I’ll give you a few examples. One of the areas where I thought it was too hard to get stuff into the literature was in the area of structure prediction. People would try to write programs that could predict the structures of proteins. And the fact is these programs don’t work all that well now, and they certainly didn’t work all that well in those days. So any reasonable reviewer could always criticize a protein-structure prediction paper to death, and these papers would never get accepted.

To get around this problem I created something called structure-prediction reports. These were papers that used new techniques to predict the structures of proteins. The ground rules were that reviewers couldn’t criticize these on the basis that they didn’t believe in the method. The idea was to get the results of the methods out in the literature for people to see. So the reviewers could criticize these papers for other reasons, but it wasn’t fair game to say that they just didn’t think this method worked. That’s an example of the kind of thing we did to let people get somewhat less-formed ideas out in the literature. And some of these ideas then took off, of course.

Another thing is that I just tend to be generous about papers in which reviewers are divided and the principal criticism is that the paper is too speculative. If it has good data, I’ll accept what other people might consider excessive speculation. That’s just my personal philosophy. I tend to let authors get away with a little bit more, in terms of authors saying what they’re thinking.

Let me give you a little history of our citation rate. We had the kind of climb in citation rate in the early days that’s typical of a new journal in a new field. But then we took a tremendous hit in the early 1990s for the following reason. In the early days of the journal, we used to publish many x-ray crystallography papers describing protein structures. Then we had some strong competitors come into the market place, like Structure and Nature Structural Biology. These journals allowed to publish some number of color figures without a charge. My publisher had a different philosophy about this, and we were required to charge authors these color fees. 

The result was a tremendous flow of protein structure papers out of our journal into these other new journals. We would have lost some of them anyway, but we lost more than our share. And these structure papers tend to be highly cited, especially if they’re interesting proteins. So if you go look at that period, our impact factor probably went down by 50%. Since then it has been improving. So it hit bottom and it’s been coming back up.

I think that’s one of the reasons for our growth in influence. Another is that we have really a strong editorial board, which has helped us grow enormously in area of various kinds of computation: first in simulations and more recently in bioinformatics. We have editors who have attracted really good papers. They have the right balance of being tough but not too tough. I think people saw a real evolution of the journal into the broadest areas of computational biology. At the same time, we managed to maintain a significant base of experimental papers, especially papers with good data and interesting analysis. These people found this a good place to publish because we have an audience that understands both computational analysis and more physical methods.

Another factor might be our special issues on the CASP competition. CASP is a contest in which groups that work on protein structure prediction get to try their methods on targets for which the structures have been done but are kept confidential until the contest is over. We work very hard on this issue and it’s inevitably very popular.

What I meant was that these are papers whose methodology is computational rather than wet laboratory science. For example, simulating the motions of a protein in the computer or simulating the mechanism of an enzyme or trying to calculate the electrical characteristics of a protein—i.e., its electric field—things like that. More recently, we’ve had a lot of computer-based papers in the area of bioinformatics: new ways of comparing sequences, analysis of protein families from widely divergent organisms, and subjects in which the whole methodology is computation.

Recently our publisher, John Wiley & Sons, urged us to transfer our small editorial office away from Hopkins to their centralized facility in New Jersey. So we did this, and now all the manuscripts go there. And because that’s an environment where all the people work together on manuscripts for the different journals, they have the capacity for a significantly bigger work flow. We also much improved our online manuscript submission system. As a result, our work load lately has gone down to some extent in terms of the basic handling of manuscripts. There are not as many snafus as there used to be, because the system catches them before they happen.

There are two things I’d like to do fairly soon. One is that Proteins historically has never had a commentary section. I’m hoping we can introduce one within six months. Initially it will be limited to papers published in the journal, but after that, I’d like to perhaps extend it to outstanding papers that people have spotted elsewhere.

Another improvement, or at least an evolutionary step, is we may divide off the bioinformatics part of the journal and make it into a separate section. Not a separate volume, but a separate section in the issue, either in front or in back, which would have a separate editor. That might happen within the next year. It’s a way of making the bioinformatics part of the journal more visible to the bioinformatics part of the community, with an editor they can identify who’s responsible for the whole thing. Those are the two things we have on the horizon.

I think that we really are approaching the time when our knowledge of protein structure and physical chemistry is going to make important contributions in medicine, biotechnology, and industry. I think we really are almost there with a set of tools that would make rational structure-based drug design much more of a reality than it’s been in the past. I think we’re also close to being able to do things like protein design, in which you want a protein molecule to achieve a specific function, or maybe do something it’s never done before or achieved in a brand-new environment.

As an example, this could have applications for things like ethanol production from biomass. We’re making ethanol in systems that haven’t been optimized to make ethanol. I think there’s a lot of possibility from the engineering of enzymes that would optimize this whole ethanol pathway. And so one can finally imagine really pushing industrial processes like that in much more efficient directions with the help of protein design.

Open source publications obviously constitute an enormously complex and challenging issue facing publishers and authors and libraries and everybody else. I have my own personal opinion about this. Putting the technological issues aside, one of my colleagues in the chemistry department, David Draper, once said about article databases that the only search you can’t do is "RNA" and "good paper." And that is the search that journals do for you. I think that journals, good journals, contribute a tremendous amount to the value of published papers in these processes of validation and improving manuscripts. As I look at the years I spent at Proteins, I can see countless papers that were transformed from a bucket of wet wash by really terrific work by reviewers and editors.

Now this process of immediate deposition of manuscripts into databases, I think, is going to overall lower the quality of published works. I think people will have a tendency, if their paper gets criticized, to just say, "screw it," put it in a database, and leave it there. It will take time to build up a system in which papers published in these databases are really reviewed well. So, in short, I’m concerned about the quality of published papers in the coming years, and that’s something we’re all going to have to deal with. I think it’s going to be hard to keep the standards up; it’s going to be a struggle.