Almost exactly the same time iPhone 5 was released the new version of protein structures.com was uploaded to the server! Essentially most of the chapters were re-written in one or other way, the tutorials on sequence alignment and homology modeling were completely re-written and new images were added, many links updated, a new template with new navigation bars, new and better figures, which are also smaller in size (which makes them download quicker when people open the corresponding pages), etcetc, etc. But this is not all, there is still a lot to do!
I will continue the updates the coming weeks with the ambition to put together as much material, links to other sites, etc., as possible to convert this site to a general portal for structural bioinformatics and one of the best on the web on the subject! The increasing number of people visiting the site and the e-mails I get from people telling me how much they like the idea of having this type of material concentrated in one place, are my sources of inspiration!

Three months have passed since the beginning of the year. Hard to believe, time passes so fast. Interesting paradox, the future takes a lot of time to come, and then suddenly it is gone, very fast. Still, memories are left, some pleasant, some not so pleasant, but this is life, although all religions say that life is suffering. Buddhism, for example, wants us to get enlightened so that we don't get reborn. I am not sure about getting reborn, but people definitely want to stay alive. I think the expectations of the future give us the energy to continue, we all are optimistic about the future, we are convinced that we will do better in the future, that life will get better. And in many cases it really does!
In many ways life at academia is privileged, we do things we like, and in many ways we have a lot of freedom in doing these things, in choosing what we want to do. However, nowadays we are getting less and less of these freedoms. Politicians more and more want to decide what research should be about, what people in research laboratories should be doing. Very strange situation, many of these politicians, at least in Sweden, do not even have any higher education. Still, they know better what research should be about. And this is despite the fact that history has demonstrated many times that the best inventions are never planned, never come as a "work order" from politicians or anybody else. Creativity cannot be planed, does not matter how much you pay an artist, you will never get another Mona Lisa or another relativity theory!
The new trend now is to create big centers of excellence, to bring a lot of people together and let them work in a certain area, a kind of science factories. Well, let us see what the next trend will be in 5-10 years.
But there is still a lot of fun in academia. For example, my trip to a meeting in Cambridge. This was not my first trip to that city, but it was the first time I had some time to walk around. The nice surprise was that the eduroam network was essentially everywhere on the streets, simply because of all the colleges. So, I had my iPhone and Google maps on the whole time and could just follow the map wherever I wanted to go. Here is an example:


This was on my way back from the nice dinner we had in a really Cambridge-type atmosphere at this place:



"Unfortunately" I had to give a talk the day after and did not want to stay late at the pub with other people. And then, in England one needs some extra time to plan such simple things like washing your hands:



The hot water is usually really hot, while the cold is really cold! How to mix them to get a useful temperature is up to to the user!


And of course there were grant applications during these months, several of them. Somehow a year gets split into two parts, the first part goes to writing grant applications and research papers, the second is more into teaching. In-between there are meetings - during the summer and early autumn. What I miss is real scientific work, like sitting and doing my own projects, like my PhD students do. We have even got the result from two grant application evaluations, one was sent last December and the second in February, both on projects related to our company SARomics Biostructures. One of the applications was sent to the EU and it received positive response, we got above the threshold, but we still don't know if we will be invited to start negotiations, which would mean that we may get the grant. That would of course be wonderful. That is going to be a big thing, a very nice project, which involves several groups.
The other was sent to the Swedish innovation agency called Vinnova. In this case we were not so lucky, although we had a very good application, as much as I can see. The project is about finding a new treatment for one cancer type, and it is going to be run in collaboration with a company from North America. However, this innovation agency decided not to give us any funds, and I don't know why, we still have not received the motivation for their decision. Interestingly, among the projects, which did get funded was, for example, a new automatic system for renting trailers. You know, those you can get at gas stations. Apparently that was more important than treatment of cancer. Still, quite disappointing. Eventually we do that project, in one or other way, it is too interesting to let it go just because someone not so clever did not like it. Perhaps the treatment, which we will eventually produce will save the life of one of these people or someone from their family, who knows. I hope they will regret their decision when that happens.

