Reaction-field electrostatics in molecular dynamics simulations: development of a conservative scheme compatible with an atomic cutoff

Alžbeta Kubincová, Sereina Riniker and Philippe H. Hünenberger

Phys. Chem. Chem. Phys., 2020, 22, 26419
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Molecular Graphics: Bridging Structural Biologists and Computer Scientists

Xavier Martinez, Michael Krone, Naif Alharbi, Alexander S. Rose, Robert S. Laramee, Sean O'Donoghue, Marc Baaden and Matthieu Chavent

Structure, 2019, 27, 1617
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Trends & Opportunities in Visualization for Physiology: A Multiscale Overview

Laura A. Garrison, Ivan Kolesar, Ivan Viola, Helwig Hauser and Stefan Bruckner

Computer Graphics Forum, 2022, 41, 609
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Effects of site-directed mutagenesis of L469 in helix-5 of human papillomavirus 16 L1 on pentamer formation

Dong Pan, Lincong Wang, Meiyi Liu, Shi Jin, Liyan Wang, Xianghui Yu, Xiao Zha and Yuqing Wu

Chem. Res. Chin. Univ., 2017, 33, 392
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Bringing chemical structures to life with augmented reality, machine learning, and quantum chemistry

Sukolsak Sakshuwong, Hayley Weir, Umberto Raucci and Todd J. Martínez

The Journal of Chemical Physics, 2022, 156
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Protein flexibility in the light of structural alphabets

Pierrick Craveur, Agnel P. Joseph, Jeremy Esque, Tarun J. Narwani, Floriane NoÃ«l, Nicolas Shinada, Matthieu Goguet, Sylvain Leonard, Pierre Poulain, Olivier Bertrand, Guilhem Faure, Joseph Rebehmed, Amine Ghozlane, Lakshmipuram S. Swapna, Ramachandra M. Bhaskara, Jonathan Barnoud, StÃ©phane TÃ©letchÃ©a, Vincent Jallu, Jiri Cerny, Bohdan Schneider, Catherine Etchebest, Narayanaswamy Srinivasan, Jean-Christophe Gelly and Alexandre G. de Brevern

Front. Mol. Biosci., 2015, 2
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MoSDeF-dihedral-fit: A lightweight software for fitting dihedrals within MoSDeF

Brad Crawford, Co D. Quach, Nicholas C. Craven, Christopher R. Iacovella, Clare McCabe, Peter T. Cummings and Jeffrey J. Potoff

JOSS, 2024, 9, 6970
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Comparison of the United- and All-Atom Representations of (Halo)alkanes Based on Two Condensed-Phase Force Fields Optimized against the Same Experimental Data Set

Marina P. Oliveira, Yan M. H. Gonçalves, S. Kashef Ol Gheta, Salomé R. Rieder, Bruno A. C. Horta and Philippe H. Hünenberger

J. Chem. Theory Comput., 2022, 18, 6757
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Visualizing Biological Membrane Organization and Dynamics

Marc Baaden

Journal of Molecular Biology, 2019, 431, 1889
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Bringing Molecular Dynamics Simulation Data into View

Peter W. Hildebrand, Alexander S. Rose and Johanna K.S. Tiemann

Trends in Biochemical Sciences, 2019, 44, 902
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An animated visualization of orbital angular momentum and spin‐orbit coupling

James R. Asher

Int J of Quantum Chemistry, 2018, 118
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Influence of the Lennard-Jones Combination Rules on the Simulated Properties of Organic Liquids at Optimal Force-Field Parametrization

Marina P. Oliveira and Philippe H. Hünenberger

J. Chem. Theory Comput., 2023, 19, 2048
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Applications of in Silico Methods for Design and Development of Drugs Targeting Protein-Protein Interactions

Vittoria Cicaloni, Alfonso Trezza, Francesco Pettini and Ottavia Spiga

CTMC, 2019, 19, 534
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Semantics for an Integrative and Immersive Pipeline Combining Visualization and Analysis of Molecular Data

Mikael Trellet, Nicolas Férey, Jakub Flotyński, Marc Baaden and Patrick Bourdot

Journal of Integrative Bioinformatics, 2018, 15
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MoleculARweb: A Web Site for Chemistry and Structural Biology Education through Interactive Augmented Reality out of the Box in Commodity Devices

Fabio Cortés Rodríguez, Gianfranco Frattini, Lucien F. Krapp, Hassan Martinez-Hung, Diego M. Moreno, Mariana Roldán, Jorge Salomón, Lee Stemkoski, Sylvain Traeger, Matteo Dal Peraro and Luciano A. Abriata

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Temporally Coherent Backmapping of Molecular Trajectories From Coarse-Grained to Atomistic Resolution

Kirill Shmilovich, Marc Stieffenhofer, Nicholas E. Charron and Moritz Hoffmann

J. Phys. Chem. A, 2022, 126, 9124
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Computational design, fabrication and evaluation of rubber protein models

Thomas Alderighi, Daniela Giorgi, Luigi Malomo, Paolo Cignoni and Monica Zoppè

Computers & Graphics, 2021, 98, 177
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Diving into chemical bonding: An immersive analysis of the electron charge rearrangement through virtual reality

Andrea Salvadori, Marco Fusè, Giordano Mancini, Sergio Rampino and Vincenzo Barone

J Comput Chem, 2018, 39, 2607
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Girsanov Reweighting Enhanced Sampling Technique (GREST): On-the-Fly Data-Driven Discovery of and Enhanced Sampling in Slow Collective Variables

Kirill Shmilovich and Andrew L. Ferguson

J. Phys. Chem. A, 2023, 127, 3497
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Evaluating Classical Force Fields against Experimental Cross-Solvation Free Energies

Sadra Kashefolgheta, Marina P. Oliveira, Salomé R. Rieder, Bruno A. C. Horta, William E. Acree and Philippe H. Hünenberger

J. Chem. Theory Comput., 2020, 16, 7556
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Immersive virtual reality in computational chemistry: Applications to the analysis of QM and MM data

Andrea Salvadori, Gianluca Del Frate, Marco Pagliai, Giordano Mancini and Vincenzo Barone

Int J of Quantum Chemistry, 2016, 116, 1731
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Seeing the unseen: Comparison study of representation approaches for biochemical processes in education

Hana Pokojná, Barbora Kozlíková, Drew Berry, Simone Kriglstein, Katarína Furmanová and Anastassia Zabrodskaja

PLoS ONE, 2023, 18, e0293592
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Accuracy and Interpretability: The Devil and the Holy Grail. New Routes across Old Boundaries in Computational Spectroscopy

Cristina Puzzarini, Julien Bloino, Nicola Tasinato and Vincenzo Barone

Chem. Rev., 2019, 119, 8131
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Building blocks for commodity augmented reality-based molecular visualization and modeling in web browsers

Luciano A. Abriata

PeerJ Computer Science, 2020, 6, e260
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Systematic Optimization of a Fragment-Based Force Field against Experimental Pure-Liquid Properties Considering Large Compound Families: Application to Saturated Haloalkanes

Marina P. Oliveira, Maurice Andrey, Salomé R. Rieder, Leyla Kern, David F. Hahn, Sereina Riniker, Bruno A. C. Horta and Philippe H. Hünenberger

J. Chem. Theory Comput., 2020, 16, 7525
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