A collection of bookmarks (in fact, my
complete bookmarks file).
Things I do and did:
(one could even consider this to be a resume...)
- Analyzing and (hopefully) predicting protein-protein
interactions from sequence information, using coarse-grained and/or
automated protein homology-model building at the
of the Faculty of Sciences of the
Free University with
Prof. Jaap Heringa. The
first three manuscripts on Sequence Harmony, two together with Walter Pirovano and one
with Elena Marchiori, have already
been published (or in print).
||Exploring the balance between Conservation
and Diversity in sequence comparison of protein families,
using Sequence Harmony and a Feature Selection algorithm.
Especially when functional differences are of interest,
diversity may be more important than conservation.
(Nucleic Acids Res., 34, 6540-6548, 2006;
Bio-ICMLA06, accepted ,2006;
NIC Series, Vol 34, 2006 pp 73-68).
- Rationalizing and predicting stereo specificity of mutatant
enzymes using (amongst others) molecular dynamics simulations,
essential dynamics analysis, homology building, automated docking
procedures and free energy calculations at the Free
University in Amsterdam at the Pharmaochemistry
group in the Chemistry Devision of
the Faculty of Sciences. This also involves the Chemistry of Complex
Molecules project, and the Leiden
||Building a Homology Model of the Styre
Mono-oxygenase enzyme, with predicted binding modes
characteristic of the correct enantiomer of the product
(Biophys. J. 91(9), Nov. 2006)
||Rationalizing Cyp 102 (P450 BM3) substrate
binding and reactivity using MD simulations and QM
calculations (Prot. Sci., 2007 16: 420-431)
in combination with experimental
characterization of turnover and product formation.
(ChemBioChem 7 345-350, 2006).
||Analyzing dynamics of Cyp 2D6 substrate
binding and dynamics using MD simulations and NMR experiments
(J. Med. Chem., 48 6117-27, 2005)
||Reviewing the state of the art in Modeling
Cytochrome P450 enzymes, which is done by quantum-mechanics
calculations, pharmacophore ('classical' and 3D-QSAR) models, homology
model building, ligand docking
and molecular dynamics simulations. A trend towards (multi-)integrated
modelling approaches is evident in many recent publications. (J.
Med. Chem., 48 2725-55, 2005, and in Drug Metabolism /
Discovery & Development, Ed.
Paul W. Erhardt, Univ. of Toledo, in press 2004.)
- Hacking away at the Gromacs
Molecular Dynamics program
package source code. This is a highly sophisticated package featuring
a high-performace single and multiple CPU simulation engine that is
optimized for most of the current hardware platforms (GROMACS is a
recursive acronym for "Gromacs Runs On Most Of All Computer Systems"
:-), and various analysis tools, most of which are also fairly well
optimized for performance, flexibility and user-friendliness.
- Supporting open source (code and standards). Read a vivid plea for both open and (human)
readable file formats.
- Unraveling the riddles and mysteries of Protein Folding and
Dynamics (which, in early 2002 has lead to my PhD
at the Molecular Dynamics (MD)
Group of the Biophysical Chemistry Department at the State
University of Groningen
(RuG) in the Netherlands. More precisely I am
looking at specific features of protein hydrophobic cores which may be
vital to a correct folding of the protein. Some results up to now
||Analysing peptide dynamics, looking at one of the
motionally coherent elements (described below) in isolation using MD
simulations and NMR experiments. Special attention goes to proper
methods for comparison of experimental and simulated data (J.
NMR 23, 181-194, 2002).
||Analysing protein dynamics in terms of motionally
(identified using the method described below). These elements are
organised in a hierarchical fashion, which might be related to
hierarchical organisation of the protein folding process. (on hold)
||Breaking down the protein into smaller segments which
regarded as separate (rigid-body like) entities, which might be used
in some kind of simplified discription of protein dynamics. (in: Monte
Carlo approach to biopolymers and protein folding.
pp. 255-267. Eds. P. Grassberger, G.T. Barkema and W. Nadler,
Höchstleistungsrechenzentrum Jülich, Germany; World
Scientific, London, 1998.)
||Improving the efficiency of Molecular Dynamics (MD)
removing the fastest motions (vis. hydrogen atom motions) from the
system, which leads to an increase in possible timestep of about a
factor of 3.5. (J. Comput. Chem. 20 (8), pp 786-798,
||Not directly related to proteins, but interesting in
its own right, are the dynamics of a fluorescent co-factor FAD. The
fluorescent behavior is directly linked to its dynamical behavior. This
makes the combined experimental fluorescence and MD simulation approach
very succesful. (J. Phys. Chem. B 106, 8858-8869, 2002).
