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I tend to gravitate towards computer modeling, simulations of protein folding, drug mechanisms, that sort of thing. Got any suggestions? The bioinformatics programs I've looked at seemed to ignore this field.

Yes, I forgot to mention. Due to my lack of research and publication experience I'm applying to MS programs though ultimately I would like to go for a PhD. I'm going to hit up my old professors for just the sort of info you spoke about this week in fact.

I'm basically just looking for some advice here as to how to direct my search for a program in molecular bio or biochemistry. I'm also interested in computational biology as I used to be a computer programmer. My stats are GPA 3.68 from a second tier state U and GRE 690Q, 710V. I don't have my AW scores yet. I took the GRE about 6 years ago and got 750Q, 760V, 6/6 AW though so I know I could probably do better on a retake. Anyway, I'm applying to a couple schools locally but am also looking out of state. I have 4 references, all very good but they are just from people I took classes from. In one case I was the 2nd highest class grade though. I also did an internship but it didn't work out due to some problems coordinating things with a person in the lab who didn't like me, so I'm not going to use that PI as a reference. Anyone have suggestions about where I might apply with a high probability of success? I have very little money to spend on application fees and of course not much time left to get in for Fall 2011.

Let me preface this by saying that my goal is a PhD and my field in molecular biology. Ideally I would just apply as a PhD candidate. The problem is that I bounced around at different schools before I was studying biology and though I have a high GPA in biology (3.68) and high GRE scores (1510) I have a number of "W" grades due to some health problems (since resolved). My thinking is that it might be easier to get into a program as a Master's candidate and then upgrade into the PhD or go elsewhere for it. I have heard, however, that it can be easier to get in as a PhD candidate. I find this hard to believe due to the fact that the school usually pays your way as a PhD student while Masters students don't get support but I'm open to hearing otherwise.