Jon Wright's Home page.

Work related bits.

I'm working in the Carmay Lim group in the Institute of Biomedical Sciences at Academia Sinica Taiwan. A brief CV is online here At the moment my research is mainly in the area of protein-protein and protein-DNA insteractions. Recent papers have looked at engineered modifications of ColE7 to enable it to bind to different DNA sequences and also papers on why two relativly minor mutations from Ile/Leu to Gly distant from the major binding interface prevented GGPPS from forming dimers. Applications of this have been used to probe protein-protein Docking via the EMAP modules in CHARMM. For a while I was looking at protein-DNA interactions and in particular mutations of the p53 protein and how they prevent p53 from binding to DNA. It is believed that over 50% of cancers occur because of these mutations. We hope in the long term to design a drug to allow the mutated p53 to bind to DNA and restore its activity. A picture of the wildtype p53 bound to DNA is to the side with the two most frequenty mutated residues in green. Another picture of this solvated and with the counter ions can be found here. The first and second parts of this work has been published in Nucleic Acids Research and The Journal of Physical Chemistry B in 2002.

Before this I studied the interactions of IgE with the FcR1 receptor and a protein designed by Tanox Biosystems Inc to inhibit the binding of IgE and FcR1. A picture of my current model of the Ch2 and Ch3 domains of IgE docked to the Tanox Anti-IgE is to the side, this work has been published in Protein Engineering (1998). In June 2003 the anti-IgE was accepted by the American Federal Drug Administration for use as an anti-asthma agent and is now available under the brand name Xolair. This work is restarting in 2009 with the X-Ray structure of the Xolair FAb being solved and the modelling of full length IgE.

The work is being performed using theoretical means - namely homology modeling, molecular dynamics and protein docking. All the computations are being carried out in house on our Linux based cluster. A list of machines and programs being used is here.

As well as my research I also manage the computer systems that the group uses and spend time writing software related to group research. I use Perl scripts and standard UNIX commands such as awk and sed as far as possible. For large projects involving number crunching or graphics I use Fortran90 and the pgplot libraries, for portabilty any parallel codes are written using the Fortran interface to the MPI system. If you want to know why I use these for my programming look over on this page.

Previous to working at the Institute of Biomedical Sciences I obtained my Ph.D. working in the Chris Reynolds group at the University of Essex, UK and my B.Sc. from the University of Keele, UK. My PhD title was Computational Studies of Hypoxia-Selective Bioreductive Agents, and a pdf version of my thesis can be found online. An example of this type of agent and its reduction pathway is below:

I am a member of the The Royal Society of Chemistry and also subscribe to the Computational Chemistry List, CHARMm and Amber mailing lists.

Non-work related bits.

In 1997 I went on a trip to Latin America where I visited Bolivia and Chile, Chile wasn't that great but Bolivia is a wonderful place and I really wish I could have spent longer there. Some pictures of the trip can be found on this page. Also I've been over to mainland China about 6 times and down to the Philippines 3 times just to see some more of Asia.

So what else have I done since I've been here, survived eleven Chinese new years, visited hot springs in Tarako gorge that you could boil eggs in, I've been coral reef diving off the islands of Penghu (half way between China and Taiwan). I was here when China played war games in 1996 around the Taiwan coast and the Americans sent two carriers to `help out'. The earthquake in 1999 was a very intersting time, typhoons also add to the variety of life here as well. I think though the best part of Taiwan has to be the food however.

As a hobby I play bass guitar, guitar and abit of drums. 

I have a three basses, the big one is a beautiful natural satin finish Yamaha BBN5-II (5-string) with the soapbar pickups. I then picked up a 2nd hand OLP MM2 copy of a MusicMan, the main difference being in the pickups, so I fitted a Seymor Duncan Basslines SMB-4d pickup with a STC-3M3pre-amp to get a bass very much like the MM. The next addition was a cheap acoustic electric bass guitar because we're now playing more and more acoustic sets. The ABG is from the Essex (SX) company made in China model DBG-29CE, it comes with Shadow piezo bridge pickups and a preamp system. I'm not sure how that works because the pickups and preamp seem to cost more than the whole guitar did! It's a short scale bass that's only 28" between the nut and the bridge. I am sure there are much nicer ABG out there but everything else I looked at was either the same price and quality or double the price for better quality. 

For the guitars, one is an out and out electric stratocaster copy (Yamaha Pacifica 112MX) again in a natural satin finish. recently I added a Yamaha Pacifica 120SJ which is the yamaha version of the telecaster. Both of these have been out and about recently in some concerts borrowed by other band members, the 112MX played through a Zoom G2.u1 multi-effects pedal and the 120SJ played through BOSS OD-1 and DS-1 overdrive and distortion pedals.

For acoustic work I have an acoustic electric yamaha APX-5A in a translucent blue finish, then because everyone kept borrowing that and I never got to play someone gave me a natural finish APX-3T which is same size/shape as the 5 so is a great practice tool. About 2-3 months after having that my wife started to learn guitar and adopted the APX-3 as hers again leaving me with no guitar to practice with at home

All five yamaha's are are made in Taiwan except the PAC120SJ which is from Indonesia and they all sound excellent, in fact better than some of the more popular makes that were USD 100-200 more pricey. However I did try 2-3 basses and 3-4 different yamaha guitars before picking these one. Funnily enough the more expensive yamaha electric guitars I tried didn't sound as good as the 112MX. At the time I bought the bass and electric guitars I bought a cheapish amp to go with them.

At home the bass plays thro a noname 35W bass amp and the guitar thro a Aria 20W amp. When playing at church the bass goes thro a Laney HardCore HCM120B and the electric thro a 65W fender with the acoustic being plugged directly into the sound board.

Being a trainee drummer I also have a electronic drum kit set up in the spare room which is a Yamaha DTXPressIII drum kit. Its perfect for near silent practice, ideal for recording and alot easier to move to venues than a real drum kit although real drums have a presence that these will never have.

Since my wife plays piano we have an electric piano in the house as well which is a Roland RD-100, this and the DTXPressIII are connected to a Behringer Eurorack UB802 mixer and then the speakers are a set of Yamaha MSP-3s. I'm having loads of fun with these at the moment but I'm not sure the neighbours are. Since none of them speak English I don't really know what they think! One interesting thing is that start playing a bass guitar and the older cat runs away, pluck a guitar and she stays but the younger one runs.

Links you might find interesting.

• Linux, a unix for PC's, Actually I think this link is better.
• Redhat Linux probably the most popular commercial version of Gnu/Linux around.
• If you use vi you will love VIM.
• The Electronic Telegraph, the expats link to the UK.
• BBC online news, much better than CNN
• Leif Laaksonen's comp chem site list.
• A very useful Fortran link.
• A very useful Perl link.
• Samba, exports unix filesystems to Win9x.
• O'Reilly's homepage - for the best computer manuals.

Opinions on these pages are generally not Academia Sinica's.