Macromolecular Modeling Blog ™

In this weekly digest – relevant titles form current issues of Nature Structural and Molecular Biology, Bioinformatics, BMC Bioinformatics, Plos Computational Biology and Journal of Computational Biology. If you want to initiate in a public discussion on one of these, let us know in the comments.

 Journal of Computational Biology:

• Minimizing and Learning Energy Functions for Side-Chain Prediction. Chen Yanover, Ora Schueler-Furman, and Yair Weiss.
• Free Energy Estimates of All-Atom Protein Structures Using Generalized Belief Propagation. Hetunandan Kamisetty, Eric P. Xing, and Christopher J. Langmead.
• Shift-Invariant Adaptive Double Threading: Learning MHC II-Peptide Binding. Noah Zaitlen, Manuel Reyes-Gomez, David Heckerman, and Nebojsa Jojic.

BMC Bioinformatics:

• Impact of residue accessible surface area on the prediction of protein secondary structures. Momen-Roknabadi A, Sadeghi M, Pezeshk H, Marashi S.
• Alignment of protein structures in the presence of domain motions. Mosca R, Brannetti B, Schneider T.
• Protein structure search and local structure characterization. Ku S, Hu Y.
• An enhanced partial order curve comparison algorithm and its application to analyzing protein folding trajectories. Sun H, Ferhatosmanoglu H, Ota M, Wang Y.

Nature Structural and Molecular Biology:

• Mapping a molecular link between allosteric inhibition and activation of the glycine receptor. Paul S Miller, Maya Topf and Trevor G Smart.
• Activation of tyrosine kinases by mutation of the gatekeeper threonine. Mohammad Azam, Markus A Seeliger, Nathanael S Gray, John Kuriyan and George Q Daley.

Bionformatics:

• Protein-ligand interaction prediction: an improved chemogenomics approach. Laurent Jacob and Jean-Philippe Vert.
• Mixture models for protein structure ensembles. Michael Hirsch and Michael Habeck.
• PRODECOMPv3: decompositions of NMR projections for protein backbone and side-chain assignments and structural studies. Doroteya K. Staykova, Jonas Fredriksson, and Martin Billeter.
• Optimal contact map alignment of protein-protein interfaces. Vinay Pulim, Bonnie Berger, and Jadwiga Bienkowska.
• Accurate sequence-based prediction of catalytic residues. Tuo Zhang, Hua Zhang, Ke Chen, Shiyi Shen, Jishou Ruan, and Lukasz Kurgan.
• Optimal design of thermally stable proteins. Ryan M. Bannen, Vanitha Suresh, George N. Phillips, Jr, Stephen J. Wright, and Julie C. Mitchell.
• Protein function prediction and annotation in an integrated environment powered by web services (AFAWE). Anika Jöcker, Fabian Hoffmann, Andreas Groscurth, and Heiko Schoof.

PLOS Computational Biology:

• (Review) Structure-Guided Comparative Analysis of Proteins: Principles, Tools, and Applications for Predicting Function. Raja Mazumder et al.
• (Review) Structural Biology by NMR: Structure, Dynamics, and Interactions. Phineus R. L. Markwick et al.