Posts

The eternal debate – one score function to rule them all?

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~ contributed by Julia Koehler Leman Molecular modeling packages use various types of score functions, depending on the task and their required atomistic level descriptions. For instance, molecular dynamics simulation packages often use a molecular mechanics force field to model small molecules, peptides and small proteins, and allow exploring the folding trajectory of the latter two. The modeling of chemical reactions requires a description of the electron configurations through quantum-mechanical force fields, which are expensive to compute and only possible for small systems. A combined QM/MM (quantum mechanics / molecular mechanics) approach allows modeling chemical reactions in larger systems such as enzymes. Monte-Carlo simulation packages often rely (at least partly) on knowledge-based score functions that are statistically derived from experimentally validated datasets through an inverse Boltzmann relationship (see Figure).   Figure: Most prevalent scor

Standing up against hate and acts of violence

~ contributed by the Rosetta JEDI committee~ Dear all, Along with all members of our community, we are heartbroken by the recent murders, acts of violence, and discrimination against people of Asian and Asian-American descent. We condemn the increased racism and xenophobia directed at people of Asian and Asian American descent. We stand in solidarity and support with the Asian, Desi, Pacific Islander, and Asian-American members of our community, condemn these acts, and mourn those lost. The recent attacks are the latest forms of bias rooted in hate against people based on their race, religion, ethnicity, socio-economic status, gender identity or expression, and sexual orientation. We call on the entire Rosetta Commons community to stand up against all forms of hate, bias, and bigotry and to eliminate xenophobic rhetoric when it arises. For anyone in the RC community who may feel unease or anxiety as a result of these and other incidents, we hope you will seek support through your unive

Rosetta Commons Black Lives Matter Statement

Trigger warning: mentions acts of violence and racism We, as members of the Rosetta Commons, recognize the grief and frustration of many members of our community and reaffirm our commitment to the safety and dignity of Black lives. The past few months have been traumatic. The recent murders of George Floyd, Breonna Taylor, Tony McDade, Sean Reed, Nina Pop, and Ahmaud Arbery, among others, have highlighted, once again, the pervasiveness of anti-Black racism and police brutality in the United States of America. We condemn these hateful acts in no uncertain terms and stand with the Black community. Black lives matter. In addition, the global COVID-19 pandemic continues to devastate our society and we acknowledge that Black and Indigenous communities have taken the brunt of the public health impact, putting their lives at risk while working in front-line roles, without protection or recognition. We affirm that these are all manifestations of structural racism. To our Black c

Parametric disasters

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~ published by Brian Weitzner ( original post from 09/03/2018 ) ~ I recently got a new computer and I have been (slowly) going through my old files to try to maintain a little order around here. So, while I was doing the ol’ twenty-first century upkeep, I stumbled across a file called “nope_nope_nope.mov”. Here’s what was in that file: There’s another one called “strand_fail.mov” that looks like this: W hat each of these movies show is a failed initial attempt at extending the parametric bundle design methods used in Rosetta. A little while ago, Vikram Mulligan and I sat down to think about what would be needed to describe a β barrel. We started off noting that a strand could be thought of as a helix in which every residue flips 180º, and that we would need to describe a “squishing” parameter to describe non-circular barrel systems. Vikram recently moved on to the  Flatiron Institute  in New York, but this was a fun little project that kind of went nowhere so I thought I would share it