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Table of Contents

October 2015

By adding global "ambient occlusion" illumination to a scene, large macromolecular systems look much more natural. Wahle and Wriggers (pcbi.1004516) introduce a novel size-specificity of the shaded features in the Sculptor molecular graphics and modeling software). Shown is a composite of CCMV images (PDB ID 1CWP) with three different scale settings. The illumination can be tuned in real time for pockets and cavities of a user-defined size, making it useful for visualizing large biomolecular systems, comprising e.g. hundreds of thousands of atoms or Mega-Dalton size electron microscopy maps. Wahle et al.

Image Credit: Wahle and Wriggers

Editorials

Ten Simple Rules for Experiments’ Provenance

Toni Kazic

Ten Simple Rules for Writing a Reply Paper

Mark P. Simmons

Ten Simple Rules for Protecting Research Integrity

David M. Shaw, Thomas C. Erren

Perspective

Ten Simple Rules for Creating a Good Data Management Plan

William K. Michener

Research Articles

Deconstructing Interocular Suppression: Attention and Divisive Normalization

Hsin-Hung Li, Marisa Carrasco, David J. Heeger

Doubly Bayesian Analysis of Confidence in Perceptual Decision-Making

Laurence Aitchison, Dan Bang, Bahador Bahrami, Peter E. Latham

Membrane Mechanics of Endocytosis in Cells with Turgor

Serge Dmitrieff, François Nédélec

Oxygen-Driven Tumour Growth Model: A Pathology-Relevant Mathematical Approach

Juan A. Delgado-SanMartin, Jennifer I. Hare, Alessandro P. S. de Moura, James W. T. Yates

Emergence of Shared Intentionality Is Coupled to the Advance of Cumulative Culture

Simon D. Angus, Jonathan Newton

Extracting Diffusive States of Rho GTPase in Live Cells: Towards In Vivo Biochemistry

Peter K. Koo, Matthew Weitzman, Chandran R. Sabanaygam, Kenneth L. van Golen, Simon G. J. Mochrie

The Trigger Factor Chaperone Encapsulates and Stabilizes Partial Folds of Substrate Proteins

Kushagra Singhal, Jocelyne Vreede, Alireza Mashaghi, Sander J. Tans, Peter G. Bolhuis

Combining Search, Social Media, and Traditional Data Sources to Improve Influenza Surveillance

Mauricio Santillana, André T. Nguyen, Mark Dredze, Michael J. Paul, Elaine O. Nsoesie, John S. Brownstein

Comparisons of Allergenic and Metazoan Parasite Proteins: Allergy the Price of Immunity

Nidhi Tyagi, Edward J Farnell, Colin M Fitzsimmons, Stephanie Ryan, Edridah Tukahebwa, Rick M Maizels, David W Dunne, Janet M Thornton, Nicholas Furnham

Relating Cortical Atrophy in Temporal Lobe Epilepsy with Graph Diffusion-Based Network Models

Farras Abdelnour, Susanne Mueller, Ashish Raj

Conformational Dynamics and Binding Free Energies of Inhibitors of BACE-1: From the Perspective of Protonation Equilibria

M. Olivia Kim, Patrick G. Blachly, J. Andrew McCammon

ApoE4-specific Misfolded Intermediate Identified by Molecular Dynamics Simulations

Benfeard Williams II, Marino Convertino, Jhuma Das, Nikolay V. Dokholyan

Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments

Rong Shen, Wei Han, Giacomo Fiorin, Shahidul M. Islam, Klaus Schulten, Benoît Roux

ENCORE: Software for Quantitative Ensemble Comparison

Matteo Tiberti, Elena Papaleo, Tone Bengtsen, Wouter Boomsma, Kresten Lindorff-Larsen

Mapping the Protein Fold Universe Using the CamTube Force Field in Molecular Dynamics Simulations

Predrag Kukic, Arvind Kannan, Maurits J. J. Dijkstra, Sanne Abeln, Carlo Camilloni, Michele Vendruscolo

Parsimonious Model of Vascular Patterning Links Transverse Hormone Fluxes to Lateral Root Initiation: Auxin Leads the Way, while Cytokinin Levels Out

Sedeer el-Showk, Hanna Help-Rinta-Rahko, Tiina Blomster, Riccardo Siligato, Athanasius F. M. Marée, Ari Pekka Mähönen, Verônica A. Grieneisen

DynaFace: Discrimination between Obligatory and Non-obligatory Protein-Protein Interactions Based on the Complex’s Dynamics

Seren Soner, Pemra Ozbek, Jose Ignacio Garzon, Nir Ben-Tal, Turkan Haliloglu

pMD-Membrane: A Method for Ligand Binding Site Identification in Membrane-Bound Proteins

Priyanka Prakash, Abdallah Sayyed-Ahmad, Alemayehu A. Gorfe

Broad CTL Response in Early HIV Infection Drives Multiple Concurrent CTL Escapes

Sivan Leviyang, Vitaly V. Ganusov

Exposing Hidden Alternative Backbone Conformations in X-ray Crystallography Using qFit

