Table of Contents

September 2006

A protein's shape can be described by a series of points on the unit sphere. The blue regions at the poles of this spherical histogram do not occur in proteins (see Hamelryck et al).

Image Credit: Histogram made using R by Wouter Boomsma. Ray-traced version of the histogram mapped to spheres using POVRAY by Thomas Hamelryck.


Ten Simple Rules for Reviewers

Philip E Bourne, Alon Korngreen


Scientific Software Development Is Not an Oxymoron

Susan M Baxter, Steven W Day, Jacquelyn S Fetrow, Stephanie J Reisinger

Research Articles

Evidence of Influence of Genomic DNA Sequence on Human X Chromosome Inactivation

Zhong Wang, Huntington F Willard, Sayan Mukherjee, Terrence S Furey

Model-Based Design of Growth-Attenuated Viruses

Kwang-il Lim, Tobias Lang, Vy Lam, John Yin

Oscillatory Regulation of Hes1: Discrete Stochastic Delay Modelling and Simulation

Manuel Barrio, Kevin Burrage, André Leier, Tianhai Tian

Imitating Manual Curation of Text-Mined Facts in Biomedicine

Raul Rodriguez-Esteban, Ivan Iossifov, Andrey Rzhetsky

Transient Calcium and Dopamine Increase PKA Activity and DARPP-32 Phosphorylation

Maria Lindskog, MyungSook Kim, Martin A Wikström, Kim T Blackwell, Jeanette Hellgren Kotaleski

Mathematical Modeling Identifies Inhibitors of Apoptosis as Mediators of Positive Feedback and Bistability

Stefan Legewie, Nils Blüthgen, Hanspeter Herzel

Intricate Knots in Proteins: Function and Evolution

Peter Virnau, Leonid A Mirny, Mehran Kardar

Transcriptional Dynamics of the Embryonic Stem Cell Switch

Vijay Chickarmane, Carl Troein, Ulrike A Nuber, Herbert M Sauro, Carsten Peterson

The Many Faces of Protein–Protein Interactions: A Compendium of Interface Geometry

Wan Kyu Kim, Andreas Henschel, Christof Winter, Michael Schroeder

Computational Model of Vascular Endothelial Growth Factor Spatial Distribution in Muscle and Pro-Angiogenic Cell Therapy

Feilim Mac Gabhann, James W Ji, Aleksander S Popel

Can Transgenic Maize Affect Soil Microbial Communities?

Christian Mulder, Marja Wouterse, Markus Raubuch, Willem Roelofs, Michiel Rutgers

Sampling Realistic Protein Conformations Using Local Structural Bias

Thomas Hamelryck, John T Kent, Anders Krogh

Targeted Molecular Dynamics Study of C-Loop Closure and Channel Gating in Nicotinic Receptors

Xiaolin Cheng, Hailong Wang, Barry Grant, Steven M Sine, J. Andrew McCammon