Macromolecular Modeling Blog ™

Another compilation of forty some titles from the recent literature all about your favorite computational structural biology science. Two of the papers are by Rosetta Design Group’s members – see if you can find waldo. Enjoy.

• Will Widgets and Semantic Tagging Change Computational Biology? from PLoS Computational Biology: New Articles by Philip E. Bourne et al.
• Unfolding Simulations Reveal the Mechanism of Extreme Unfolding Cooperativity in the Kinetically Stable ?-Lytic Protease from PLoS Computational Biology: New Articles by Neema L. Salimi et al.
• The Overlap of Small Molecule and Protein Binding Sites within Families of Protein Structures from PLoS Computational Biology: New Articles by Fred P. Davis et al.
• The Structural Basis of Peptide-Protein Binding Strategies from Structure by Nir London, Dana Movshovitz-Attias, Ora Schueler-Furman.
• Improving protein secondary structure prediction using a simple k-mer model from Bioinformatics by Madera, M., Calmus, R., Thiltgen, G., Karplus, K., Gough, J.
• Active site prediction using evolutionary and structural information from Bioinformatics by Sankararaman, S., Sha, F., Kirsch, J. F., Jordan, M. I., Sjolander, K.
• Protein secondary structure appears to be robust under in silico evolution while protein disorder appears not to be from Bioinformatics by Schaefer, C., Schlessinger, A., Rost, B.
• PSiFR: an integrated resource for prediction of protein structure and function from Bioinformatics by Pandit, S. B., Brylinski, M., Zhou, H., Gao, M., Arakaki, A. K., Skolnick, J.
• PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta from Bioinformatics by Chaudhury, S., Lyskov, S., Gray, J. J.
• iDBPs: a web server for the identification of DNA binding proteins from Bioinformatics by Nimrod, G., Schushan, M., Szilagyi, A., Leslie, C., Ben-Tal, N.
• A novel method for accurate one-dimensional protein structure prediction based on fragment matching from Bioinformatics by Zhou, T., Shu, N., Hovmoller, S.
• Globally, unrelated protein sequences appear random from Bioinformatics by Lavelle, D. T., Pearson, W. R.
• Optimization of minimum set of protein-DNA interactions: a quasi exact solution with minimum over-fitting from Bioinformatics by Temiz, N. A., Trapp, A., Prokopyev, O. A., Camacho, C. J.
• FoldAmyloid: a method of prediction of amyloidogenic regions from protein sequence from Bioinformatics by Garbuzynskiy, S. O., Lobanov, M. Yu., Galzitskaya, O. V.
• Thermodynamic resolution: How do errors in modeled protein structures affect binding affinity predictions? from Proteins by Manoj Kumar Singh, Brian N. Dominy
• Current status of membrane protein structure classification from Proteins by Sindy Neumann, Angelika Fuchs, Armen Mulkidjanian, Dmitrij Frishman
• New computational method for prediction of interacting protein loop regions from Proteins by Matthew L. Danielson, Markus A. Lill
• A comprehensive examination of the contributions to the binding entropy of protein-ligand complexes from Proteins by Nidhi Singh, Arieh Warshel
• Helix-sheet packing in proteins from Proteins by Chengcheng Hu, Patrice Koehl
• Absolute binding free energy calculations: On the accuracy of computational scoring of protein-ligand interactions from Proteins by Nidhi Singh, Arieh Warshel
• Studying pressure denaturation of a protein by molecular dynamics simulations from Proteins by Sapna Sarupria, Tuhin Ghosh, Angel E. García, Shekhar Garde
• Feature space resampling for protein conformational search from Proteins by Ben Blum, Michael I. Jordan, David Baker
• The subunit interfaces of weakly associated homodimeric proteins from JMB by Sucharita, Dey , Arumay, Pal , Pinak, Chakrabarti , Joël, Janin
• Protein folding requires crowd control in a simulated cell from JMB by Benjamin R., Jefferys , Lawrence A., Kelley , Michael J.E., Sternberg
• Prediction of structures of zinc-binding proteins through explicit modeling of metal coordination geometry from Protein Science by Chu Wang, Robert Vernon, Oliver Lange, Michael Tyka, David Baker
• Conserved tertiary couplings stabilize elements in the PDZ fold, leading to characteristic patterns of domain conformational flexibility from Protein Science by Bosco K. Ho, David A. Agard
• Accounting for conformational changes during protein–protein docking from Curr. op. in Struct. Biol. by Martin, Zacharias
• Targeting biomolecular flexibility with metadynamics from Curr. op. in Struct. Biol. by Vanessa, Leone , Fabrizio, Marinelli , Paolo, Carloni , Michele, Parrinello
• Nature and nurture in protein folding and binding from Curr. op. in Struct. Biol. by Laura, Itzhaki , Peter, Wolynes
• Structure-based design of kinetic stabilizers that ameliorate the transthyretin amyloidoses from Curr. op. in Struct. Biol. by Stephen, Connelly , Sungwook, Choi , Steven M, Johnson , Jeffery W, Kelly , Ian A, Wilson
• Understanding Kinase Selectivity Through Energetic Analysis of Binding Site Waters from ChemMedChem by Daniel D. Robinson, Woody Sherman, Ramy Farid
• Modeling of loops in proteins: a multi-method approach from BMC Structural Biology – Latest articles by Andrzej Kolinski
• Identification of recurring protein structure microenvironments and discovery of novel functional sites around CYS residues from BMC Structural Biology – Latest articles by Russ Altman
• Automatic prediction of catalytic residues by modeling residue structural neighborhood from BMC Bioinformatics – Latest articles by Andrea Passerini
• A new protein binding pocket similarity measure based on comparison of clouds of atoms in 3D: application to ligand prediction from BMC Bioinformatics – Latest articles by Veronique Stoven
• Potentials’R'Us web-server for protein energy estimations with coarse-grained knowledge-based potentials from BMC Bioinformatics – Latest articles by Robert Jernigan
• Mining protein loops using a structural alphabet and statistical exceptionality from BMC Bioinformatics – Latest articles by Anne-claude Camproux
• Multiple structure alignment and consensus identification for proteins from BMC Bioinformatics – Latest articles by Ravi Janardan
• De Novo Self-Assembling Collagen Heterotrimers Using Explicit Positive and Negative Design from Biochemistry by Fei Xu et al
• FragBag, an accurate representation of protein structure, retrieves structural neighbors from the entire PDB quickly and accurately from PNAS by Budowski-Tal, I., Nov, Y., Kolodny, R.
• Identifying the amylome, proteins capable of forming amyloid-like fibrils from PNAS by Goldschmidt, L., Teng, P. K., Riek, R., Eisenberg, D.
• Capillarity theory for the fly-casting mechanism from PNAS by Trizac, E., Levy, Y., Wolynes, P. G.
• Competition between native topology and nonnative interactions in simple and complex folding kinetics of natural and designed proteins from PNAS by Zhang, Z., Chan, H. S.
• Metal templated design of protein interfaces from PNAS by Salgado, E. N., Ambroggio, X. I., Brodin, J. D., Lewis, R. A., Kuhlman, B., Tezcan, F. A.
• Protein interactions and ligand binding: From protein subfamilies to functional specificity from PNAS by Rausell, A., Juan, D., Pazos, F., Valencia, A.
• Ubiquitin not only serves as a tag but also assists degradation by inducing protein unfolding from PNAS by Hagai, T., Levy, Y.

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