Funny, when I start thinking of occasions when I wished people would after some time realize how wrong they were in taken a certain decision, I can remember quite a few. Once we sent a manuscript to Nature Structural Biology, it was about a pi-helix, a special type of a helix in proteins. It came back just after few days with a letter that they were not interested. I was disappointed, just because I was sure that we had a great work and that it would also give them the citation’s number they want. And since I was very naive at that time and believed that people at academia were doing things primarily for promoting science, I wrote an angry letter (because I was angry :-)) to the journal and sent a copy to the persons I recommended as referees for the manuscript, when I submitted it to the journal. I still don’t understand why I did this (sending the letter to the potential referees), probably hoped I would hear some compassion ☺. Of course nobody contacted me with regard to the letter. However, that was not the end of the story. We submitted the same manuscript to Structure, and you know what? After a few days it came back from Structure with a letter stating that they did not want our paper and pointed to my angry letter to the previous journal as the reason. I couldn't believe this! Apparently they sent the manuscript for initial review to one of the persons, to whom I sent a copy of the angry e-mail in the hope for some compassion, and that person decided to punish me by sending that mail to Structure! And Structure editors decided to show some solidarity with their colleagues at Nat. Struc. Biol.! Anyway, the manuscript was accepted in Protein Engineering without any comments and currently we have something like 80 citations to that paper. Actually, we were recently asked to write a review on the pi-helix, something like "The pi-helix, 10 years later". This is something we are doing now together with my former student Michel. The take-home lesson was: do not expect any compassion from people outside the departmental coffee room (the main and probably only location where we can complain to each other and get some compassion:-)!
I don’t know why I always get into stories like this, but on the other hand, there is something to tell afterwords! As Oscar Wild wrote once, the only thing, which is worse than being talked about is not being talked about ☺. And I think the only thing that is worse than having stories to tell is not having any stories to tell!
Have a nice spring!

What is credibility? I don't mean i everyday life, I mean in science. Sometimes it is a real mystery how people decide that for example somebody is credible, but that other guy is not. Some years ago I applied for a grant to a Swedish agency called FORMAS, which gives money to research related to plants and agriculture. The project was about obtaining structural information on an enzyme called magnesium chelatase, which catalyses the first committed reaction in chlorophyll biosynthesis, the insertion of a magnesium ion into a porphyrin ring. I received about half a page evaluation of the project, where the person who did the evaluation wrote that the project was very interesting, but he (or she) doubted that I had the competence to carry it on. By other words I was not credible. Eventually, together with my PhD students we did what we planned in that grant application and now it is published. And all that without the help from FORMAS. A second story is about another enzyme called spermidine synthase from the malaria parasite Plasmodium falciparum. I applied at least 3 times to the Swedish agency called SIDA, which supports research related to third-world countries, for funds to determine the structure of this enzyme, which is a potential drug target for the treatment of malaria. And what do you think? All possible excuses and explanations of why I could not work with this project. The last time I applied we already had crystals and the person who evaluated my application actually recommended funding the project. Do you think I got the money? You would never guess the answer I received from that research council, only a few words: too premature!!! Was it too premature for millions of children who die due to malaria? Or was it too premature because they also thought I did not have the competence, "low credibility"? Eventually we determined the structure without their funds and currently running a project on a design of new inhibitors for that enzyme. The list could go on, but I just take one last example. Last year I applied for a grant to get a SAXS machine to our department. The idea was that having a machine in-house will stimulate more people to use the method and eventually we could build a competence in Bio-SAXS and have an active group by the time the new synchrotron (MAX IV) is built in Lund. I don't need to tell you the rest of the story. Actually I did not even get any beamtime at MAX lab to run SAXS experiments when I applied last spring. In June last year I wrote to the director of the synchrotron and demanded some explanation and the names of the persons who evaluated my beamtime application. What do you think the answer was? Well, I don't know, I did not get any answer, but I am still waiting :-). Meanwhile we drive to Hamburg for SAXS data collection, and I enjoy these trips enormously.

And now a very recent example. We plan an application for EU program on industrial PhDs. Within this program the student is supposed to spend half of his time at a company and the second half at an academic institution. It is an exciting and also challenging project. I made a mistake to discuss it with some people I know, I am not going to name them. And guess what was their reaction, no credibility of course. In a control experiment one would let, for example, a Swedish person talk to the same people and suggest the same project to see if their reaction would be the same. Unfortunately one would probably need to enter a parallel world, which was not affected by the results of the first happening to get a correct answer. But we still don't know who to do that.
However, everything was not so dark last week. That is because Marco was here again! Marco has one student in Lund working on organic synthesis of inhibitors of another enzyme from the malaria parasite, dihydroorotate devydrogenase (DHODH). He will also be part of the planned "mission impossible" EU project for which we had the first planning meeting. I had someone who listened to my complains to about the people who thought the project was impossible and those who thought we did not have the credibility. And guess what? He did not agree with them :-).
Here you see Marco when he just arrived from the airport to the meeting we had at DTU in Copenhagen:




What do you think people? Are we going to make it or mission impossible?

Ciao for now!

