Macromolecular Modeling Blog ™

The latest crop of interesting literature in our field. There are a bunch of papers about protein dynamics (and its conservation) and another bunch on protein design. And if you search carefully there is also one paper by us on peptide docking with a new Rosetta protocol.

• Neighbor-Dependent Ramachandran Probability Distributions of Amino Acids Developed from a Hierarchical Dirichlet Process Model from PLoS Computational Biology: New Articles by Daniel Ting et al.

• On the Conservation of the Slow Conformational Dynamics within the Amino Acid Kinase Family: NAGK the Paradigm from PLoS Computational Biology: New Articles by Enrique Marcos et al.

• Watching Biomolecular Machines in Action from Structure Ron Elber.

• Dynameomics: A Comprehensive Database of Protein Dynamics from Structure Marc W. van der Kamp, R. Dustin Schaeffer, Amanda L. Jonsson, Alexander D. Scouras, Andrew M. Simms, Rudesh D. Toofanny, Noah C. Benson, Peter C. Anderson, Eric D. Merkley, Steven Rysavy, Dennis Bromley, David A.C. Beck, Valerie Daggett.

• Quality assessment of protein model-structures using evolutionary conservation from Bioinformatics by Kalman, M., Ben-Tal, N.

• ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment from Bioinformatics by Konc, J., Janezic, D.

• A machine learning approach to predicting protein-ligand binding affinity with applications to molecular docking from Bioinformatics by Ballester, P. J., Mitchell, J. B. O.

• Alignment-free local structural search by writhe decomposition from Bioinformatics by Zhi, D., Shatsky, M., Brenner, S. E.

• SeSAW: balancing sequence and structural information in protein functional mapping from Bioinformatics by Standley, D. M., Yamashita, R., Kinjo, A. R., Toh, H., Nakamura, H.

• SLiM on Diet: finding short linear motifs on domain interaction interfaces in Protein Data Bank from Bioinformatics by Hugo, W., Song, F., Aung, Z., Ng, S. K., Sung, W. K.

• ESBTL: efficient PDB parser and data structure for the structural and geometric analysis of biological macromolecules from Bioinformatics by Loriot, S., Cazals, F., Bernauer, J.

• FoldGPCR: Structure prediction protocol for the transmembrane domain of G protein-coupled receptors from class A from Proteins by Mayako Michino, Jianhan Chen, Raymond C. Stevens, Charles L. Brooks III

• Structural characterization of two pore-forming peptides: Consequences of introducing a C-terminal tryptophan from Proteins by Alvaro I. Herrera, Ahlam Al-Rawi, Gabriel A. Cook, Jian Gao, Takeo Iwamoto, Om Prakash, John M. Tomich, Jianhan Chen

• Sub-angstrom modeling of complexes between flexible peptides and globular proteins from Proteins by Barak Raveh, Nir London, Ora Schueler-Furman

• Accurate prediction of protein folding rates from sequence and sequence-derived residue flexibility and solvent accessibility from Proteins by Jianzhao Gao, Tuo Zhang, Hua Zhang, Shiyi Shen, Jishou Ruan, Lukasz Kurgan

• Improving threading algorithms for remote homology modeling by combining fragment and template comparisons from Proteins by Hongyi Zhou, Jeffrey Skolnick

• Real-time ligand binding pocket database search using local surface descriptors from Proteins by Rayan Chikhi, Lee Sael, Daisuke Kihara

• Homology Modelling Protein-Ligand Interactions: Allowing for Ligand-Induced Conformational Change from JMB James A.R., Dalton , Richard M., Jackson

• Consensus Protein Design Without Phylogenetic Bias from JMB Christian, Jäckel , Jesse D., Bloom , Peter, Kast , Frances H., Arnold , Donald, Hilvert

• Geometric similarities of protein-protein interfaces at atomic resolution are only observed within homologous families: An exhaustive structural classification study from JMB Akira R., Kinjo , Haruki, Nakamura

• Combinatorial Enzyme Design Probes Allostery and Cooperativity in the Trypsin Fold from JMB Michael J., Page , Enrico, Di Cera

• Contributions of Conserved TPLH Tetrapeptides to the Conformational Stability of Ankyrin Repeat Proteins from JMB Yi, Guo , Chunhua, Yuan , Feng, Tian , Kun, Huang , Christopher M., Weghorst , …

• Elimination of a cis-proline-containing loop and turn optimization stabilizes a protein and accelerates its folding from JMB Roman P., Jakob , Bettina K., Zierer , Ulrich, Weininger , Stefanie D., Hofmann , Stefan H., Lorenz , …

• Higher-Order Assembly of Collagen Peptides into Nano- and Microscale Materials from Biochemistry by David E. Przybyla et al

