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

Computational Methods for Exploration and Analysis of Macromolecular Structure and Dynamics

Amarda Shehu, Ruth Nussinov

PLOS Computational Biology: published October 27, 2015 | https://doi.org/10.1371/journal.pcbi.1004585

Ten Simple Rules for Experiments’ Provenance

Toni Kazic

PLOS Computational Biology: published October 20, 2015 | https://doi.org/10.1371/journal.pcbi.1004384

Ten Simple Rules for Establishing International Research Collaborations

Richard de Grijs

PLOS Computational Biology: published October 8, 2015 | https://doi.org/10.1371/journal.pcbi.1004311

Ten Simple Rules for Writing a Reply Paper

Mark P. Simmons

PLOS Computational Biology: published October 8, 2015 | https://doi.org/10.1371/journal.pcbi.1004536

Ten Simple Rules for Protecting Research Integrity

David M. Shaw, Thomas C. Erren

PLOS Computational Biology: published October 1, 2015 | https://doi.org/10.1371/journal.pcbi.1004388

Perspective

Ten Simple Rules for Creating a Good Data Management Plan

William K. Michener

PLOS Computational Biology: published October 22, 2015 | https://doi.org/10.1371/journal.pcbi.1004525

Research Articles

Deconstructing Interocular Suppression: Attention and Divisive Normalization

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

PLOS Computational Biology: published October 30, 2015 | https://doi.org/10.1371/journal.pcbi.1004510

Doubly Bayesian Analysis of Confidence in Perceptual Decision-Making

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

PLOS Computational Biology: published October 30, 2015 | https://doi.org/10.1371/journal.pcbi.1004519

Membrane Mechanics of Endocytosis in Cells with Turgor

Serge Dmitrieff, François Nédélec

PLOS Computational Biology: published October 30, 2015 | https://doi.org/10.1371/journal.pcbi.1004538

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

PLOS Computational Biology: published October 30, 2015 | https://doi.org/10.1371/journal.pcbi.1004550

Temporal Gillespie Algorithm: Fast Simulation of Contagion Processes on Time-Varying Networks

Christian L. Vestergaard, Mathieu Génois

PLOS Computational Biology: published October 30, 2015 | https://doi.org/10.1371/journal.pcbi.1004579

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

Simon D. Angus, Jonathan Newton

PLOS Computational Biology: published October 30, 2015 | https://doi.org/10.1371/journal.pcbi.1004587

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

PLOS Computational Biology: published October 29, 2015 | https://doi.org/10.1371/journal.pcbi.1004297

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

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

PLOS Computational Biology: published October 29, 2015 | https://doi.org/10.1371/journal.pcbi.1004444

Dendritic Pooling of Noisy Threshold Processes Can Explain Many Properties of a Collision-Sensitive Visual Neuron

Matthias S. Keil

PLOS Computational Biology: published October 29, 2015 | https://doi.org/10.1371/journal.pcbi.1004479

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

PLOS Computational Biology: published October 29, 2015 | https://doi.org/10.1371/journal.pcbi.1004513

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

PLOS Computational Biology: published October 29, 2015 | https://doi.org/10.1371/journal.pcbi.1004546

Structural Insights into Separase Architecture and Substrate Recognition through Computational Modelling of Caspase-Like and Death Domains

Anja Winter, Ralf Schmid, Richard Bayliss

PLOS Computational Biology: published October 29, 2015 | https://doi.org/10.1371/journal.pcbi.1004548

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

Farras Abdelnour, Susanne Mueller, Ashish Raj

PLOS Computational Biology: published October 29, 2015 | https://doi.org/10.1371/journal.pcbi.1004564

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

PLOS Computational Biology: published October 27, 2015 | https://doi.org/10.1371/journal.pcbi.1004341

ApoE4-specific Misfolded Intermediate Identified by Molecular Dynamics Simulations

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

PLOS Computational Biology: published October 27, 2015 | https://doi.org/10.1371/journal.pcbi.1004359

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

PLOS Computational Biology: published October 27, 2015 | https://doi.org/10.1371/journal.pcbi.1004368

Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning

Lane W. Votapka, Rommie E. Amaro

PLOS Computational Biology: published October 27, 2015 | https://doi.org/10.1371/journal.pcbi.1004381

ENCORE: Software for Quantitative Ensemble Comparison

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

PLOS Computational Biology: published October 27, 2015 | https://doi.org/10.1371/journal.pcbi.1004415