For some reason people look very much towards the end of the year and then become very happy and wish each other happiness when the new year finally arrives :-). The end of the year is also a time to look back, trying to assess the accomplishments of the last 12 months. One could of course do this just for nostalgic reasons. Whatever the reason was, I decided to do it and then I could see what a tremendous year I have had, so much packed it was with happenings. Could this be predicted 12 months ago? Hardly, however, I had a vague plan and at least some idea on where I wanted to get. The rest started to unfold by some mechanisms driven by some, for me unknown forces. Things happen and we have to make the best use of them. That is why it is good to have a plan, which may help us and teach us to use the things which may happen and let them take us where we want to go.
Now, looking back on the most memorable of 2011, what was the most memorable?

My two visits to Moscow of course, the first to try to prepare the bioinformtatics course, and the second was actually to run the course. I was hoping that among other things, the contact with my Alma Mater would lead to some collaboration, joint grants, etc. However, I quickly learned that the almighty Russian bureaucracy was nothing to play with. Handling bureaucracy is generally not my strongest side and spending time learning how to deal with Russian bureaucracy is definitely nothing I am looking forward to. Perhaps around 10 signatures were needed to get me a room at the university guest house. I am not going more into the details, but here is the guest house house I was going to stayed at, that April 2011, as seen by my iPhone :-). There was also this nice old Volga-car, probably forgotten at this parking by its owner and standing there since the soviet time. In some way this is rather characteristic of Russia: Nobody cares.



Actually, we also visited some friends at the Institute of Protein Research in Puschino, a research centre just outside Moscow. By that time Anders Liljas joined me in Moscow and gave some lectures for the students at the course. On the left we are eating lunch together with our friends in Puschino. On the right Anders is being prepared for a TV program which we recorded while there. It was about science in general and Nobel Prices (Anders served for many years as a member of the Nobel Committee for Chemistry). However, this program was never translated, perhaps the Russian authorities did not like our free talks about the state of science in Russia. Anyway, this is just a guess, nobody gave us any explanation, which is again typical for Russia. But at least we had fun recording the program:




I was back in Lund at the end of April, but soon, namely at the very beginning of May we were going to Hamburg to collect some SAXS data at the EMBL outstation at the DESY synchrotron. And here we are, late evening having dinner at a chines restaurant:



Very nice food indeed! I warmly recommend this place. Did I get back to Lund after this? No! We went directly to Strasbourg for a meeting on frataxin and Freidrich's ataxia. This was a view from my hotel window 6th of May early in the morning and next to it is Grazia from Mayo Clinic and with whom we collaborate on frataxin, standing together with Annalisa Pastore from the MRC National Inst of Medical Research in London:



Then there was Marco. Marco is from the University of Turin. He contacted me and suggested a collaboration on some kinases. And here is he sitting outside while I was preparing the dinner, talking to his family back in Turin, perhaps discussing which Lego he should get for his son Francesco, on the right is the day after when we went to a restaurant in Malmö together with Maria Prostova from Moscow, who visited us to discuss a project on some virus RNA-protein interactions:



This contact resulted in a great grant application to the EU together with some companies and other academic groups. However, that was in December, before that there was the summer and the autumn, again full of traveling and meetings. At the end of June I went to visit my sister who stayed for a while in the far North in Norway in a place called Budö. Then we went for a one day trip to Lofoten, an area with unbelievably beautiful nature far far in the North. It was +12 degrees in the end of june! Probably the warmest temperature of the year:




A lot happened during the summer, among the memorable moments was this visit to the Danish museum of modern art called Arken. Here you can see a couple of modern art creations. The one I liked most was that with the broken stairs to the administration. Taken into account the overhead we pay the university from our grants (60%), the main part of which goes to keeping the beurocrats going, you can understand that I don't have many positive associations with the word "administration". Concerning the other two "junky" pieces, you may judged the artistic quality by yourself, I am not going to comment that for obvious reasons.




Then there was the carbonic anhydrase meeting followed by the SFBM meeting in Tällberg, a very nice place with fantastic nature. Every year, since 1996, the Swedish Structural Biology Network (SBNET) has had its meeting at this place. And this year for the first time we had the meeting of the Swedish Society for Biochemistry and Molecular Biology (SFBM). The pictures below may give an idea of that place:



And finally there was Freiburg. There we had a meeting with all the members of the EU project I mentioned earlier to discuss the details of the project. I have not been to Freiburg before, but with all Christmas lights it was definitely very charming. ALthough I must say, I did not go to the Scottish dancing event you see below. And Marco was there of course.




