Meet the classic paper: Sorin and Pande 2005
We revisit a classic paper from Folding@home’s early days in which the supposedly simple dynamics of a simple peptide turns out to be much more exciting than expected.
Read moreAuthor: Vincent Voelz
NEW COVID-19 SMALL MOLECULE SCREENING SIMULATIONS ARE RUNNING ON FULL FOLDING@HOME!
We are excited to announce a new batch of small molecule screening simulations are now up and running on Folding@home! These simulations will help prioritize which molecules will be synthesized and assayed…
Read moreNew paper: predicting how mutations perturb folding
In a new article published in the Journal of Chemical Theory and Computation, researchers from the Voelz Lab address an important challenge for molecular simulation: how to efficiently predict the effects…
Read moreNew paper on MDM2: lid region dynamics and computational docking
The so-called “guardian of the genome”, p53 is a tumor suppression protein involved in regulating cell repair and apoptosis. Many cancer cells are able to proliferate because they have mutations…
Read moreNew paper on non-native salt-bridge effects on folding
Salt−bridges are electrostatic interactions between positively charged residue side chains (like arginine or lysine) and negatively-charged side chains (like aspartic and glutamic acids). They play an important role in stabilizing…
Read moreNew paper on peptoid helix folding from the Voelz Lab
Nature relies on the remarkable folding properties of proteins and nucleic acids to perform vital chemical work. Not surprisingly, synthetic chemists have long set their sights on developing non-natural molecules—called…
Read moreSimulating protein dynamics to find binding-competent states
Mutation to the tumor-suppressor protein p53 is a common feature in most cancers. MDM2–a protein whose job it is to downregulate p53 via their direct binding interaction–has therefore become a…
Read moreUsing MSMs to study the effect of tryptophan mutations on folding
In a new paper, we describe our efforts to use Markov State Models (MSMs) to study the how tryptophan mutations affect the folding and conformational dynamics of a series of…
Read moreModeling cyclic RGD peptides
RGD peptides (those which contain a conserved Arg-Gly-Asp sequence) can adopt a hairpin loop structure found in integrin-binding proteins such as fibronectin, fibrinogen, and vitronectin. Over the last few decades,…
Read moreExploring how mutations affect folding using Markov State Models
A powerful method to understand folding and conformational change in proteins has been the Markov State Model (MSM) approach, in which protein dynamics can be described as a network of…
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