Daniel A. Keedy, James S. Fraser, Henry van den Bedem

Sensorimotor Model of Obstacle Avoidance in Echolocating Bats

Dieter Vanderelst, Marc W. Holderied, Herbert Peremans

The Invariance Hypothesis Implies Domain-Specific Regions in Visual Cortex

Joel Z. Leibo, Qianli Liao, Fabio Anselmi, Tomaso Poggio

Reinforcement Learning of Linking and Tracing Contours in Recurrent Neural Networks

Tobias Brosch, Heiko Neumann, Pieter R. Roelfsema

Critical Roles of the Direct GABAergic Pallido-cortical Pathway in Controlling Absence Seizures

Mingming Chen, Daqing Guo, Min Li, Tao Ma, Shengdun Wu, Jingling Ma, Yan Cui, Yang Xia, Peng Xu, Dezhong Yao

An Exploration of the Universe of Polyglutamine Structures

Àngel Gómez-Sicilia, Mateusz Sikora, Marek Cieplak, Mariano Carrión-Vázquez

Modeling the Evolution of Beliefs Using an Attentional Focus Mechanism

Dimitrije Marković, Jan Gläscher, Peter Bossaerts, John O’Doherty, Stefan J. Kiebel

Signaling and Adaptation Modulate the Dynamics of the Photosensoric Complex of Natronomonas pharaonis

Philipp S. Orekhov, Daniel Klose, Armen Y. Mulkidjanian, Konstantin V. Shaitan, Martin Engelhard, Johann P. Klare, Heinz-Jürgen Steinhoff

Qualitative and Quantitative Protein Complex Prediction Through Proteome-Wide Simulations

Simone Rizzetto, Corrado Priami, Attila Csikász-Nagy

Laminar Neural Field Model of Laterally Propagating Waves of Orientation Selectivity

Paul C. Bressloff, Samuel R. Carroll

Intracellular Information Processing through Encoding and Decoding of Dynamic Signaling Features

Hirenkumar K. Makadia, James S. Schwaber, Rajanikanth Vadigepalli

Crawling and Gliding: A Computational Model for Shape-Driven Cell Migration

Ioana Niculescu, Johannes Textor, Rob J. de Boer

The Impact of Different Sources of Fluctuations on Mutual Information in Biochemical Networks

Michael Chevalier, Ophelia Venturelli, Hana El-Samad

Perm-seq: Mapping Protein-DNA Interactions in Segmental Duplication and Highly Repetitive Regions of Genomes with Prior-Enhanced Read Mapping

Xin Zeng, Bo Li, Rene Welch, Constanza Rojo, Ye Zheng, Colin N. Dewey, Sündüz Keleş

A Pan-Cancer Catalogue of Cancer Driver Protein Interaction Interfaces

Eduard Porta-Pardo, Luz Garcia-Alonso, Thomas Hrabe, Joaquin Dopazo, Adam Godzik

Established Microbial Colonies Can Survive Type VI Secretion Assault

David Bruce Borenstein, Peter Ringel, Marek Basler, Ned S. Wingreen

Refinement of the Central Steps of Substrate Transport by the Aspartate Transporter GltPh: Elucidating the Role of the Na2 Sodium Binding Site

SanthoshKannan Venkatesan, Kusumika Saha, Azmat Sohail, Walter Sandtner, Michael Freissmuth, Gerhard F. Ecker, Harald H. Sitte, Thomas Stockner

Integrative Genomics-Based Discovery of Novel Regulators of the Innate Antiviral Response

Robin van der Lee, Qian Feng, Martijn A. Langereis, Rob ter Horst, Radek Szklarczyk, Mihai G. Netea, Arno C. Andeweg, Frank J. M. van Kuppeveld, Martijn A. Huynen

Transcriptional Bursting in Gene Expression: Analytical Results for General Stochastic Models

Niraj Kumar, Abhyudai Singh, Rahul V. Kulkarni

Electrosensory Midbrain Neurons Display Feature Invariant Responses to Natural Communication Stimuli

Tristan Aumentado-Armstrong, Michael G. Metzen, Michael K. J. Sproule, Maurice J. Chacron

Quantitative Live Imaging of Human Embryonic Stem Cell Derived Neural Rosettes Reveals Structure-Function Dynamics Coupled to Cortical Development

Omer Ziv, Assaf Zaritsky, Yakey Yaffe, Naresh Mutukula, Reuven Edri, Yechiel Elkabetz

Bridging between NMA and Elastic Network Models: Preserving All-Atom Accuracy in Coarse-Grained Models

Hyuntae Na, Robert L. Jernigan, Guang Song

The Structural Basis for Activation and Inhibition of ZAP-70 Kinase Domain

Roland G. Huber, Hao Fan, Peter J. Bond

PF2 fit: Polar Fast Fourier Matched Alignment of Atomistic Structures with 3D Electron Microscopy Maps

Radhakrishna Bettadapura, Muhibur Rasheed, Antje Vollrath, Chandrajit Bajaj

A Neutrophil Phenotype Model for Extracorporeal Treatment of Sepsis

Alexander D. Malkin, Robert P. Sheehan, Shibin Mathew, William J. Federspiel, Heinz Redl, Gilles Clermont

Efficient "Shotgun" Inference of Neural Connectivity from Highly Sub-sampled Activity Data

Daniel Soudry, Suraj Keshri, Patrick Stinson, Min-hwan Oh, Garud Iyengar, Liam Paninski

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