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

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