April 2016

Investigation of macromolecular structure and dynamics is fundamental to understanding how macromolecules carry out their functions in the cell. Significant advances have been made toward this end in silico, with a growing number of computational methods proposed yearly to study and simulate various aspects of macromolecular structure and dynamics. This review aims to provide an overview of recent advances, focusing primarily on methods proposed for exploring the structure space of macromolecules in isolation and in assemblies for the purpose of characterizing equilibrium structure and dynamics. Shehu et al.

Image Credit: Lei Chen and Yan Liang (L2Molecule.com, Bruce Donald Laboratory [See Reference 452])

Topic Page

Hypercycle

Natalia Szostak, Szymon Wasik, Jacek Blazewicz

PLOS Computational Biology: published April 7, 2016 | https://doi.org/10.1371/journal.pcbi.1004853

Review

Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics

Tatiana Maximova, Ryan Moffatt, Buyong Ma, Ruth Nussinov, Amarda Shehu

PLOS Computational Biology: published April 28, 2016 | https://doi.org/10.1371/journal.pcbi.1004619

Research Articles

The Interaction between Vector Life History and Short Vector Life in Vector-Borne Disease Transmission and Control

Samuel P. C. Brand, Kat S. Rock, Matt J. Keeling

PLOS Computational Biology: published April 29, 2016 | https://doi.org/10.1371/journal.pcbi.1004837

Quorum-Sensing Synchronization of Synthetic Toggle Switches: A Design Based on Monotone Dynamical Systems Theory

Evgeni V. Nikolaev, Eduardo D. Sontag

PLOS Computational Biology: published April 29, 2016 | https://doi.org/10.1371/journal.pcbi.1004881

A Drug-Centric View of Drug Development: How Drugs Spread from Disease to Disease

Raul Rodriguez-Esteban

PLOS Computational Biology: published April 28, 2016 | https://doi.org/10.1371/journal.pcbi.1004852

A Network Biology Approach Identifies Molecular Cross-Talk between Normal Prostate Epithelial and Prostate Carcinoma Cells

Victor Trevino, Alberto Cassese, Zsuzsanna Nagy, Xiaodong Zhuang, John Herbert, Philipp Antzack, Kim Clarke, Nicholas Davies, Ayesha Rahman, Moray J. Campbell, Michele Guindani, Roy Bicknell, Marina Vannucci, Francesco Falciani

PLOS Computational Biology: published April 28, 2016 | https://doi.org/10.1371/journal.pcbi.1004884

Nucleosome Presence at AML-1 Binding Sites Inversely Correlates with Ly49 Expression: Revelations from an Informatics Analysis of Nucleosomes and Immune Cell Transcription Factors

Andrew Wight, Doo Yang, Ilya Ioshikhes, Andrew P. Makrigiannis

PLOS Computational Biology: published April 28, 2016 | https://doi.org/10.1371/journal.pcbi.1004894

Deep Neural Networks as a Computational Model for Human Shape Sensitivity

Jonas Kubilius, Stefania Bracci, Hans P. Op de Beeck

PLOS Computational Biology: published April 28, 2016 | https://doi.org/10.1371/journal.pcbi.1004896

HepatoDyn: A Dynamic Model of Hepatocyte Metabolism That Integrates ¹³C Isotopomer Data

Carles Foguet, Silvia Marin, Vitaly A. Selivanov, Eric Fanchon, Wai-Nang Paul Lee, Joan J. Guinovart, Pedro de Atauri, Marta Cascante

PLOS Computational Biology: published April 28, 2016 | https://doi.org/10.1371/journal.pcbi.1004899

An Electrostatic Funnel in the GABA-Binding Pathway

Timothy S. Carpenter, Felice C. Lightstone

PLOS Computational Biology: published April 27, 2016 | https://doi.org/10.1371/journal.pcbi.1004831

The Evolution of Quorum Sensing as a Mechanism to Infer Kinship

Jonas Schluter, Armin P. Schoech, Kevin R. Foster, Sara Mitri

PLOS Computational Biology: published April 27, 2016 | https://doi.org/10.1371/journal.pcbi.1004848

MEDYAN: Mechanochemical Simulations of Contraction and Polarity Alignment in Actomyosin Networks

Konstantin Popov, James Komianos, Garegin A. Papoian

PLOS Computational Biology: published April 27, 2016 | https://doi.org/10.1371/journal.pcbi.1004877

Parasites Sustain and Enhance RNA-Like Replicators through Spatial Self-Organisation

