Literature Review 22/01/10

Jan
22
2010

You know the drill… a collection of relevant titles from the recent literature, if you want to discuss any of these, or expand on them, we’ll be more than happy.

Conformational Transitions upon Ligand Binding: Holo-Structure Prediction from Apo Conformations

from PLoS Computational Biology: New Articles by Daniel Seeliger et al.

Combining Structure and Sequence Information Allows Automated Prediction of Substrate Specificities within Enzyme Families

from PLoS Computational Biology: New Articles by Marc Röttig et al.

Disentangling Direct from Indirect Co-Evolution of Residues in Protein Alignments

from PLoS Computational Biology: New Articles by Lukas Burger et al.

Design Principles for Ligand-Sensing, Conformation-Switching Ribozymes

from PLoS Computational Biology: New Articles by Xi Chen et al.

Rational Mutational Analysis of a Multidrug MFS Transporter CaMdr1p of Candida albicans by Employing a Membrane Environment Based Computational Approach

from PLoS Computational Biology: New Articles by Khyati Kapoor et al.

Tradeoff Between Stability and Multispecificity in the Design of Promiscuous Proteins

from PLoS Computational Biology: New Articles by Menachem Fromer et al.

Warren L. DeLano 21 June 1972–3 November 2009

from NSMB by James A Wells

Rapid model quality assessment for protein structure predictions using the comparison of multiple models without structural alignments

from Bioinformatics by McGuffin, L. J., Roche, D. B.

Identification of substrates for Ser/Thr kinases using residue-based statistical pair potentials

from Bioinformatics by Kumar, N., Mohanty, D.

Kinase selectivity potential for inhibitors targeting the ATP binding site: a network analysis

from Bioinformatics by Huang, D., Zhou, T., Lafleur, K., Nevado, C., Caflisch, A.

AQUA: automated quality improvement for multiple sequence alignments

from Bioinformatics by Muller, J., Creevey, C. J., Thompson, J. D., Arendt, D., Bork, P.

Roll: a new algorithm for the detection of protein pockets and cavities with a rolling probe sphere

from Bioinformatics by Yu, J., Zhou, Y., Tanaka, I., Yao, M.

Automatic clustering of docking poses in virtual screening process using self-organizing map

from Bioinformatics by Bouvier, G., Evrard-Todeschi, N., Girault, J.-P., Bertho, G.

Modeling the interplay of single-stranded binding proteins and nucleic acid secondary structure

from Bioinformatics by Forties, R. A., Bundschuh, R.

Multiscale simulations of protein landscapes: Using coarse-grained models as reference potentials to full explicit models

from Proteins by Benjamin M. Messer, Maite Roca, Zhen T. Chu, Spyridon Vicatos, Alexandra Vardi Kilshtain, Arieh Warshel

Information-theoretic analysis of the reference state in contact potentials used for protein structure prediction

from Proteins by Armando D. Solis, Shalom R. Rackovsky

FREAD revisited: Accurate loop structure prediction using a database search algorithm

from Proteins by Yoonjoo Choi, Charlotte M. Deane

Mapping of ligand-binding cavities in proteins

from Proteins by C. David Andersson, Brian Y. Chen, Anna Linusson

A discriminative approach for identifying domain-domain interactions from protein-protein interactions

from Proteins by Xing-Ming Zhao, Luonan Chen, Kazuyuki Aihara

De novo backbone scaffolds for protein design

from Proteins by James T. MacDonald, Katarzyna Maksimiak, Michael I. Sadowski, William R. Taylor

DynaDock: A new molecular dynamics-based algorithm for protein-peptide docking including receptor flexibility

from Proteins by Iris Antes

Model-guided mutagenesis drives functional studies of human NHA2, implicated in hypertension

from JMB Maya, Schushan , Minghui, Xiang , Pavel, Bogomiakov , Etana, Padan , Rajini, Rao , …

Rapid structural characterization of human antibody-antigen complexes through experimentally validated computational docking

from JMB Luca, Simonelli , Martina, Beltramello , Zinaida, Yudina , Annalisa, Macagno , Luigi, Calzolai , …

Evolutionary optimization of computationally designed enzymes: Kemp eliminases of the KE07 series

from JMB Olga Khersonsky, Daniela Röthlisberger, Orly Dym, Shira Albeck, Colin J. Jackson, David Baker and Dan S. Tawfik

Backbone model of an aquareovirus virion by cryo-electron microscopy and bioinformatics

from JMB

Lingpeng, Cheng , Jiang, Zhu , Wong Hoi, Hui , Xiaokang, Zhang , Barry, Honig , …

Evolutionary Trace Annotation of Protein Function in the Structural Proteome

from JMB Serkan, Erdin , R. Matthew, Ward , Eric, Venner , Olivier, Lichtarge

Functional Studies and Modeling of Pore-Lining Residue Mutants of the Influenza A Virus M2 Ion Channel

from Biochemistry by Victoria Balannik et al

A galaxy of folds

from Protein Science by Vikram Alva, Michael Remmert, Andreas Biegert, Andrei N. Lupas, Johannes Söding

Analysis of galactosemia-linked mutations of GALT enzyme using a computational biology approach

from PEDS by Facchiano, A., Marabotti, A.

Large conformational changes in proteins: signaling and other functions

from Curr. op. in Struct. Biol. Barry J, Grant , Alemayehu A, Gorfe , J Andrew, McCammon

A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA

from NAR by Lavery, R., Zakrzewska, K., Beveridge, D., Bishop, T. C., Case, D. A., Cheatham, T., Dixit, S., Jayaram, B., Lankas, F., Laughton, C., Maddocks, J. H., Michon, A., Osman, R., Orozco, M., Perez, A., Singh, T., Spackova, N., Sponer, J.