Macromolecular Modeling Blog ™

 In this Bi-weekly digest a novel O2 transport protein designed from first principals (on which we’ll elaborate in an upcoming post – stay tuned) and a nice over-representation of Bioinformatics papres. 

Nature:

• Design and engineering of an O(2) transport protein. Koder RL, Anderson JL, Solomon LA, Reddy KS, Moser CC, Dutton PL.
• Transmembrane passage of hydrophobic compounds through a protein channel wall. Hearn EM, Patel DR, Lepore BW, Indic M, van den Berg B.

 Journal of Computational Biology:

• Optimizing Energy Potential for Protein Fold Recognition with Parametric Evaluation Function. Junfeng Gu et al.

Proteins:

• A new prediction strategy for long local protein structures using an original description. Aurélie Bornot, Catherine Etchebest, Alexandre G. de Brevern.
• REMO: A new protocol to refine full atomic protein models from C-alpha traces by optimizing hydrogen-bonding networks. Yunqi Li, Yang Zhang.
• A coarse-grained potential for fold recognition and molecular dynamics simulations of proteins. Peter Májek, Ron Elber
• Graphical models of protein-protein interaction specificity from correlated mutations and interaction data. John Thomas, Naren Ramakrishnan, Chris Bailey-Kellogg

Biophysical Journal:

• Protein structure prediction by pro-Sp3-TASSER. Zhou H, Skolnick J.
• Coupling between normal modes drives protein conformational dynamics: illustrations using allosteric transitions in myosin II. Zheng W, Thirumalai D.

• Structural alphabets for protein structure classification: a comparison study. Le Q, Pollastri G, Koehl P.
• Predicting Protein Function and Binding Profile via Matching of Local Evolutionary and Geometric Surface Patterns. Tseng YY, Dundas J, Liang J.
• Structural and Functional Studies of the Biotin Protein Ligase from Aquifex aeolicus Reveal a Critical Role for a Conserved Residue in Target Specificity. Cecile M. Tron, Iain W. McNae, Margaret Nutley, David J. Clarke, Alan Cooper, Malcolm D. Walkinshaw, Robert L. Baxter, Dominic J. Campopiano
• Sequence and Structural Features of Enzymes and their Active Sites by EC Class. Bray T, Doig AJ, Warwicker J.
• Signatures of protein-DNA recognition in free DNA binding sites. Locasale JW, Napoli AA, Chen S, Berman HM, Lawson CL.

Bioinformatics:

• Double water exclusion : a hypothesis refining the O-ring theory for the hot spots at protein interfaces. Jinyan Li and Qian Liu.
• Sequence-based prediction of protein interaction sites with an integrative method. Xue-wen Chen and Jong Cheol Jeong
• Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): insights into functional dynamics. Lee-Wei Yang, Eran Eyal, Ivet Bahar, and Akio Kitao.
• The protein–small-molecule database, a non-redundant structural resource for the analysis of protein-ligand binding. Izhar Wallach and Ryan Lilien.
• Fragment-based identification of druggable hot spots of proteins using Fourier domain correlation techniques. Ryan Brenke, Dima Kozakov, Gwo-Yu Chuang, Dmitri Beglov, David Hall, Melissa R. Landon, Carla Mattos, and Sandor Vajda.
• DTA: dihedral transition analysis for characterization of the effects of large main-chain dihedral changes in proteins. Wataru Nishima, Guoying Qi, Steven Hayward, and Akio Kitao.
• SECISaln, a web-based tool for the creation of structure-based alignments of eukaryotic SECIS elements. Charles E. Chapple, Roderic Guigó, and Alain Krol.
• CPSP-web-tools: a server for 3D lattice protein studies. Martin Mann, Cameron Smith, Mohamad Rabbath, Marlien Edwards, Sebastian Will, and Rolf Backofen.
• MatrixDB, a database focused on extracellular protein–protein and protein–carbohydrate interactions. Emilie Chautard, Lionel Ballut, Nicolas Thierry-Mieg, and Sylvie Ricard-Blum.

PLoS Computational Biology:

• Rapid Sampling of Molecular Motions with Prior Information Constraints. Barak Raveh et al.
• Conformational Changes and Slow Dynamics through Microsecond Polarized Atomistic Molecular Simulation of an Integral Kv1.2 Ion Channel. Pär Bjelkmar et al.
• Allosteric Communication Occurs via Networks of Tertiary and Quaternary Motions in Proteins. Michael D. Daily et al.
• Predicting Peptide Structures in Native Proteins from Physical Simulations of Fragments. Vincent A. Voelz et al.

Nature Structural and Molecular Biology:

• The mechanism of folding of Im7 reveals competition between functional and kinetic evolutionary constraints. Claire T Friel, D Alastair Smith, Michele Vendruscolo, Joerg Gsponer and Sheena E Radford

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