Enrico Sandro Colizzi, Paulien Hogeweg

PLOS Computational Biology: published April 27, 2016 | https://doi.org/10.1371/journal.pcbi.1004902

A Geometrically-Constrained Mathematical Model of Mammary Gland Ductal Elongation Reveals Novel Cellular Dynamics within the Terminal End Bud

Ingrid Paine, Arnaud Chauviere, John Landua, Amulya Sreekumar, Vittorio Cristini, Jeffrey Rosen, Michael T. Lewis

PLOS Computational Biology: published April 26, 2016 | https://doi.org/10.1371/journal.pcbi.1004839

Constraints on Biological Mechanism from Disease Comorbidity Using Electronic Medical Records and Database of Genetic Variants

Steven C. Bagley, Marina Sirota, Richard Chen, Atul J. Butte, Russ B. Altman

PLOS Computational Biology: published April 26, 2016 | https://doi.org/10.1371/journal.pcbi.1004885

Rigid Residue Scan Simulations Systematically Reveal Residue Entropic Roles in Protein Allostery

Robert Kalescky, Hongyu Zhou, Jin Liu, Peng Tao

PLOS Computational Biology: published April 26, 2016 | https://doi.org/10.1371/journal.pcbi.1004893

Bulk Genotyping of Biopsies Can Create Spurious Evidence for Hetereogeneity in Mutation Content

Rumen Kostadinov, Carlo C. Maley, Mary K. Kuhner

PLOS Computational Biology: published April 22, 2016 | https://doi.org/10.1371/journal.pcbi.1004413

Reconstruction of Cell Surface Densities of Ion Pumps, Exchangers, and Channels from mRNA Expression, Conductance Kinetics, Whole-Cell Calcium, and Current-Clamp Voltage Recordings, with an Application to Human Uterine Smooth Muscle Cells

Jolene Atia, Conor McCloskey, Anatoly S. Shmygol, David A. Rand, Hugo A. van den Berg, Andrew M. Blanks

PLOS Computational Biology: published April 22, 2016 | https://doi.org/10.1371/journal.pcbi.1004828

Modularity Induced Gating and Delays in Neuronal Networks

Mark Shein-Idelson, Gilad Cohen, Eshel Ben-Jacob, Yael Hanein

PLOS Computational Biology: published April 22, 2016 | https://doi.org/10.1371/journal.pcbi.1004883

The Role of Genome Accessibility in Transcription Factor Binding in Bacteria

Antonio L. C. Gomes, Harris H. Wang

PLOS Computational Biology: published April 22, 2016 | https://doi.org/10.1371/journal.pcbi.1004891

CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing

Eric Talevich, A. Hunter Shain, Thomas Botton, Boris C. Bastian

PLOS Computational Biology: published April 21, 2016 | https://doi.org/10.1371/journal.pcbi.1004873

Single-Cell Co-expression Analysis Reveals Distinct Functional Modules, Co-regulation Mechanisms and Clinical Outcomes

Jie Wang, Shuli Xia, Brian Arand, Heng Zhu, Raghu Machiraju, Kun Huang, Hongkai Ji, Jiang Qian

PLOS Computational Biology: published April 21, 2016 | https://doi.org/10.1371/journal.pcbi.1004892

Effective Design of Multifunctional Peptides by Combining Compatible Functions

Christian Diener, Georgina Garza Ramos Martínez, Daniel Moreno Blas, David A. Castillo González, Gerardo Corzo, Susana Castro-Obregon, Gabriel Del Rio

PLOS Computational Biology: published April 20, 2016 | https://doi.org/10.1371/journal.pcbi.1004786

A Computational Model of the Rainbow Trout Hypothalamus-Pituitary-Ovary-Liver Axis

Kendall Gillies, Stephen M. Krone, James J. Nagler, Irvin R. Schultz

PLOS Computational Biology: published April 20, 2016 | https://doi.org/10.1371/journal.pcbi.1004874

Network-Based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package

Nurcan Tuncbag, Sara J. C. Gosline, Amanda Kedaigle, Anthony R. Soltis, Anthony Gitter, Ernest Fraenkel

PLOS Computational Biology: published April 20, 2016 | https://doi.org/10.1371/journal.pcbi.1004879

