A new XSEDE award for supercomputing resources

posted Mar 15, 2017, 8:24 AM by Vincent Voelz

Good news: our renewal request for the XSEDE supercomputing allocation was renewed March 2017!  The allocation, comprising over 6.2 million processor-hours on TACC Stampede, PSC Bridges and SDSC Comet supports our continuing work on "Molecular simulation and kinetic network modeling of protein folding mechanisms", funded through the NSF (MCB140270), and new work on simulating protein binding pathways and kinetics.   The estimated value of the allocation is over $222K, and represents a significant investment by the NSF in advances computing infrastructure for the U.S.

New JCTC paper on MaxCal modeling of protein mutations

posted Nov 28, 2016, 3:31 PM by Vincent Voelz   [ updated Nov 28, 2016, 4:10 PM ]

Congrats to Hongbin Wan and Guangfeng Zhou on their new paper published in the Journal of Chemical Theory and Computation!  

This new work describes a new statistical mechanical technique to compute changes in folding kinetics directly from changes in equilibrium state populations.  Our current approach to modeling folding kinetics for different protein sequences is to perform large-scale simulations, from which we construct transition network models of folding called Markov State Models.  In the future, this new method could be used to infer how mutations and other perturbations affect folding, and avoid the expense of having to do so many simulations for each sequence.

Wan, H., Zhou, G., & Voelz, V. A. (2016). A Maximum-Caliber Approach to Predicting Perturbed Folding Kinetics Due to Mutations. Journal of Chemical Theory and Computation, Article ASAP.


Happy Halloween from the Voelz lab

posted Oct 31, 2016, 3:09 PM by Vincent Voelz

New paper on MDM2: lid region dynamics and computational docking

posted Sep 16, 2016, 11:31 AM by Vincent Voelz   [ updated Sep 16, 2016, 11:32 AM ]

Congrats to Sudipto Mukherjee and George Pantelopulos on their new paper published in Scientific Reports on MDM2 lid region dynamics and its role in computational docking. You can read a research summary on the ever-popular Folding@home blog, or check out the following link to the full manuscript:

Mukherjee, S., Pantelopulos, G. A., & Voelz, V. A. (2016). Markov models of the apo-MDM2 lid region reveal diffuse yet two-state binding dynamics and receptor poses for computational docking. Scientific Reports, 6: 31631. doi:10.1038/srep31631

Voelz Lab takes Philadelphia ACS Meeting by storm

posted Sep 7, 2016, 2:24 PM by Vincent Voelz   [ updated Sep 7, 2016, 2:25 PM ]

Congrats to Voelz lab graduate students presenting at the 252nd National Meeting of the American Chemical Society in Philadelphia, PA, August 21-25, 2016
  • Guangfeng Zhou, invited talk in PHYS: Intrinsically Disordered Proteins: Structure, Function & Interactions, "Understanding MDM2-p53 binding through Markov state model approaches"
  • Matt Hurley, COMP poster: "Probing the effects of N-methylation on peptide-protein interactions using alchemical free energy perturbation."
  • Yunhui Ge, COMP poster: "Computational screening and selection of linear peptide hairpin mimetics by implicit solvent molecular simulation"
  • Hongbin Wan, COMP poster: "Using Markov state models to better understand the effects of mutations on folding"

XSEDE supercomputing allocation awarded to Voelz Lab

posted Mar 26, 2016, 9:56 PM by Vincent Voelz   [ updated Mar 15, 2017, 8:11 AM ]

Our group was recently awarded with an XSEDE supercomputing allocation on TACC Stampede for our continuing work on "Molecular simulation and kinetic network modeling of protein folding mechanisms", funded through the NSF (MCB140270).  The renewal is about twice the amount as our previous allocation, with an estimated value of over $217K, representing a significant investment by the NSF in advances computing infrastructure for the U.S.

Asghar defends thesis

posted Jan 29, 2016, 11:02 PM by Vincent Voelz   [ updated Jan 29, 2016, 11:02 PM ]

Congrats to Dr. Asghar Razavi!  

Asghar successfully defended his thesis “Markov State Models and Their Applications In Protein Folding Simulations, Small Molecule Design, and Membrane Protein Modeling” on November 2.     He is the first student in the Voelz Lab to receive their Ph.D. 

Asghar leaves behind an impressive spate of first-author publications (several still under review), and will no doubt go on to great success in his postdoc with Harel Weinstein in the Institute for Computational Biomedicine, Weill Cornell Medical College in New York City.  

Asghar and Vince, post-hooding ceremony 

Welcome Matt!

posted Jan 29, 2016, 10:20 PM by Vincent Voelz   [ updated Jan 29, 2016, 11:02 PM ]

A (belated) welcome to Matt Hurley, who joined the Voelz Lab this December.  Matt is currently working on binding free energy calculations of integrin inhibitors.

New paper on non-native salt-bridge effects on folding

posted Jan 29, 2016, 9:51 PM by Vincent Voelz

Congrats to Guangfeng Zhou on his first-author paper in the Journal of Physical Chemistry B!

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 many protein structures, and have been shown to be designable features for protein design. 

In a new, we study the effects of non-native salt bridges on the folding of a soluble alanine-based peptide helix (Fs peptide) using extensive all-atom molecular dynamics simulations performed on the Folding@home distributed computing platform. Using Markov State Models, we show how non-native salt-bridges affect the folding kinetics of Fs peptide by perturbing specific conformational states. Furthermore, we present methods for the automatic detection and analysis of such states. 

Why are these results important to our understanding of protein folding? It used to be thought that protein unfolded states resembled a “random coil” with few structural features.  We now know that salt-bridges forming in unfolded states can significantly affect folding stability and dynamics. Our work shows that we can quantitatively predict these effects.  Eventually, we hope to be able to use such knowledge to engineer the folding properties of proteins. 

New paper on peptoid helix folding

posted Nov 22, 2015, 5:13 PM by Vincent Voelz   [ updated Nov 22, 2015, 5:15 PM ]

Peptoids (N-substituted oligoglycines) are bio-inspired synthetic heteropolymers that can fold into a number of diverse structural scaffolds.  In a new paper by Mukherjee et al., we report on improved simulation potentials that better model peptoid helices, a key motif for peptide mimics.  We then use a statistical mechanical helix-coil  model to examine the thermodynamic forces that drive helix formation.  We find that, unlike peptides, peptoid helices can  increase their entropy upon folding, indicating that steric bulk of plays a large role in stabilizing helices.  These findings will help future efforts in computational peptoid design.  

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