Macromolecular Modeling Blog ™

In a first digest of 2009: two new Rosetta protocols – A new RosettaLigand – docking with full ligand and receptor flexibility, and an improved design protocol to recover native protein-protein interface sequences. Also a new structure of the NaK channel and analysis of its selectivity.

Nature Structural and Molecular Biology:

• High-resolution structure of the open NaK channel. Amer Alam and Youxing Jiang
• Structural analysis of ion selectivity in the NaK channel. Amer Alam and Youxing Jiang

Structure:

• Prediction of Protein-Protein Interface Sequence Diversity Using Flexible Backbone Computational Protein Design. Elisabeth L. Humphris and Tanja Kortemme

JMB:

• RosettaLigand Docking with Full Ligand and Receptor Flexibility. Davis IW, Baker D.
• Structural basis of restoring sequence-specific DNA binding and transactivation to mutant p53 by suppressor mutations. Suad O, Rozenberg H, Brosh R, Diskin-Posner Y, Kessler N, Shimon LJ, Frolow F, Liran A, Rotter V, Shakked Z.
• Principal component analysis for protein folding dynamics. Maisuradze GG, Liwo A, Scheraga HA.

PLoS Computational Biology:

• Disordered Flanks Prevent Peptide Aggregation. Sanne Abeln et al.
• Association Rate Constants of Ras-Effector Interactions Are Evolutionarily Conserved. Christina Kiel et al.
• Formation and Growth of Oligomers: A Monte Carlo Study of an Amyloid Tau Fragment. Da-Wei Li et al.

Current Opinions in Chemical Biology:

• Peptides as protein binding site mimetics. Jutta Eichler
• Electron transfer in peptides and proteins. Bernd Giese, Michael Graber, Meike Cordes

Bioinformatics:

• Predicting small ligand binding sites in proteins using backbone structure. Andrew J. Bordner

Know of any hot literature that’s not here ? Want to hear more about a specific research/field ? Tell us in the comments.

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