APP Is a Context-Sensitive Regulator of the Hippocampal Presynaptic Active Zone

Melanie Laßek, Jens Weingarten, Martin Wegner, Benjamin F. Mueller, Marion Rohmer, Dominic Baeumlisberger, Tabiwang N. Arrey, Meike Hick, Jörg Ackermann, Amparo Acker-Palmer, Ina Koch, Ulrike Müller, Michael Karas, Walter Volknandt

PLOS Computational Biology: published April 19, 2016 | https://doi.org/10.1371/journal.pcbi.1004832

Rapid Prediction of Bacterial Heterotrophic Fluxomics Using Machine Learning and Constraint Programming

Stephen Gang Wu, Yuxuan Wang, Wu Jiang, Tolutola Oyetunde, Ruilian Yao, Xuehong Zhang, Kazuyuki Shimizu, Yinjie J. Tang, Forrest Sheng Bao

PLOS Computational Biology: published April 19, 2016 | https://doi.org/10.1371/journal.pcbi.1004838

Hippocampal CA1 Ripples as Inhibitory Transients

Paola Malerba, Giri P Krishnan, Jean-Marc Fellous, Maxim Bazhenov

PLOS Computational Biology: published April 19, 2016 | https://doi.org/10.1371/journal.pcbi.1004880

AuPairWise: A Method to Estimate RNA-Seq Replicability through Co-expression

Sara Ballouz, Jesse Gillis

PLOS Computational Biology: published April 15, 2016 | https://doi.org/10.1371/journal.pcbi.1004868

Visualization of Metabolic Interaction Networks in Microbial Communities Using VisANT 5.0

Brian R. Granger, Yi-Chien Chang, Yan Wang, Charles DeLisi, Daniel Segrè, Zhenjun Hu

PLOS Computational Biology: published April 15, 2016 | https://doi.org/10.1371/journal.pcbi.1004875

Oscillations via Spike-Timing Dependent Plasticity in a Feed-Forward Model

Yotam Luz, Maoz Shamir

PLOS Computational Biology: published April 15, 2016 | https://doi.org/10.1371/journal.pcbi.1004878

A Predictive Model for Yeast Cell Polarization in Pheromone Gradients

Nicolas Muller, Matthieu Piel, Vincent Calvez, Raphaël Voituriez, Joana Gonçalves-Sá, Chin-Lin Guo, Xingyu Jiang, Andrew Murray, Nicolas Meunier

PLOS Computational Biology: published April 14, 2016 | https://doi.org/10.1371/journal.pcbi.1004795

Computational Reconstruction of NFκB Pathway Interaction Mechanisms during Prostate Cancer

Daniela Börnigen, Svitlana Tyekucheva, Xiaodong Wang, Jennifer R. Rider, Gwo-Shu Lee, Lorelei A. Mucci, Christopher Sweeney, Curtis Huttenhower

PLOS Computational Biology: published April 14, 2016 | https://doi.org/10.1371/journal.pcbi.1004820

Ups and Downs of Poised RNA Polymerase II in B-Cells

Phuong Dao, Damian Wojtowicz, Steevenson Nelson, David Levens, Teresa M. Przytycka

PLOS Computational Biology: published April 14, 2016 | https://doi.org/10.1371/journal.pcbi.1004821

Mathematical Model for Length Control by the Timing of Substrate Switching in the Type III Secretion System

Maulik K. Nariya, Johnny Israeli, Jack J. Shi, Eric J. Deeds

PLOS Computational Biology: published April 14, 2016 | https://doi.org/10.1371/journal.pcbi.1004851

Integrating Antimicrobial Therapy with Host Immunity to Fight Drug-Resistant Infections: Classical vs. Adaptive Treatment

Erida Gjini, Patricia H. Brito

PLOS Computational Biology: published April 14, 2016 | https://doi.org/10.1371/journal.pcbi.1004857

The Development of Audio-Visual Integration for Temporal Judgements

Wendy J. Adams

PLOS Computational Biology: published April 14, 2016 | https://doi.org/10.1371/journal.pcbi.1004865

Mechanical Stress Induces Remodeling of Vascular Networks in Growing Leaves

Yohai Bar-Sinai, Jean-Daniel Julien, Eran Sharon, Shahaf Armon, Naomi Nakayama, Mokhtar Adda-Bedia, Arezki Boudaoud

PLOS Computational Biology: published April 13, 2016 | https://doi.org/10.1371/journal.pcbi.1004819

Problem Solving as Probabilistic Inference with Subgoaling: Explaining Human Successes and Pitfalls in the Tower of Hanoi

