Macromolecular Modeling Blog ™

In this Bi-Weekly digest – relevant titles form current issues of molecular and computational biology literature, amongst featured titles: Surface Sites for Engineering Allosteric Control in Proteins and The RNA Polymerase ”Switch Region” Is a Target for Inhibitors. If you want to initiate in a public discussion on one of these, let us know in the comments.

Nature:

• Crystal structure of a stable dimer reveals the molecular basis of serpin polymerization. Yamasaki M, Li W, Johnson DJ, Huntington JA.
• Crystal structure of opsin in its G-protein-interacting conformation. Scheerer P, Park JH, Hildebrand PW, Kim YJ, Krauss N, Choe HW, Hofmann KP, Ernst OP.

Cell:

• The RNA Polymerase ”Switch Region” Is a Target for Inhibitors. J. Mukhopadhyay, K. Das, S. Ismail, D. Koppstein, M. Jang, B. Hudson, S. Sarafianos, S. Tuske, J. Patel, R. Jansen, H. Irschik, E. Arnold, and R.H. Ebright
• Cytokine-Induced Signaling Networks Prioritize Dynamic Range over Signal Strength. K.A. Janes, H.C. Reinhardt, and M.B. Yaffe

Structure:

• Structural analysis of the interactions between paxillin LD motifs and alpha-parvin. Lorenz S, Vakonakis I, Lowe ED, Campbell ID, Noble ME, Hoellerer MK.

Nucleic Acids Research:

• Predicting transcription factor specificity with all-atom models. Jamal Rahi S, Virnau P, Mirny LA, Kardar M.
• The whole alignment and nothing but the alignment: the problem of spurious alignment flanks. Frith MC, Park Y, Sheetlin SL, Spouge JL.
• Protein-DNA interactions: structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins. Ahmad S, Keskin O, Sarai A, Nussinov R.
• A probabilistic generative model for GO enrichment analysis. Lu Y, Rosenfeld R, Simon I, Nau GJ, Bar-Joseph Z.

Journal of Molecular Biology:

• Computational redesign of a protein-protein interface for high affinity and binding specificity using modular architecture and naturally occurring template fragments. Potapov V, Reichmann D, Abramovich R, Filchtinski D, Zohar N, Ben Halevy D, Edelman M, Sobolev V, Schreiber G.
• Structural basis for the substrate specificity of bone morphogenetic protein1/tolloid-like metalloproteases. Mac Sweeney A, Gil-Parrado S, Vinzenz D, Bernardi A, Hein A, Bodendorf U, Erbel P, Logel C, Gerhartz B.
• Substrate Preference of Transglutaminase 2 Revealed by Logistic Regression Analysis and Intrinsic Disorder Examination. Csosz E, Bagossi P, Nagy Z, Dosztanyi Z, Simon I, Fesus L.
• Increased folding stability of TEM-1 beta-lactamase by in vitro selection. Kather I, Jakob RP, Dobbek H, Schmid FX.
• A molecular dynamics study of the interaction of D-peptide amyloid inhibitors with their target sequence reveals a potential inhibitory pharmacophore conformation. Esteras-Chopo A, Morra G, Moroni E, Serrano L, de la Paz ML, Colombo G.
• Determination of the topology of the hydrophobic segment of mammalian diacylglycerol kinase epsilon in a cell membrane and its relationship to predictions from modeling. Decaffmeyer M, Shulga YV, Dicu AO, Thomas A, Truant R, Topham MK, Brasseur R, Epand RM.

Protein Science:

• How well can the accuracy of comparative protein structure models be predicted? David Eramian, Narayanan Eswar, Min-Yi Shen, and Andrej Sali.
• Fragment-HMM: A new approach to protein structure prediction. Shuai Cheng Li, Dongbo Bu, Jinbo Xu, and Ming Li

Proteins:

• Guiding conformation space search with an all-atom energy potential. TJ Brunette, Oliver Brock.

BMC Bioinformatics:

• Identification of hot-spot residues in protein-protein interactions by computational docking. Grosdidier S, Fernandez-Recio J
• Structural assembly of two-domain proteins by rigid-body docking. Cheng T, Blundell T, Fernandez-Recio J
• Homology modelling of protein-protein complexes: a simple method and its possibilities and limitations. Launay G, Simonson T
• MetaMQAP: a meta-server for the quality assessment of protein models. Pawlowski M, Gajda M, Matlak R, Bujnicki J

Bioinformatics:

• TESE: generating specific protein structure test set ensembles. Francesco Sirocco and Silvio C. E. Tosatto
• DOCKGROUND protein-protein docking decoy set. Shiyong Liu, Ying Gao, and Ilya A. Vakser
• PREDICT-2ND: a tool for generalized protein local structure prediction. Sol Katzman, Christian Barrett, Grant Thiltgen, Rachel Karchin, and
  Kevin Karplus
• Biomolecular pleiomorphism probed by spatial interpolation of coarse models. Mirabela Rusu, Stefan Birmanns, and Willy Wriggers

PLOS computational biology:

• Protein Docking by the Underestimation of Free Energy Funnels in the Space of Encounter Complexes. Yang Shen, Ioannis Ch. Paschalidis, Pirooz Vakili, Sandor Vajda.
• Discarding Functional Residues from the Substitution Table Improves Predictions of Active Sites within Three-Dimensional Structures. Sungsam Gong, Tom L. Blundell.

Be Sociable, Share!

•