyone", with an option to change for individual elements.

Things I like/use about the current system (delivered by ITS Learning and called Absalon)
Quiz. I give use reading quizzes extensively.  There are two things about the I really like about the Absalon implementation.  One is that you can label the quiz "obligatory" (it's just a word that appear)s. Students really take this seriously even though there are no explicit penalties for not taking the quiz. Another very useful feature is that I can send email only to students who haven't taken the quiz.

Bulletin board. The bulletin board is very prominently displayed and you can mostly count of students seeing it when they log in.

Planner. Absalon has a rudimentary planner/calendar with links directly to assignments and quizzes.

Mathjax. Very useful for typing equations

Plagiarism detection. Very useful for reports.

Student activity. List of who has logged in when or taken quizzes.

Copy from last year. Of course it's very useful to copy quizzes etc from last years course page.

In-active files/view as student. Files and folders can be made active or inactive where the latter can be viewed only by instructors and TAs.  Very handy for sharing solution sets, etc.  It is pretty easy to see  if a file or folder is inactive, but if I doubt I can choose "view as student".

Things I miss
1. Option to schedule the email to students who haven't taken the quiz at a particular time and date.
2. Option to have the answer to a quiz question revealed immediately after the answer.
3. Some kind of badge system for quizzes, e.g. Genius badge = 10 correct answers in a row, etc.
4. For questions with free text answers: option to see answers from all student on one question at once.
Open.  The course page is completely closed to students who are not signed up.  It would be very helpful to give access to other students so they can see what the course is about before they sign up.

SMS or other notification/reminder feature.  Right now every interaction with students is through email, but what good is an email notification about a quiz that is due in two hours if the email is not read.  Actually, iPhone one can mark email contacts as VIP and get notifications when VIP emails arrive, so that might fix it.  Not sure if that works on Android or if students have set up forwarding. Also, next time I teach I'll set up and share a Google calendar for the course, which might help and/or use the remind app.

Integration with social media.  Some way to automatically share announcements, etc. on Twitter, Facebook, Google+, etc.  E.g. with Twitter I am thinking something send directly to their Twitter address, so they get alerted - not some hashtag.

Better discussion forum. I wrote about that here.

Dropbox integration. I spend a lot of time uploading files to the system.  I already keep my course material on dropbox, so it would be great of one could mirror drop-box folders (with some control over what files are visible to the students).

Mobile friendly/app. It is very important to be able access and work on the site with a smartphone or tablet.

In-active files/view as student. More detail is needed on student activity. Who has downloaded what file when?  Create contact lists for groups of students who match certain criteria.  E.g. who has not downloaded the last homework problem yet.  Also overview of single student's activity.

Extract student identifiers to create accounts on other systems.  This is currently amazingly complicated.

Comments and questions very welcome.

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Saturday, January 10, 2015

Blog posts, videos and "other publications" for 2014

Every year I have to fill out several "what have you accomplished last year?" forms. I've just send in one of them. There is a section on "other publications", which, I guess, is intended for non-refereed articles and books. But there are now many other ways to disseminate information so I added:

http://molecularmodelingbasics.blogspot.com 69,537 pageviews in 2014
http://proteinsandwavefunctions.blogspot.com 17,964 pageviews in 2014 (group-blog, includes contributions from others)

Active Learning: Tools and Tips (https://sites.google.com/site/jhdou363/) 1850 pageviews in 2014

http://www.youtube.com/user/MolModBasics 45,074 views in 2014

http://www.slideshare.net/molmodbasics/ 10,397 views in 2014

http://propka.org ca 30,000 pageviews in 2014
http://molcalc.org 44,679 pageviews in 2014

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Monday, January 5, 2015

Planned papers for 2015

Last month I participated in a departmental retreat and one of the things we talked about was planning publications. It never hurts to have a plan (as long as you don't feel you have to follow it slavishly) and the first day at work in 2015 seems like a good time to make plans.

1. Søs Torpenholt, Leonardo De Maria, Mats H. M. Olsson, Lars H. Christensen, Michael Skjøt, Peter Westh, Jan H. Jensen and Leila Lo Leggio "Effect of mutations on the thermostability of Aspergillus aculeatus β-1,4-galactanase" Computational and Structural Biotechnology Journal, submitted
2. Lars A. Bratholm, Anders S. Christensen, Thomas Hamelryck, and Jan H. Jensen "Bayesian inference of protein structure from chemical shift data" PeerJ, submitted. Preprint

3. Automated prediction of the NMR structure of the protein CI-2.
4. Linear scaling HF-3c calculations by interface to FMO2 in GAMESS
5. Thermodynamics of binding. I plan to turn my recent blogposts (with 2 more to come) on this topic into a perspective article.
6. ProCS14. I need to turn this masters thesis into a paper (how will I find the time?).
7. NMR structure of the protein AKMT.
8. Benchmarking of PM6 and DFTB3 for barrier heights computed using enzyme active site models.
9. Predicting binding free energies for CB7
10. Probabilistic treatment of distance restraints in protein structure determination

Maybe, but probably not in 2015.
11. PCM/DFTB3 or PM6 in GAMESS
12. Anharmonic effects on vibrational entropy
13. Prediction of HD-exchange in proteins
14. PELE sampling and enzyme barrier heights

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Sunday, December 14, 2014

A discussion forum for on-line office hours

The problem
I would like to hold virtual office hours.  I have considered Skype and Adobe Connect but it's not clear how they would show me their work, how I can give feedback quickly and effectively, and avoid answering the same question again and again.

I anticipate that most questions will be a photo of their handwritten work with the question "What am I doing wrong?"

The solution

* A discussion forum with threads on different subjects like, e.g. Reddit.

* Login is required to post questions and I control who can log in

* There is a teacher mode and a student mode

Student mode:

* Text-entry that supports equations (e.g. Mathjax)

* Students can easily post photos of their work, so seamless integration with webcam, tablet and smartphone is needed.

* It should also be possible to write/draw using a tablet.

Additional features in the teacher mode

* When answering the question, the question, including any pictures, is copied and it is possible to write/draw on the picture using a tablet.

* When answering questions it is possible to record the screen + audio and embed the resulting video automatically.

I need this feature so I can answer quickly, but I don't want the students to be able to pose questions as recordings because I can read the question much faster.

* Optionally: a feature where I can choose to get email notification when a new questions is asked (for off-peak hours).

To the extent possible under law, the person who associated CC0 with this work has waived all copyright and related or neighboring rights to this work.

Smartphone wireless microphone apps for asking questions in large lecture halls

Just came across this app called Crowd Mics.  The price is pretty steep but they leave the door open for negotiations with academic institutions.

The same search also uncovered Beekast, but there is very little information to be had at the web site.

If you have used these or similar apps please share your experience in the comment section.

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Monday, November 17, 2014

Book chapter on my flipped classroom

I am writing a book chapter on my flipped classroom for a book on university pedagogy.  Normally I decline invitations for book chapters of any kind, but I was working on a web-book anyway so I thought I could just reformat part of that as a chapter.

Here is a draft.  Comments welcome.  Use either the comment function in Google Docs or the comment section below.

This work is licensed under a Creative Commons Attribution 4.0