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

PLOS Computational Biology: published October 27, 2015 | https://doi.org/10.1371/journal.pcbi.1004435

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

PLOS Computational Biology: published October 27, 2015 | https://doi.org/10.1371/journal.pcbi.1004450

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

PLOS Computational Biology: published October 27, 2015 | https://doi.org/10.1371/journal.pcbi.1004461

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

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

PLOS Computational Biology: published October 27, 2015 | https://doi.org/10.1371/journal.pcbi.1004469

A Virtual Mixture Approach to the Study of Multistate Equilibrium: Application to Constant pH Simulation in Explicit Water

Xiongwu Wu, Bernard R. Brooks

PLOS Computational Biology: published October 27, 2015 | https://doi.org/10.1371/journal.pcbi.1004480

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

Sivan Leviyang, Vitaly V. Ganusov

PLOS Computational Biology: published October 27, 2015 | https://doi.org/10.1371/journal.pcbi.1004492

Predicting the Effect of Mutations on Protein-Protein Binding Interactions through Structure-Based Interface Profiles

Jeffrey R. Brender, Yang Zhang

PLOS Computational Biology: published October 27, 2015 | https://doi.org/10.1371/journal.pcbi.1004494

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

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

PLOS Computational Biology: published October 27, 2015 | https://doi.org/10.1371/journal.pcbi.1004507

Multi-scale Visualization of Molecular Architecture Using Real-Time Ambient Occlusion in Sculptor

Manuel Wahle, Willy Wriggers

PLOS Computational Biology: published October 27, 2015 | https://doi.org/10.1371/journal.pcbi.1004516

Sensorimotor Model of Obstacle Avoidance in Echolocating Bats

Dieter Vanderelst, Marc W. Holderied, Herbert Peremans

PLOS Computational Biology: published October 26, 2015 | https://doi.org/10.1371/journal.pcbi.1004484

Automatic Prediction of Protein 3D Structures by Probabilistic Multi-template Homology Modeling

Armin Meier, Johannes Söding

PLOS Computational Biology: published October 23, 2015 | https://doi.org/10.1371/journal.pcbi.1004343

The Invariance Hypothesis Implies Domain-Specific Regions in Visual Cortex

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

PLOS Computational Biology: published October 23, 2015 | https://doi.org/10.1371/journal.pcbi.1004390

Reinforcement Learning of Linking and Tracing Contours in Recurrent Neural Networks

Tobias Brosch, Heiko Neumann, Pieter R. Roelfsema

PLOS Computational Biology: published October 23, 2015 | https://doi.org/10.1371/journal.pcbi.1004489

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

PLOS Computational Biology: published October 23, 2015 | https://doi.org/10.1371/journal.pcbi.1004539

An Exploration of the Universe of Polyglutamine Structures

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

PLOS Computational Biology: published October 23, 2015 | https://doi.org/10.1371/journal.pcbi.1004541

Modeling the Evolution of Beliefs Using an Attentional Focus Mechanism

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

PLOS Computational Biology: published October 23, 2015 | https://doi.org/10.1371/journal.pcbi.1004558

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

PLOS Computational Biology: published October 23, 2015 | https://doi.org/10.1371/journal.pcbi.1004561

Qualitative and Quantitative Protein Complex Prediction Through Proteome-Wide Simulations

Simone Rizzetto, Corrado Priami, Attila Csikász-Nagy

PLOS Computational Biology: published October 22, 2015 | https://doi.org/10.1371/journal.pcbi.1004424

Laminar Neural Field Model of Laterally Propagating Waves of Orientation Selectivity

Paul C. Bressloff, Samuel R. Carroll

PLOS Computational Biology: published October 22, 2015 | https://doi.org/10.1371/journal.pcbi.1004545

Intracellular Information Processing through Encoding and Decoding of Dynamic Signaling Features

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

PLOS Computational Biology: published October 22, 2015 | https://doi.org/10.1371/journal.pcbi.1004563

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

Ioana Niculescu, Johannes Textor, Rob J. de Boer

PLOS Computational Biology: published October 21, 2015 | https://doi.org/10.1371/journal.pcbi.1004280

Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways

Sean L. Seyler, Avishek Kumar, M. F. Thorpe, Oliver Beckstein

PLOS Computational Biology: published October 21, 2015 | https://doi.org/10.1371/journal.pcbi.1004568

