Table of Contents

July 2008

AF-2 domains of nuclear receptors mediate crucial protein–protein interactions with transcriptional coactivators. The AF-2 domains (magenta) of the human nuclear xenobiotic receptor PXR (cyan) were demonstrated using molecular dynamics to move together in an "active-ready" conformation, poised to bind to their cognate protein partners (see Teotico et al. pcbi.1000111). Other nuclear receptors were also shown to follow suit.

Image Credit: Monica Frazier and Matthew Redinbo

Message from ISCB

ISCB Honors David Haussler and Aviv Regev

Clare Sansom, B. J. Morrison McKay


Computational Biology Resources Lack Persistence and Usability

Stella Veretnik, J. Lynn Fink, Philip E. Bourne

Outlook on Thailand's Genomics and Computational Biology Research and Development

Wannipha Tongsima, Sissades Tongsima, Prasit Palittapongarnpim

Research Articles

Kinetic Modeling of the Assembly, Dynamic Steady State, and Contraction of the FtsZ Ring in Prokaryotic Cytokinesis

Ivan V. Surovtsev, Jeffrey J. Morgan, Paul A. Lindahl

Dynamics of Immune Escape during HIV/SIV Infection

Christian L. Althaus, Rob J. De Boer

Circadian Phase Resetting via Single and Multiple Control Targets

Neda Bagheri, Jörg Stelling, Francis J. Doyle III

Local Function Conservation in Sequence and Structure Space

Nils Weinhold, Oliver Sander, Francisco S. Domingues, Thomas Lengauer, Ingolf Sommer

Increased Brain Signal Variability Accompanies Lower Behavioral Variability in Development

Anthony Randal McIntosh, Natasa Kovacevic, Roxane J. Itier

Quantitative Predictions of Peptide Binding to Any HLA-DR Molecule of Known Sequence: NetMHCIIpan

Morten Nielsen, Claus Lundegaard, Thomas Blicher, Bjoern Peters, Alessandro Sette, Sune Justesen, Søren Buus, Ole Lund

Unraveling Protein Networks with Power Graph Analysis

Loïc Royer, Matthias Reimann, Bill Andreopoulos, Michael Schroeder

The Generation of Promoter-Mediated Transcriptional Noise in Bacteria

Namiko Mitarai, Ian B. Dodd, Michael T. Crooks, Kim Sneppen

The Ascent of the Abundant: How Mutational Networks Constrain Evolution

Matthew C. Cowperthwaite, Evan P. Economo, William R. Harcombe, Eric L. Miller, Lauren Ancel Meyers

Active Nuclear Receptors Exhibit Highly Correlated AF-2 Domain Motions

Denise G. Teotico, Monica L. Frazier, Feng Ding, Nikolay V. Dokholyan, Brenda R. S. Temple, Matthew R. Redinbo

Evolution of Evolvability in Gene Regulatory Networks

Anton Crombach, Paulien Hogeweg

Probing the Extent of Randomness in Protein Interaction Networks

Joseph Ivanic, Anders Wallqvist, Jaques Reifman

Similarity Queries for Temporal Toxicogenomic Expression Profiles

Adam A. Smith, Aaron Vollrath, Christopher A. Bradfield, Mark Craven

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