April 2006

A dipeptide nanotube, composed of 2,000 diphenylalanine molecules, is optimized under a two-dimensional lattice wrapping system (see Tsai et al) with an all-atom force field. The constructed tube can be used as a foundation for building an atomic model with the tube geometry observed experimentally.

Image Credit: Image created by Chung-Jung Tsai with graphics software, BioChem.

Education

Practical Strategies for Discovering Regulatory DNA Sequence Motifs

Kenzie D MacIsaac, Ernest Fraenkel

PLOS Computational Biology: published April 28, 2006 | https://doi.org/10.1371/journal.pcbi.0020036

Research Articles

A Model for Integrating Elementary Neural Functions into Delayed-Response Behavior

Thomas Gisiger, Michel Kerszberg

PLOS Computational Biology: published April 7, 2006 | https://doi.org/10.1371/journal.pcbi.0020025

Folding Very Short Peptides Using Molecular Dynamics

Bosco K Ho, Ken A Dill

PLOS Computational Biology: published April 14, 2006 | https://doi.org/10.1371/journal.pcbi.0020027

Conformational Changes in Protein Loops and Helices Induced by Post-Translational Phosphorylation

Eli S Groban, Arjun Narayanan, Matthew P Jacobson

PLOS Computational Biology: published April 21, 2006 | https://doi.org/10.1371/journal.pcbi.0020032

Identification and Classification of Conserved RNA Secondary Structures in the Human Genome

Jakob Skou Pedersen, Gill Bejerano, Adam Siepel, Kate Rosenbloom, Kerstin Lindblad-Toh, Eric S Lander, Jim Kent, Webb Miller, David Haussler

PLOS Computational Biology: published April 21, 2006 | https://doi.org/10.1371/journal.pcbi.0020033

SAGE2Splice: Unmapped SAGE Tags Reveal Novel Splice Junctions

Byron Yu-Lin Kuo, Ying Chen, Slavita Bohacec, Öjvind Johansson, Wyeth W Wasserman, Elizabeth M Simpson

PLOS Computational Biology: published April 28, 2006 | https://doi.org/10.1371/journal.pcbi.0020034

Codon Usage Domains over Bacterial Chromosomes

Marc Bailly-Bechet, Antoine Danchin, Mudassar Iqbal, Matteo Marsili, Massimo Vergassola

PLOS Computational Biology: published April 21, 2006 | https://doi.org/10.1371/journal.pcbi.0020037

Positive Selection, Relaxation, and Acceleration in the Evolution of the Human and Chimp Genome

Leonardo Arbiza, Joaquín Dopazo, Hernán Dopazo

PLOS Computational Biology: published April 28, 2006 | https://doi.org/10.1371/journal.pcbi.0020038

Changing Cellular Location of CheZ Predicted by Molecular Simulations

Karen Lipkow

PLOS Computational Biology: published April 28, 2006 | https://doi.org/10.1371/journal.pcbi.0020039

Designing a Nanotube Using Naturally Occurring Protein Building Blocks

Chung-Jung Tsai, Jie Zheng, Ruth Nussinov

PLOS Computational Biology: published April 28, 2006 | https://doi.org/10.1371/journal.pcbi.0020042

Correspondence

The Signal in the Genomes

David Sankoff

PLOS Computational Biology: published April 28, 2006 | https://doi.org/10.1371/journal.pcbi.0020035

Cover

Optimized dipeptide nanotube