Macromolecular Modeling Blog ™

A collection of interesting papers from the recent literature – there’s something for everyone here. Enjoy.

• Predicting protein structures with a multiplayer online game from Nature by Seth Cooper, Firas Khatib, Adrien Treuille, Janos Barbero, Jeehyung Lee, Michael Beenen, Andrew Leaver-Fay, David Baker, Zoran Popovi? & Foldit players

• Structural basis for high-affinity HER2 receptor binding by an engineered protein [Biochemistry] from PNAS by Eigenbrot, C., Ultsch, M., Dubnovitsky, A., Abrahmsen, L., Hard, T.

• Charge interactions can dominate the dimensions of intrinsically disordered proteins [Biophysics_And_Computational_Biology] from PNAS by Muller-Spath, S., Soranno, A., Hirschfeld, V., Hofmann, H., Ruegger, S., Reymond, L., Nettels, D., Schuler, B.

• Hollow core of Alzheimer’s A{beta}42 amyloid observed by cryoEM is relevant at physiological pH [Biophysics_And_Computational_Biology] from PNAS by Miller, Y., Ma, B., Tsai, C.-J., Nussinov, R.

• Predicting resistance mutations using protein design algorithms [Biophysics_And_Computational_Biology] from PNAS by Frey, K. M., Georgiev, I., Donald, B. R., Anderson, A. C.

• Computational glycoscience: characterizing the spatial and temporal properties of glycans and glycan–protein complexes from Curr. op. in Struct. Biol. by Robert J, Woods , Matthew B, Tessier

• Protein engineering and design: from first principles to new technologies from Curr. op. in Struct. Biol. by Jane, Clarke , Lynne, Regan

• Growth and excitement in membrane protein structural biology from Curr. op. in Struct. Biol. by Christopher G, Tate , Raymond C, Stevens

• Computational Analysis of Phosphopeptide Binding to the Polo-Box Domain of the Mitotic Kinase PLK1 Using Molecular Dynamics Simulation from PLoS Computational Biology: New Articles by David J. Huggins et al.

• VASP: A Volumetric Analysis of Surface Properties Yields Insights into Protein-Ligand Binding Specificity from PLoS Computational Biology: New Articles by Brian Y. Chen et al.

• Lysine120 Interactions with p53 Response Elements can Allosterically Direct p53 Organization from PLoS Computational Biology: New Articles by Yongping Pan et al.

• Knotted vs. Unknotted Proteins: Evidence of Knot-Promoting Loops from PLoS Computational Biology: New Articles by Raffaello Potestio et al.

• More Than 1,001 Problems with Protein Domain Databases: Transmembrane Regions, Signal Peptides and the Issue of Sequence Homology from PLoS Computational Biology: New Articles by Wing-Cheong Wong et al.

• Using NMR Chemical Shifts as Structural Restraints in Molecular Dynamics Simulations of Proteins from Structure by Paul Robustelli, Kai Kohlhoff, Andrea Cavalli, Michele Vendruscolo.

• First insight into the prediction of protein folding rate change upon point mutation from Bioinformatics by Huang, L.-T., Gromiha, M. M.

• A highly accurate statistical approach for the prediction of transmembrane {beta}-barrels from Bioinformatics by Freeman, T. C., Wimley, W. C.

• Structure-based kernels for the prediction of catalytic residues and their involvement in human inherited disease from Bioinformatics by Xin, F., Myers, S., Li, Y. F., Cooper, D. N., Mooney, S. D., Radivojac, P.

• Molecular signatures-based prediction of enzyme promiscuity from Bioinformatics by Carbonell, P., Faulon, J.-L.

• Why are polar residues within the membrane core evolutionary conserved? from Proteins by Arne Elofsson

• Blind predictions of protein interfaces by docking calculations in CAPRI from Proteins by Shoshana J. Wodak

• Structure-based prediction of protein-peptide specificity in Rosetta from Proteins by Philip Bradley

• How different from random are docking predictions when ranked by scoring functions? from Proteins by Baldomero Oliva

• Determining macromolecular assembly structures by molecular docking and fitting into an electron density map from Proteins by Haim J. Wolfson

• Protein loop modeling by using fragment assembly and analytical loop closure from Proteins by Chaok Seok

• Fluctuations of backbone torsion angles obtained from NMR-determined structures and their prediction from Proteins by Yaoqi Zhou

• Geometrically centered region: A “wet” model of protein binding hot spots not excluding water molecules from Proteins by Jinyan Li