• Computational Study of the Resistance Shown by the Subtype B/HIV-1 Protease to Currently Known Inhibitors from Biochemistry by Alessandro Genoni et al

• Conformational Preferences of a 14-Residue Fibrillogenic Peptide from Acetylcholinesterase from Biochemistry by Ranjit Vijayan et al

• Analysis and prediction of calcium-binding pockets from apo-protein structures exhibiting calcium-induced localized conformational changes from Protein Science by Xue Wang, Kun Zhao, Michael Kirberger, Hing Wong, Guantao Chen, Jenny J. Yang

• Use of amino acid composition to predict epitope residues of individual antibodies from PEDS by Soga, S., Kuroda, D., Shirai, H., Kobori, M., Hirayama, N.

• Creating novel proteins by combining design and selection from PEDS by Grove, T. Z., Hands, M., Regan, L.

• Improving thermostability of papain through structure-based protein engineering from PEDS by Choudhury, D., Biswas, S., Roy, S., Dattagupta, J. K.

• Engineering a two-helix bundle protein for folding studies from PEDS by Dodson, C. A., Ferguson, N., Rutherford, T. J., Johnson, C. M., Fersht, A. R.

• Ubiquitin—molecular mechanisms for recognition of different structures from Curr. op. in Struct. Biol. Tina, Perica , Cyrus, Chothia

• RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures from BMC Bioinformatics – Latest articles by Ryszard Adamiak

• Creating PWMs of transcription factors using 3D structure-based computation of protein-DNA free binding energies from BMC Bioinformatics – Latest articles by Alexander Kel

• Structural fragment clustering reveals novel structural and functional motifs in alpha-helical transmembrane proteins from BMC Bioinformatics – Latest articles by Michael Schroeder

• Predictors of natively unfolded proteins: unanimous consensus score to detect a twilight zone between order and disorder in generic datasets. from BMC Bioinformatics – Latest articles by Andrea Giansanti

• A knowledge-guided strategy for improving the accuracy of scoring functions in binding affinity prediction from BMC Bioinformatics – Latest articles by Renxiao Wang

• Orientation-dependent backbone-only residue pair scoring functions for fixed backbone protein design from BMC Bioinformatics – Latest articles by Andrew Bordner

• Dynamics-based alignment of proteins: An alternative approach to quantify dynamic similarity. from BMC Bioinformatics – Latest articles by Philip Biggin

• LowModeMD—Implicit Low-Mode Velocity Filtering Applied to Conformational Search of Macrocycles and Protein Loops from Journal of Chemical Information and Modeling: Latest Articles (ACS Publications) by Paul Labute

• A Novel Evaluation of Residue and Protein Volumes by Means of Laguerre Tessellation from Journal of Chemical Information and Modeling: Latest Articles (ACS Publications) by Jeremy Esque et al

• Electrostatic hot spot on DNA-binding domains mediates phosphate desolvation and the pre-organization of specificity determinant side chains from NAR by Temiz, A. N., Benos, P. V., Camacho, C. J.

• Mutation Bias Favors Protein Folding Stability in the Evolution of Small Populations from PLoS Computational Biology: New Articles by Raul Mendez et al.

• Net charge per residue modulates conformational ensembles of intrinsically disordered proteins [Biophysics_And_Computational_Biology] from PNAS by Mao, A. H., Crick, S. L., Vitalis, A., Chicoine, C. L., Pappu, R. V.

• Experimental detection of knotted conformations in denatured proteins [Biophysics_And_Computational_Biology] from PNAS by Mallam, A. L., Rogers, J. M., Jackson, S. E.

• Experimental snapshots of a protein-DNA binding landscape [Biophysics_And_Computational_Biology] from PNAS by Sanchez, I. E., Ferreiro, D. U., Dellarole, M., de Prat-Gay, G.

• Entropic mechanism of large fluctuation in allosteric transition [Biophysics_And_Computational_Biology] from PNAS by Itoh, K., Sasai, M.

• Evolution-guided discovery and recoding of allosteric pathway specificity determinants in psychoactive bioamine receptors [Biophysics_And_Computational_Biology] from PNAS by Rodriguez, G. J., Yao, R., Lichtarge, O., Wensel, T. G.

• Protein structural dynamics in solution unveiled via 100-ps time-resolved x-ray scattering [Biophysics_And_Computational_Biology] from PNAS by Cho, H. S., Dashdorj, N., Schotte, F., Graber, T., Henning, R., Anfinrud, P.

• Metamorphic proteins mediate evolutionary transitions of structure [Biophysics_And_Computational_Biology] from PNAS by Yadid, I., Kirshenbaum, N., Sharon, M., Dym, O., Tawfik, D. S.

Be Sociable, Share!

•