Activation pathway of Src kinase reveals intermediate states as targets for drug design

2014-shukla-src-kinase

Diwakar Shukla; Yilin Meng; Benoît Roux; Vijay S. Pande

2014-03-03 (online)

Nature Communications (Nat. Commun.). 5, doi:10.1038/ncomms4397

Description

MSM analysis of c-Src kinase. The MSMBuilder paper uses the dataset from this paper as an example.

msm-applications

Protein kinases: evolution of dynamic regulatory proteins

2011-kinase-review

Susan S. Taylor; Alexandr P. Kornev

2011-02-01 (print)

Trends in Biochemical Sciences (Trends Biochem. Sci.). 36, 2, 65-77. doi:10.1016/j.tibs.2010.09.006

Description

Review of protein kinases. The MSMBuilder paper uses a kinase MD dataset as an example.

review

Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations

2009-noe-equilibrium-from-short

F. Noe; C. Schutte; E. Vanden-Eijnden; L. Reich; T. R. Weikl

2009-11-03 (online) – 2009-11-10 (print)

Proceedings of the National Academy of Sciences (Proc. Natl. Acad. Sci. U.S.A.). 106, 45, 19011-19016. doi:10.1073/pnas.0905466106

Reactive flux and folding pathways in network models of coarse-grained protein dynamics

2009-berezhkovskii-reactive-flux

Alexander Berezhkovskii; Gerhard Hummer; Attila Szabo

2009-05-28 (print)

The Journal of Chemical Physics (J. Chem. Phys.). 130, 20, 205102. doi:10.1063/1.3139063

Transition Path Theory for Markov Jump Processes

2009-metzner-tpt

Philipp Metzner; Christof Schütte; Eric Vanden-Eijnden

2009-01-01 (print)

Multiscale Modeling & Simulation (Multiscale Model. Simul.). 7, 3, 1192-1219. doi:10.1137/070699500

Description

Transition path theory (TPT).

msm-theory msm-postprocessing

Cα-based torsion angles: A simple tool to analyze protein conformational changes

1995-alpha-carbon

Maria M. Flocco; Sherry L. Mowbray

1995-10-01 (print)

Protein Science (Protein Sci.). 4, 10, 2118-2122. doi:10.1002/pro.5560041017

Description

Alpha carbon featurization

features