• Achieving reliability and high accuracy in automated protein docking: ClusPro, PIPER, SDU, and stability analysis in CAPRI rounds 13-19 from Proteins by Sandor Vajda

• Protein-protein docking with binding site patch prediction and network-based terms enhanced combinatorial scoring from Proteins by Cun Xin Wang

• Protein-protein docking benchmark version 4.0 from Proteins by Zhiping Weng

• Smoothing molecular interactions: The “kinetic buffer” effect of intrinsically disordered proteins from Proteins by Zhirong Liu

• Side-chain rotamer transitions at protein-protein interfaces from Proteins by Charles H. Robert

• Docking and scoring protein interactions: CAPRI 2009 from Proteins by Shoshana J. Wodak

• Strengths and weaknesses of data-driven docking in critical assessment of prediction of interactions from Proteins by Alexandre M. J. J. Bonvin

• Docking by structural similarity at protein-protein interfaces from Proteins by Ilya A. Vakser

• A structural dissection of amino acid substitutions in helical transmembrane proteins from Proteins by Kenji Mizuguchi

• RepliCopter: A replicate optimizer for flexible docking from Proteins by Julie C Mitchell

• Binding site prediction and improved scoring during flexible protein–protein docking with ATTRACT from Proteins by Martin Zacharias

• Measuring “Un-measurable” Folding Kinetics of Proteins by Single-Molecule Force Spectroscopy from JMB by Ashlee, Jollymore , Hongbin, Li

• Proteome-Level Relationship between Folding and Aggregation Propensities of Proteins from JMB by GianGaetano, Tartaglia , Michele, Vendruscolo

• Micelle-like architecture of the monomeric ensemble of Alzheimer’s amyloid-? peptide in aqueous solution and its implications for A? aggregation from JMB by Andreas, Vitalis , Amedeo, Caflisch

• Context-Dependent Remodeling of Structure in Two Large Protein Fragments from JMB by Matthew J., Schellenberg , Dustin B., Ritchie , Tao, Wu , Craig J., Markin , Leo, Spyracopoulos , …

• Engineering allosteric regulation into the hinge region of a circularly permuted TEM-1 {beta}-lactamase from PEDS by Mathieu, V., Fastrez, J., Soumillion, P.

• Analysis and prediction of VH/VL packing in antibodies from PEDS by Abhinandan, K. R., Martin, A. C. R.

• A lead discovery strategy driven by a comprehensive analysis of proteases in the peptide substrate space from Protein Science by Meir Glick

• An exciting but challenging road ahead for computational enzyme design from Protein Science by David Baker

• Evaluation and ranking of enzyme designs from Protein Science by K. N. Houk

• Helicity of short E-R/K peptides from Protein Science by James A. Spudich

• RosettaHoles2: A volumetric packing measure for protein structure refinement and validation from Protein Science by David Baker

• Domain motion and interdomain hot spots in a multidomain enzyme from Protein Science by Lesa J. Beamer

• T-Analyst: a program for efficient analysis of protein conformational changes by torsion angles from Journal of Computer-Aided Molecular Design

• Pocket Similarity: Are alpha Carbons Enough? from Journal of Chemical Information and Modeling by Howard J Feldman et al

• Comparing interfacial dynamics in protein-protein complexes: an elastic network approach from BMC Structural Biology – Latest articles by Ruth Nussinov

• Systematic analysis of short internal indels and their impact on protein folding from BMC Structural Biology – Latest articles by Jun-tao Guo

• CMASA: an accurate algorithm for detecting local protein structural similarity and its application to enzyme catalytic site annotation from BMC Bioinformatics – Latest articles by Jing-Fei Huang

• TOPSAN: a collaborative annotation environment for structural genomics. from BMC Bioinformatics – Latest articles by John Wooley

• Predicting beta-turns and their types using predicted backbone
  dihedral angles and secondary structures from BMC Bioinformatics – Latest articles by Jonathan Hirst

• Sequence-based identification of interface residues by an integrative profile combining hydrophobic and evolutionary information from BMC Bioinformatics – Latest articles by Jinyan Li

• A structural-alphabet-based strategy for finding structural motifs across protein families from NAR by Wu, C. Y., Chen, Y. C., Lim, C.

• Evidence of Adaptability in Metal Coordination Geometry and Active-Site Loop Conformation among B1 Metallo-beta-lactamases from Biochemistry by Javier M. Gonzalez et al

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