Computer & Information Sciences

Macromolecular Structure and Dynamics

Published June 8, 2016 Curated Collections

In this collection of newly published research articles, Ruth Nussinov (Editor-in-Chief) and Amarda Shehu (George Mason University, USA) highlight some of the latest advancements in computational treatments of macromolecules focusing upon recent computational methods investigating various aspects of the relationship between macromolecular structure, dynamics, and function. Through this the editors hope to convey and celebrate the tremendous progress that computational structural biology has made over the last two decades.

Image Credit: Wahle and Wriggers (pcbi.1004516)

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From the blogs
Editorial
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From the blogs

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Wahle and Wriggers (pcbi.1004516)

Biologue The PLOS Comp Biol Macromolecular Structure and Dynamics Collection
October 27, 2015 Ruth Nussinov, Amarda Shehu

Editorial

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Wriggers et al. (pcbi.1004516)

PLOS Computational Biology Computational Methods for Exploration and Analysis of Macromolecular Structure and Dynamics
October 27, 2015 Amarda Shehu, Ruth Nussinov

Research

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10.1371/journal.pcbi.1004611

PLOS Computational Biology Unbiased Rare Event Sampling in Spatial Stochastic Systems Biology Models Using a Weighted Ensemble of Trajectories
February 4, 2016 Rory M. Donovan, Jose-Juan Tapia, Devin P. Sullivan, James R. Faeder, Robert F. Murphy, Markus Dittrich, Daniel M. Zuckerman
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pcbi.1004368

PLOS Computational Biology Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments
October 27, 2015 Rong Shen, Wei Han, Giacomo Fiorin, Shahid Islam, Klaus Schulten, Benoît Roux
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10.1371/journal.pcbi.1004469

PLOS Computational Biology pMD-Membrane: A Method for Ligand Binding Site Identification in Membrane-Bound Proteins
October 27, 2015 Priyanka Prakash, Abdallah Sayyed-Ahmad, Alemayehu Gorfe
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10.1371/journal.pcbi.1004507

PLOS Computational Biology Exposing Hidden Alternative Backbone Conformations in X-ray Crystallography Using qFit
October 27, 2015 Daniel Keedy, James Fraser, Henry van den Bedem
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10.1371/journal.pcbi.1004461

PLOS Computational Biology DynaFace: Discrimination between Obligatory and Non-obligatory Protein-Protein Interactions Based on the Complex’s Dynamics
October 27, 2015 Seren Soner, Pemra Ozbek, Jose Ignacio Garzon, Nir Ben-Tal, Turkan Haliloglu
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10.1371/journal.pcbi.1004341

PLOS Computational Biology Conformational Dynamics and Binding Free Energies of Inhibitors of BACE-1: From the Perspective of Protonation Equilibria
October 27, 2015 M Kim, Patrick Blachly, J McCammon
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10.1371/journal.pcbi.1004494

PLOS Computational Biology Predicting the Effect of Mutations on Protein-Protein Binding Interactions through Structure-Based Interface Profiles
October 27, 2015 Jeffrey Brender, Yang Zhang
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10.1371/journal.pcbi.1004480

PLOS Computational Biology A Virtual Mixture Approach to the Study of Multistate Equilibrium: Application to Constant pH Simulation in Explicit Water
October 27, 2015 Xiongwu Wu, Bernard Brooks
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10.1371/journal.pcbi.1004516

PLOS Computational Biology Multi-scale Visualization of Molecular Architecture Using Real-Time Ambient Occlusion in Sculptor
October 27, 2015 Manuel Wahle, Willy Wriggers
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10.1371/journal.pcbi.1004415

PLOS Computational Biology ENCORE: Software for Quantitative Ensemble Comparison
October 27, 2015 Matteo Tiberti, Elena Papaleo, Tone Bengtsen, Wouter Boomsma, Kresten Lindorff-Larsen
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pcbi.1004359

PLOS Computational Biology ApoE4-specific Misfolded Intermediate Identified by Molecular Dynamics Simulations
October 27, 2015 Benfeard Williams II, Marino Convertino, Jhuma Das, Nikolay Dokholyan
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pcbi.1004381

PLOS Computational Biology Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning
October 27, 2015 Lane Votapka, Rommie Amaro
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10.1371/journal.pcbi.1004435

PLOS Computational Biology Mapping the Protein Fold Universe Using the CamTube Force Field in Molecular Dynamics Simulations
October 27, 2015 Predrag Kukic, Arvind Kannan, Maurits Dijkstra, Sanne Abeln, Carlo Camilloni, Michele Vendruscolo
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10.1371/journal.pcbi.1004470

PLOS Computational Biology Mapping the Conformation Space of Wildtype and Mutant H-Ras with a Memetic, Cellular, and Multiscale Evolutionary Algorithm
September 1, 2015 Rudy Clausen, Buyong Ma, Ruth Nussinov, Amarda Shehu

Collection Editors

The Collection Editors are Ruth Nussinov, Tel Aviv University and Amarda Shehu, George Mason University.

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