EDITORIAL: Chemical Compound Space Exploration by Multiscale High-Throughput Screening and Machine Learning

Ganna Gryn’ova, Tristan Bereau, Carolin Müller, Pascal Friederich, Rebecca C. Wade, Ariane Nunes-Alves, Thereza A. Soares, Kenneth Jr. Merz

Journal of Chemical Information and Modeling, vol. 64, 2024, pp. 5737-5738

Characterization of the Bottlenecks and Pathways for Inhibitor Dissociation from [NiFe] Hydrogenase

Farzin Sohraby, Ariane Nunes-Alves

Journal of Chemical Information and Modeling, vol. 64, 2024, pp. 4193-4203

pH-dependence of the Plasmodium falciparum chloroquine resistance transporter is linked to the transport cycle

Fiona Berger, Guillermo M. Gomez, Cecilia P. Sanchez, Britta Posch, Gabrielle Planelles, Farzin Sohraby, Ariane Nunes-Alves, Michael Lanzer

Nature Communications, 2023

Advances in computational methods for ligand binding kinetics

Farzin Sohraby, Ariane Nunes-Alves

Trends in Biochemical Sciences, 2023

AlphaFold2 in Molecular Discovery

Ariane Nunes-Alves, Kenneth Merz

Journal of Chemical Information and Modeling, vol. 63, 2023, pp. 5947-5949

Molecular characterization of AIFM2/FSP1 inhibition by iFSP1-like molecules

T. N. Xavier da Silva, Clemens Schulte, Ariane Nunes-Alves, H. Maric, José Pedro Friedmann Angeli

Cell Death and Disease, 2023

Diffusion of small molecule drugs is affected by surface interactions and crowder proteins

Debabrata Dey, Ariane Nunes-Alves, Rebecca C. Wade, Gideon Schreiber

iScience, vol. 25, 2022, p. 105088

The Non-phosphorylating Glyceraldehyde-3-Phosphate Dehydrogenase GapN Is a Potential New Drug Target in Streptococcus pyogenes

Philip Eisenberg, Leon Albert, Jonathan Teuffel, Eric Zitzow, Claudia Michaelis, Jane Jarick, Clemens Sehlke, Lisa Große, Nicole Bader, Ariane Nunes-Alves, Bernd Kreikemeyer, Hermann Schindelin, Rebecca C. Wade, Tomas Fiedler

Frontiers in Microbiology, vol. 13, 2022

The (Re)-Evolution of Quantitative Structure–Activity Relationship (QSAR) Studies Propelled by the Surge of Machine Learning Methods

Thereza A. Soares, Ariane Nunes-Alves, Angelica Mazzolari, Fiorella Ruggiu, Guo-Wei Wei, Kenneth Merz

Journal of Chemical Information and Modeling, vol. 62, 2022, pp. 5317-5320

Structure-kinetic relationship reveals the mechanism of selectivity of FAK inhibitors over PYK2

Benedict-Tilman Berger, Marta Amaral, Daria B. Kokh, Ariane Nunes-Alves, Djordje Musil, Timo Heinrich, Martin Schröder, Rebecca Neil, Jing Wang, Iva Navratilova, Joerg Bomke, Jonathan M. Elkins, Susanne Müller, Matthias Frech, Rebecca C. Wade, Stefan Knapp

Cell Chemical Biology, 2021

Line-FRAP, A Versatile Method to Measure Diffusion Rates In Vitro and In Vivo

Debabrata Dey, Shir Marciano, Ariane Nunes-Alves, Vladimir Kiss, Rebecca C. Wade, Gideon Schreiber

Journal of Molecular Biology, vol. 433, 2021, p. 166898

A Protocol to Use Comparative Binding Energy Analysis to Estimate Drug-Target Residence Time

Gaurav K Ganotra, Ariane Nunes-Alves, Rebecca C Wade

Methods in molecular biology (Clifton, N.J.), vol. 2266, 2021, pp. 171—186

Ligand Unbinding Mechanisms and Kinetics for T4 Lysozyme Mutants from τRAMD Simulations