Last, but not least, we were approaching Christmas, we had a company Christmas party at my place and I had to give it the look which was appropriate for the occasion:



This was a quick summary of 2011. I promise (this is my New Year promise) that next year I will update the blog in a more regular fashion, to keep the december summary short.
Best wishes and Happy New Year!

I am a bit ashamed for not writing much for this blog. I just noticed that the last time I was here was 8th of February, 9 months ago! What happened? A lot. But perhaps moving from one place to another (I am at a walking distance from my work now) was the largest disaster, which kept me out of reach. However, my energy is returning (after all the heavy stuff I had to move around) and with the energy comes the wish to have some fun! And publishing on the blog is fun! May be the recent renewal of my grant by the Research Council made a substantial contribution to the new energy flow. Or the recent paper we published I J. Mol. Biol. I don’t know.

There is one thing I have a bad feeling about, I have only made minor updates at the site during this period. I have big plans, but they need time. Although I have installed new blog software to replace the one I had before. The new blog has a better appearance and it is synchronised with with Blogspot. I want to update a lot of other stuff, but, always that “but”. I have to finish a grant application I am busy writing now, deadline 6th of December. After that I can have fun, like updating my blog, adding material to the site, etc!
Meanwhile, you may see me on the photo below, with my former supervisor from Moscow State University, Vsevolod Tverdislov at his 70th birthday party. There seems to be some resemblance between us:

Long break, too long. It is actually the first time and I don't understand what happened. But now, NOW suddenly my writing energy is back. I wonder if this has to do with the cycles of the sun. In few days it is going to be exactly one year since I published this site and started to fill it with information! Strange, and now one year later the same energy is back, and I am prepared again to work here! I should admit that the best pages were created at the end of February, while I was on vacation in Thailand with my sister, her kids and my daughter. It was fantastic to get away from the winter and the snow and suddenly be able to drink cocktails with fresh tropical fruits!

Anyway, much has happened since the year started, perhaps the most exciting was my visit to Moscow. I am going to give a course at Lomonosov University later this spring, and I went there for some preparations. I met a lot of old good friends, this was very nice, I enjoyed that very much. The most exciting part of the visit was my program on the Russian channel russia.ru. I talked about structural biology at the first program and about how the system in Sweden stimulates the transfer of university research to industry, also called innovation system. The second is still not published; I assume it will come in a couple of weeks. It is in Russian of course!

Another interesting thing, which happened recently, is that one of my students is back from his half-a-year paternity leave, things like this exist in Sweden! Now we can continue our work on few manuscripts, which are almost ready. Publications, publications, publications. That is the academic life, publications and grant applications.
I promise to come more often now, I like this and I don't know why I don't use this more often.

Me on russia.ru

Happy New Year! I often ask myself, why do we get so excited about the new year, why are we so happy about it? It seems to be a good occasion to forget all our problems, concerns, etc, and just celebrate. I think this is the only holyday on earth, which unites so many people and makes so many people happy, independently of religion, nationality, and all other million things, which have we invented to keep ourselves away from each other on this planet.
I had a wonderful Christmas and New Year celebration with my family, sisters, their kinds, old friends and their families. I need such occasions to remind myself that what really maters in life are the people we surround us with, all the friends we acquire during our life, and of course our loved ones, our families.
Now when we have reached 2011 I can see that almost the whole year is already scheduled with coming meetings, courses, trips to various countries, and much more. I recently got an invitation from Vietnam to go there in February and give some lectures (and they would pay the whole trip). Unfortunately I had to decline, I have already filled February with three different meetings and I also need time for my students, for writing and publishing papers, writing new grant applications, hopefully solving new structures, taking care of our company, and of course adding new pages to this site. Otherwise it would have been nice to get some sun and see some green. Here we are getting more and more snow, all efforts to keep the way to the house free from snow seems to be futile, new snow comes quicker that I can handle it.
Next will be Moscow! I am going for a few days to prepare a course on structural bioinformatics, which will be given in April at my Alma Metter, the Lomonosov Moscow State University! I am really feel excited about going to Moscow, teaching students at my old university after so many years! You will get the report of course!

A month since I wrote anything on this wall. It has been quite hectic time. I find that writing letters, or a blog, which is more or less the same thing, needs some accumulated positive energy. I think during hectic times this energy is mostly used to keep me optimistic, no matter what, and the little, which remains, is needed for the most essential communication. And the result is no blog posts. Sorry for this. Now when courses are almost over, no major grant applications ahead, the days will soon start becoming longer, etc. I am looking forward for spending more time writing on this wall.
Much happened during the past month. Victor Lamzin from EMBL-Hamburg (where the DESY synchrotron is located) visited us, gave a nice seminar which was followed by a tutorial on the Arp/Warp program package, used for automatic protein model building into electron density maps. You may read about the details of Victors work here. And here you see Victor in the computer room talking about his program:

And here before the diner at an Indian restaurant in the evening with Victors colleague Tim:

Other big events of the period include the structure determination by our company SARomics Biostructures of the Inimex Pharmaceuticals Innate Defense Regulator (IDR) IMX942 in complex with its target, the ZZ domain of human p62 (sequestosome-1). You can read more about this here.
That was a big news which went with a press release by the two companies.