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

Michael Chevalier, Ophelia Venturelli, Hana El-Samad

PLOS Computational Biology: published October 20, 2015 | https://doi.org/10.1371/journal.pcbi.1004462

The Shape of an Auxin Pulse, and What It Tells Us about the Transport Mechanism

Graeme Mitchison

PLOS Computational Biology: published October 20, 2015 | https://doi.org/10.1371/journal.pcbi.1004487

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

PLOS Computational Biology: published October 20, 2015 | https://doi.org/10.1371/journal.pcbi.1004491

At the Edge of Chaos: How Cerebellar Granular Layer Network Dynamics Can Provide the Basis for Temporal Filters

Christian Rössert, Paul Dean, John Porrill

PLOS Computational Biology: published October 20, 2015 | https://doi.org/10.1371/journal.pcbi.1004515

A Pan-Cancer Catalogue of Cancer Driver Protein Interaction Interfaces

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

PLOS Computational Biology: published October 20, 2015 | https://doi.org/10.1371/journal.pcbi.1004518

Established Microbial Colonies Can Survive Type VI Secretion Assault

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

PLOS Computational Biology: published October 20, 2015 | https://doi.org/10.1371/journal.pcbi.1004520

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

PLOS Computational Biology: published October 20, 2015 | https://doi.org/10.1371/journal.pcbi.1004551

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

PLOS Computational Biology: published October 20, 2015 | https://doi.org/10.1371/journal.pcbi.1004553

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

Niraj Kumar, Abhyudai Singh, Rahul V. Kulkarni

PLOS Computational Biology: published October 16, 2015 | https://doi.org/10.1371/journal.pcbi.1004292

Electrosensory Midbrain Neurons Display Feature Invariant Responses to Natural Communication Stimuli

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

PLOS Computational Biology: published October 16, 2015 | https://doi.org/10.1371/journal.pcbi.1004430

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

PLOS Computational Biology: published October 16, 2015 | https://doi.org/10.1371/journal.pcbi.1004453

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

Hyuntae Na, Robert L. Jernigan, Guang Song

PLOS Computational Biology: published October 16, 2015 | https://doi.org/10.1371/journal.pcbi.1004542

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

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

PLOS Computational Biology: published October 16, 2015 | https://doi.org/10.1371/journal.pcbi.1004560

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

Radhakrishna Bettadapura, Muhibur Rasheed, Antje Vollrath, Chandrajit Bajaj

PLOS Computational Biology: published October 15, 2015 | https://doi.org/10.1371/journal.pcbi.1004289

A Neutrophil Phenotype Model for Extracorporeal Treatment of Sepsis

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

PLOS Computational Biology: published October 15, 2015 | https://doi.org/10.1371/journal.pcbi.1004314

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

PLOS Computational Biology: published October 14, 2015 | https://doi.org/10.1371/journal.pcbi.1004464

The Mass-Longevity Triangle: Pareto Optimality and the Geometry of Life-History Trait Space

Pablo Szekely, Yael Korem, Uri Moran, Avi Mayo, Uri Alon

PLOS Computational Biology: published October 14, 2015 | https://doi.org/10.1371/journal.pcbi.1004524

Establishing a Statistical Link between Network Oscillations and Neural Synchrony

Pengcheng Zhou, Shawn D. Burton, Adam C. Snyder, Matthew A. Smith, Nathaniel N. Urban, Robert E. Kass

PLOS Computational Biology: published October 14, 2015 | https://doi.org/10.1371/journal.pcbi.1004549

Gene Prioritization by Compressive Data Fusion and Chaining

Marinka Žitnik, Edward A. Nam, Christopher Dinh, Adam Kuspa, Gad Shaulsky, Blaž Zupan

PLOS Computational Biology: published October 14, 2015 | https://doi.org/10.1371/journal.pcbi.1004552

A Common Mechanism Underlying Food Choice and Social Decisions

Ian Krajbich, Todd Hare, Björn Bartling, Yosuke Morishima, Ernst Fehr

PLOS Computational Biology: published October 13, 2015 | https://doi.org/10.1371/journal.pcbi.1004371

Comprehensive Meta-analysis of Ontology Annotated 16S rRNA Profiles Identifies Beta Diversity Clusters of Environmental Bacterial Communities

Andreas Henschel, Muhammad Zohaib Anwar, Vimitha Manohar

PLOS Computational Biology: published October 12, 2015 | https://doi.org/10.1371/journal.pcbi.1004468

