News – Page 31 – Folding@home

FAST Conformational Searches by Balancing Exploration/Exploitation Trade-Offs.

December 8, 2015 by Anton Thynell

Molecular dynamics simulations are a powerful means of understanding conformational changes. However, it is still difficult to simulate biologically relevant time scales without the use of specialized supercomputers. Here, we introduce a goal-oriented sampling method, called fluctuation amplification of specific traits (FAST), for extending the capabilities of commodity hardware. This algorithm rapidly searches conformational space for structures with desired properties by balancing trade-offs…

FAH's achievements in 2015, with a glimpse into 2016

December 6, 2015 by Vijay Pande

We’re reaching the end of 2015 and as in previous years, I’d like to summarize for donors what Folding@home (FAH) has done in 2015 and where we’re going. In general,…

New paper on peptoid helix folding from the Voelz Lab

November 26, 2015 by Vincent Voelz

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…

Issues with FahCore21

November 20, 2015 by Vijay Pande

We’ve discovered that the new FahCore_21 is producing more errors than we consider acceptable for some clients. The error rate seems to depend on several factors but most noticeable is…

mTOR: Projects 10491-10499

November 9, 2015 by Steven Albanese

In projects 10491-10499, the Chodera lab takes a look at mTOR, a serine/threonine kinase. The MTOR gene was originally discovered in yeast in 1991 and named TOR1/2 because it was…

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories.

October 21, 2015 by Tor Raswill

Biophys J. 2015 Oct 20;109(8):1528-32. doi: 10.1016/j.bpj.2015.08.015. McGibbon RT, Beauchamp KA, Harrigan MP, Klein C, Swails JM, Hernández CX, Schwantes CR, Wang LP, Lane TJ, Pande VS As molecular dynamics…

Heat dissipation guides activation in signaling proteins.

October 21, 2015 by Tor Raswill

Proc Natl Acad Sci U S A. 2015 Aug 18;112(33):10377-82. doi: 10.1073/pnas.1501804112. Epub 2015 Aug 3. Weber JK, Shukla D, Pande VS Life is fundamentally a nonequilibrium phenomenon. At the…

Efficient maximum likelihood parameterization of continuous-time Markov processes.

October 21, 2015 by Tor Raswill

J Chem Phys. 2015 Jul 21;143(3):034109. doi: 10.1063/1.4926516. McGibbon RT, Pande VS. Continuous-time Markov processes over finite state-spaces are widely used to model dynamical processes in many fields of natural…

United polarizable multipole water model for molecular mechanics simulation.

October 21, 2015 by Tor Raswill

J Chem Phys. 2015 Jul 7;143(1):014504. doi: 10.1063/1.4923338. Qi R, Wang LP, Wang Q, Pande VS, Ren P We report the development of a united AMOEBA (uAMOEBA) polarizable water model,…

OpenMM: A Hardware Independent Framework for Molecular Simulations.

October 21, 2015 by Tor Raswill

Comput Sci Eng. 2015 Jul 1;12(4):34-39. Eastman P, Pande VS The wide diversity of computer architectures today requires a new approach to software development. OpenMM is a framework for molecular…