A week ago I also went to Stockholm to collect some data at the SGC (structural genomics consortium), since Max lab is closed due to some technical problems and our in-house equipment needs some reparation. It was not much fun to drive 600 km on roads covered by snow, by somehow I managed to come back home safe. I even took a couple of picture on the way. Here is how it looked like at the stop I had for a coup of coffee at a place called Brahe Hus.

I actually put some extra light on the second photo, otherwise it was as dark as the first one.

And what now? You may guess from the following photo taking just outside my house in Lund:

Its Christmas time!

Two weeks of lectures and practicals, organising visits, trials to get the students understand some basic ideas, work with company questions, answering e-mails, etc., etc. Here you see Derek and Chris from iThemba Pharmaceuticals at Max Lab:

 iThemba is a South African company focus on the development of drugs against tropical diseases, and HIV, which unfortunately has become pretty much a tropical disease. We discuss some collaboration in relation to my malaria projects.

My friends on Facebook complain that I have abandoned them, I have not been to the gym for ages (yesterday went for the first time after 3 weeks), and we got the first snow! Poor students from the very South at the course! I have got some student from Egypt, Southern Europe (France and Spain), India, China, and some other countries, I don't actually know exactly. It must be a real shock for them, snow laying on the ground everywhere! That was how it loked like from my office window Friday morning:

I even managed to get a puncture in the middle of the night on my way home  back från Malmö, where I went to bring my daughter after a Haloween party! Thanks to Toyota's road assistance the problem was quickly fixed, and I could get a nice night sleep that night.

One of the most memorable events was probably the attempt to get the PhD students at the crystallography course to start using Linux. My Goodness! What a suffering that was for some of these poor people, they needed to remember about 10-15 Linux commands  and use them to organise their directories, download some files, unzip them, edit some other files and try to use a program for processing X-ray data. That was really dramatic. People often think that crystallography is like MS Office. You open the program and start solving the structure. I think at least these fellows have now changed their minds and probably will try to keep away from crystallography for the rest of their lives. We all work so hard to put our brains to sleep and awakening is of course very painful.  And the longer our brains existed asleep, the more painful the awakening is.
We are supposed to enjoy our lives, not to exert our brains. That is what happens when there is no external or interna stimuli and motivation. Animals usually have two things on their mind: Food and sex, the last one being the only way for them to get pleasure. Still, they have to work hard even for this! Since most of us are well fed and don´t need to go around hungry, what remains then? And the pleasure often is accessible in various easy forms, so what we do? Put our brains to sleep, that is what animals do when they are satisfied with their life. But some of us are more inventive of course, look at politicians and administrators (for example, university administrators). How much trouble and how many problems they cause for others? The way I understand it is that they work hard trying to keep us awake! What would we do without them?

Anyway, today we are going to watch the new Harry Potter movie. This is something I am really looking forward to!

I promised to tell the story of how I became interested in using the Internet for teaching and marketing. It all started when I got e-mail from Shaun Fawcett, a person specialised in helping people with their English writing (writing help central). More than 10 years ago I purchased from him a collection of recommendation letter templates. Being at university one has to write such letters several times per year. From time to time I kept getting e-mails from him on various subjects related to English writing, and sometimes I actually red these e-mails and still find them very useful. Anyway, about a year ago he started to market a new pdf book on how to create a website and start marketing your own stuff. I purchased his book, that was the second time I ever purchased anything from him, I red it over the Christmas holyday last year and I actually started creating my own site! That book made everything so easy and accessible, that I was difficult to resist starting the work with own website. And the first result? It is proteinstructures.com! saromics.com was my second site, by then I was pretty sure of what I was doing. I share this story because I know people like stories and because I think Shaun is really doing great job, helping people. Just to make it clear, I don't get paid for saying all this and i have actually never had any contact with him. Perhaps some day I will write to him. I can tell you what was my latest purchase from Shaun, it is a book on writing a pdf book, or e-books, as they are called on the internet. And why do I need that? I need that because I am writing en e-book related to the content of this site. Probably I will call it something like Practical Guide on Structural Bioinformatics. When it is coming? I cannot promise you now, but I am doing my best.