Ariane Nunes-Alves, Daria B. Kokh, Rebecca C. Wade

Current Research in Structural Biology, vol. 3, 2021, pp. 106-111

Prediction of the Drug–Target Binding Kinetics for Flexible Proteins by Comparative Binding Energy Analysis

Ariane Nunes-Alves, Fabian Ormersbach, Rebecca C. Wade

Journal of Chemical Information and Modeling, vol. 61, 2021, pp. 3708-3721

Molecular Dynamics Simulations in Drug Discovery and Pharmaceutical Development

Outi M. H. Salo-Ahen, Ida Alanko, Rajendra Bhadane, Alexandre M. J. J. Bonvin, Rodrigo Vargas Honorato, Shakhawath Hossain, André H. Juffer, Aleksei Kabedev, Maija Lahtela-Kakkonen, Anders Støttrup Larsen, Eveline Lescrinier, Parthiban Marimuthu, Muhammad Usman Mirza, Ghulam Mustafa, Ariane Nunes-Alves, Tatu Pantsar, Atefeh Saadabadi, Kalaimathy Singaravelu, Michiel Vanmeert

Processes, vol. 9, 2021

Impact of the Journal of Chemical Information and Modeling Special Issue on Women in Computational Chemistry

Angelica Mazzolari, Ariane Nunes-Alves, Habibah A. Wahab, Rommie E. Amaro, Zoe Cournia, Kenneth M. Merz

Journal of Chemical Information and Modeling, vol. 60, 2020, pp. 3328-3330

From Brazil to Germany: Challenges and Advantages

Ariane Nunes-Alves

Journal of Chemical Information and Modeling, vol. 60, 2020, pp. 449-451

Recent progress in molecular simulation methods for drug binding kinetics

Ariane Nunes-Alves, Daria B Kokh, Rebecca C Wade

Current Opinion in Structural Biology, vol. 64, 2020, pp. 126 - 133

What Makes a Paper Be Highly Cited? 60 Years of the Journal of Chemical Information and Modeling

Ariane Nunes-Alves, Angelica Mazzolari, Kenneth M. Merz

Journal of Chemical Information and Modeling, vol. 60, 2020, pp. 5866-5867

Myotubularin-related protein 7 activates peroxisome proliferator-activated receptor-gamma

Philip Weidner, Michaela Söhn, Torsten Schroeder, Laura Helm, Veronika Hauber, Tobias Gutting, Johannes Betge, Christoph Röcken, Florian N. Rohrbacher, Vijaya R. Pattabiraman, Jeffrey W. Bode, Rony Seger, Daniel Saar, Ariane Nunes-Alves, Rebecca C. Wade, Matthias P. A. Ebert, Elke Burgermeister

Oncogenesis, vol. 9, 2020, p. 59

Structural characterization of an Arf dimer interface: molecular mechanism of Arf-dependent membrane scission

Petra Diestelkoetter‐Bachert, Rainer Beck, Inge Reckmann, Andrea Hellwig, Ana Garcia‐Saez, Monika Zelman‐Hopf, Anton Hanke, Ariane Nunes Alves, Rebecca C. Wade, Rebecca C. Wade, Matthias P. Mayer, Felix Wieland

FEBS Letters, vol. 594(14), 2020 Jun 1, pp. 2240-2253

Mechanical Unfolding of Macromolecules Coupled to Bond Dissociation

Ariane Nunes-Alves, Guilherme Menegon Arantes

Journal of Chemical Theory and Computation, vol. 14, 2018, pp. 282-290

Escape of a Small Molecule from Inside T4 Lysozyme by Multiple Pathways

Ariane Nunes-Alves, Daniel M. Zuckerman, Guilherme Menegon Arantes

Biophysical Journal, vol. 114, 2018, pp. 1058-1066

Ligand–Receptor Affinities Computed by an Adapted Linear Interaction Model for Continuum Electrostatics and by Protein Conformational Averaging

Ariane Nunes-Alves, Guilherme Menegon Arantes

Journal of Chemical Information and Modeling, vol. 54, 2014, pp. 2309-2319

Neurotransmitters as Main Players in the Neural Differentiation and Fate Determination Game

K. Yuahasi, K. N. Gomes, M. Campos, A. A. Nery, Ariane Nunes Alves, C. Trujillo, H. Ulrich

2010