- Study Molecular Sciences at Wageningen
Agricultural University (WAU) in the Neterlands (I finished in
- Play tennis in Lunteren
(which is close to Barneveld). After having played it way back as a
(pre-)teenager, I picked it up again somewhere around late 2004.
- I relished for some time in the aftermath of my PhD work
(thesis (3.9Mb) is done, the defense was at
July 5th, 2002). (But I'm over that, now. ;-)
- Educate people in being nice and helpful
- Writing scientific articles
- Used to ride the bike, mostly between Winsum (where I lived)
and Groningen (where I
worked). The route I took can be traced on a satellite
image (90kb jpeg image) I have of
the area. Now, I sometimes (only once up to now, due to construction
works on the railroad) take the bike from Barneveld (where I live) to
Amersfoort (where I continue by train to Amsterdam, where I work).
- Finding things on Internet. I could ofcourse include a host of
to search-engines here, but I won't because that takes the magic away.
- Play Dungeons & Dragons (Third
Edition) with a group of friends from highschool. We started playing
with this group somewhere around 1984 and we still play with the same
4 people who started except for some who dropped out and in in the
- Confuse my brain
- Hobby on my computer
- Fantasy novels
(Hmm. Maybe this is too obvious. Everybody knows
that D&D players read fantasy novels...)
- J.R.R. Tolkien:
(and, yes I have seen the films!
LOVE IT LOVE IT LOVE IT.
By the way, I also once at high-school saw the cartoon-film of "The
Fellowship", or was it "The Hobbit"... What should I say?)
- The Hobbit
- The Lord of The Rings
- The Wheel of Time series (Robert Jordan):
this is a must try for anyone who is
afraid that all fantasy books after Tolkien inevitably look pale in
comparison! To give you an indication: while reading "The Eye of the
World" in the train, I failed to notice the emergency stop we
made until we had been standing still with jammed brakes after well
over an hour...
- 1. The Eye Of The World
- 2. The Great Hunt
- 3. The Dragon Reborn
- 4. The Shadow Rising
- 5. The Fires Of Heaven
- 6. Lord Of Chaos
- 7. A Crown of Swords
- 8. The Path of Daggers
- 9. Winters Heart
- 10. Crossroads of Twilight
- 11. Knife of Dreams
I wonder if this would be the last one?
- Harry Potter (J. Rowling):
- 1. The Philosopher's Stone
- 2. The Chamber of Secrets
- 3. The Prisoner of Azkaban
- 4. The Goblet of Fire
- 5. The Order of the Phenix
- 6. The Half-Blood Prince
- 7. The Deathly Hallows
- Dune series (Frank Herbert), might also be called Science
- Shannarah series (Sword of ..., Elfstones of ..., etc.,
can't remember author)
- Deathgate series (Margareth Weiss & Tracy Hickmann *
thanks Rabhin S. Jainandunsing)
- Lots of the Forgotten Realms and the Dragonlance series
- lots of others (you don't want me to list them
- Science Fiction novels
(This isn't too obvious, is it? I mean, not every fantasy freak also
reads science fiction novels..., do they?)
- Arthur C. Clarke (I can't have missed many... ;-)
- Isaac Asimov (see note above)
- Stephen Baxter
- The Light Of Other Days (with Arthur Clarke)
- several others
- Dune series (Frank Herbert), might also be called Fantasy
- The Hitchhikers Guide to the Galaxy -- DON't
(or should this be under Fantasy? Or should it have a nice
category all of it's own, like Science Fantasy?)
And, yes, I saw this film as well, and LOVED IT, leaving me in
a state that I could only describe appropriately as
flabberghasted... Now I'm waiting for the sequel(s?).
- some others, but most not nearly as good
- Other novels
- Wilbur Smith
- Birds of Prey
- Valey of Kings
- Blue Horizon
- several others
- Newspaper Scientific Section (NRC
Handelsblad Wetenschap & Onderwijs)
- Scientific American
- Dutch Literary Novels
- Harry Mulish:
- De Procedure
- Ontdekking van de hemel
(and, yes, I saw the film and
LOVED IT - is this getting boring already?)
- Voer voor psychologen
- De Toekomst van Gisteren
- De Diamant
- Lots of others I can't remember the titles of
- not: De Aanslag
- Maarten 't Hart
- J. Bernlef
- Lots of others I can't remember
- Watch Star Trek:
- Original Series (nostalgia rules)
- The Next Generation (Where no-man, er... no-one,
- Voyager - Damn! They actually made it... :-(
- Deep Space Nine (which unfortunately sometimes is
much soapy "Bold and Beautiful")
- Should I mention "Enterprise"? I've tried it a few times...
O.K. That's about it, if you want or need more info, you can
contact me at email@example.com.
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