Francesco Donnarumma, Domenico Maisto, Giovanni Pezzulo

PLOS Computational Biology: published April 13, 2016 | https://doi.org/10.1371/journal.pcbi.1004864

Maximum-Entropy Models of Sequenced Immune Repertoires Predict Antigen-Antibody Affinity

Lorenzo Asti, Guido Uguzzoni, Paolo Marcatili, Andrea Pagnani

PLOS Computational Biology: published April 13, 2016 | https://doi.org/10.1371/journal.pcbi.1004870

Quorum Sensing Desynchronization Leads to Bimodality and Patterned Behaviors

David N. Quan, Chen-Yu Tsao, Hsuan-Chen Wu, William E. Bentley

PLOS Computational Biology: published April 12, 2016 | https://doi.org/10.1371/journal.pcbi.1004781

Traveling Pulses for a Two-Species Chemotaxis Model

Casimir Emako, Charlène Gayrard, Axel Buguin, Luís Neves de Almeida, Nicolas Vauchelet

PLOS Computational Biology: published April 12, 2016 | https://doi.org/10.1371/journal.pcbi.1004843

Fast and Accurate Learning When Making Discrete Numerical Estimates

Adam N. Sanborn, Ulrik R. Beierholm

PLOS Computational Biology: published April 12, 2016 | https://doi.org/10.1371/journal.pcbi.1004859

Molecular Infectious Disease Epidemiology: Survival Analysis and Algorithms Linking Phylogenies to Transmission Trees

Eben Kenah, Tom Britton, M. Elizabeth Halloran, Ira M. Longini Jr

PLOS Computational Biology: published April 12, 2016 | https://doi.org/10.1371/journal.pcbi.1004869

Computational and Empirical Studies Predict Mycobacterium tuberculosis-Specific T Cells as a Biomarker for Infection Outcome

Simeone Marino, Hannah P. Gideon, Chang Gong, Shawn Mankad, John T. McCrone, Philana Ling Lin, Jennifer J. Linderman, JoAnne L. Flynn, Denise E. Kirschner

PLOS Computational Biology: published April 11, 2016 | https://doi.org/10.1371/journal.pcbi.1004804

A Robust Feedforward Model of the Olfactory System

Yilun Zhang, Tatyana O. Sharpee

PLOS Computational Biology: published April 11, 2016 | https://doi.org/10.1371/journal.pcbi.1004850

A Theoretical Model of Jigsaw-Puzzle Pattern Formation by Plant Leaf Epidermal Cells

Takumi Higaki, Natsumaro Kutsuna, Kae Akita, Hisako Takigawa-Imamura, Kenji Yoshimura, Takashi Miura

PLOS Computational Biology: published April 7, 2016 | https://doi.org/10.1371/journal.pcbi.1004833

A Knowledge-Based System for Display and Prediction of O-Glycosylation Network Behaviour in Response to Enzyme Knockouts

Andrew G. McDonald, Keith F. Tipton, Gavin P. Davey

PLOS Computational Biology: published April 7, 2016 | https://doi.org/10.1371/journal.pcbi.1004844

Dynamics of Cell Ensembles on Adhesive Micropatterns: Bridging the Gap between Single Cell Spreading and Collective Cell Migration

Philipp J. Albert, Ulrich S. Schwarz

PLOS Computational Biology: published April 7, 2016 | https://doi.org/10.1371/journal.pcbi.1004863

Learning Pitch with STDP: A Computational Model of Place and Temporal Pitch Perception Using Spiking Neural Networks

Nafise Erfanian Saeedi, Peter J. Blamey, Anthony N. Burkitt, David B. Grayden

PLOS Computational Biology: published April 6, 2016 | https://doi.org/10.1371/journal.pcbi.1004860

Cache Domains That are Homologous to, but Different from PAS Domains Comprise the Largest Superfamily of Extracellular Sensors in Prokaryotes

Amit A. Upadhyay, Aaron D. Fleetwood, Ogun Adebali, Robert D. Finn, Igor B. Zhulin

PLOS Computational Biology: published April 6, 2016 | https://doi.org/10.1371/journal.pcbi.1004862

Detecting Presymptomatic Infection Is Necessary to Forecast Major Epidemics in the Earliest Stages of Infectious Disease Outbreaks

Robin N. Thompson, Christopher A. Gilligan, Nik J. Cunniffe

PLOS Computational Biology: published April 5, 2016 | https://doi.org/10.1371/journal.pcbi.1004836

Cover

Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics

Topic Page

Review

Research Articles

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