Feed-Forward versus Feedback Inhibition in a Basic Olfactory Circuit

Tiffany Kee, Pavel Sanda, Nitin Gupta, Mark Stopfer, Maxim Bazhenov

PLOS Computational Biology: published October 12, 2015 | https://doi.org/10.1371/journal.pcbi.1004531

Antagonistic Coevolution Drives Whack-a-Mole Sensitivity in Gene Regulatory Networks

Jeewoen Shin, Thomas MacCarthy

PLOS Computational Biology: published October 9, 2015 | https://doi.org/10.1371/journal.pcbi.1004432

Connectivity Homology Enables Inter-Species Network Models of Synthetic Lethality

Alexandra Jacunski, Scott J. Dixon, Nicholas P. Tatonetti

PLOS Computational Biology: published October 9, 2015 | https://doi.org/10.1371/journal.pcbi.1004506

Modelling Odor Decoding in the Antennal Lobe by Combining Sequential Firing Rate Models with Bayesian Inference

Dario Cuevas Rivera, Sebastian Bitzer, Stefan J. Kiebel

PLOS Computational Biology: published October 9, 2015 | https://doi.org/10.1371/journal.pcbi.1004528

Discrete Element Framework for Modelling Extracellular Matrix, Deformable Cells and Subcellular Components

Bruce S. Gardiner, Kelvin K. L. Wong, Grand R. Joldes, Addison J. Rich, Chin Wee Tan, Antony W. Burgess, David W. Smith

PLOS Computational Biology: published October 9, 2015 | https://doi.org/10.1371/journal.pcbi.1004544

TRANSIT - A Software Tool for Himar1 TnSeq Analysis

Michael A. DeJesus, Chaitra Ambadipudi, Richard Baker, Christopher Sassetti, Thomas R. Ioerger

PLOS Computational Biology: published October 8, 2015 | https://doi.org/10.1371/journal.pcbi.1004401

An Adapting Auditory-motor Feedback Loop Can Contribute to Generating Vocal Repetition

Jason D. Wittenbach, Kristofer E. Bouchard, Michael S. Brainard, Dezhe Z. Jin

PLOS Computational Biology: published October 8, 2015 | https://doi.org/10.1371/journal.pcbi.1004471

Ligand Discovery for the Alanine-Serine-Cysteine Transporter (ASCT2, SLC1A5) from Homology Modeling and Virtual Screening

Claire Colas, Christof Grewer, Nicholas James Otte, Armanda Gameiro, Thomas Albers, Kurnvir Singh, Helen Shere, Massimiliano Bonomi, Jeff Holst, Avner Schlessinger

PLOS Computational Biology: published October 7, 2015 | https://doi.org/10.1371/journal.pcbi.1004477

Analyzing and Quantifying the Gain-of-Function Enhancement of IP₃ Receptor Gating by Familial Alzheimer’s Disease-Causing Mutants in Presenilins

Don-On Daniel Mak, King-Ho Cheung, Patrick Toglia, J. Kevin Foskett, Ghanim Ullah

PLOS Computational Biology: published October 6, 2015 | https://doi.org/10.1371/journal.pcbi.1004529

Reconciling Estimates of Cell Proliferation from Stable Isotope Labeling Experiments

Raya Ahmed, Liset Westera, Julia Drylewicz, Marjet Elemans, Yan Zhang, Elizabeth Kelly, Rajko Reljic, Kiki Tesselaar, Rob J. de Boer, Derek C. Macallan, José A. M. Borghans, Becca Asquith

PLOS Computational Biology: published October 5, 2015 | https://doi.org/10.1371/journal.pcbi.1004355

SubClonal Hierarchy Inference from Somatic Mutations: Automatic Reconstruction of Cancer Evolutionary Trees from Multi-region Next Generation Sequencing

Noushin Niknafs, Violeta Beleva-Guthrie, Daniel Q. Naiman, Rachel Karchin

PLOS Computational Biology: published October 5, 2015 | https://doi.org/10.1371/journal.pcbi.1004416

Implications of Heterogeneous Biting Exposure and Animal Hosts on Trypanosomiasis brucei gambiense Transmission and Control

Chris M. Stone, Nakul Chitnis

PLOS Computational Biology: published October 1, 2015 | https://doi.org/10.1371/journal.pcbi.1004514

Cover

Multi-scale Visualization of Molecular Architecture Using Real-Time Ambient Occlusion in Sculptor

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