OpenAlex is a bibliographic catalogue of scientific papers, authors and institutions accessible in open access mode, named after the Library of Alexandria. It's citation coverage is excellent and I hope you will find utility in this listing of citing articles!
If you click the article title, you'll navigate to the article, as listed in CrossRef. If you click the Open Access links, you'll navigate to the "best Open Access location". Clicking the citation count will open this listing for that article. Lastly at the bottom of the page, you'll find basic pagination options.
Requested Article:
Pragmatic Coarse-Graining of Proteins: Models and Applications
Luís Borges-Araújo, Ilias Patmanidis, Akhil Pratap Singh, et al.
Journal of Chemical Theory and Computation (2023) Vol. 19, Iss. 20, pp. 7112-7135
Open Access | Times Cited: 46
Luís Borges-Araújo, Ilias Patmanidis, Akhil Pratap Singh, et al.
Journal of Chemical Theory and Computation (2023) Vol. 19, Iss. 20, pp. 7112-7135
Open Access | Times Cited: 46
Showing 1-25 of 46 citing articles:
GōMartini 3: From large conformational changes in proteins to environmental bias corrections
Paulo C. T. Souza, Luís Borges-Araújo, Chris Brasnett, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2024)
Open Access | Times Cited: 20
Paulo C. T. Souza, Luís Borges-Araújo, Chris Brasnett, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2024)
Open Access | Times Cited: 20
A coarse‐grained model for disordered and multi‐domain proteins
Fan Cao, Sören von Bülow, Giulio Tesei, et al.
Protein Science (2024) Vol. 33, Iss. 11
Open Access | Times Cited: 16
Fan Cao, Sören von Bülow, Giulio Tesei, et al.
Protein Science (2024) Vol. 33, Iss. 11
Open Access | Times Cited: 16
Implementation of Time-Averaged Restraints with UNRES Coarse-Grained Model of Polypeptide Chains
Nguyen Truong Co, Cezary Czaplewski, Emilia A. Lubecka, et al.
Journal of Chemical Theory and Computation (2025)
Open Access | Times Cited: 2
Nguyen Truong Co, Cezary Czaplewski, Emilia A. Lubecka, et al.
Journal of Chemical Theory and Computation (2025)
Open Access | Times Cited: 2
Chemically Informed Coarse-Graining of Electrostatic Forces in Charge-Rich Biomolecular Condensates
Andrés R. Tejedor, Anne Aguirre Gonzalez, Maria Julia Maristany, et al.
ACS Central Science (2025) Vol. 11, Iss. 2, pp. 302-321
Open Access | Times Cited: 2
Andrés R. Tejedor, Anne Aguirre Gonzalez, Maria Julia Maristany, et al.
ACS Central Science (2025) Vol. 11, Iss. 2, pp. 302-321
Open Access | Times Cited: 2
Martini3-IDP: improved Martini 3 force field for disordered proteins
Liguo Wang, Christopher Brasnett, Luís Borges-Araújo, et al.
Nature Communications (2025) Vol. 16, Iss. 1
Open Access | Times Cited: 2
Liguo Wang, Christopher Brasnett, Luís Borges-Araújo, et al.
Nature Communications (2025) Vol. 16, Iss. 1
Open Access | Times Cited: 2
OLIVES: A Go̅-like Model for Stabilizing Protein Structure via Hydrogen Bonding Native Contacts in the Martini 3 Coarse-Grained Force Field
Kasper B. Pedersen, Luís Borges-Araújo, Amanda D. Stange, et al.
Journal of Chemical Theory and Computation (2024)
Open Access | Times Cited: 12
Kasper B. Pedersen, Luís Borges-Araújo, Amanda D. Stange, et al.
Journal of Chemical Theory and Computation (2024)
Open Access | Times Cited: 12
Assessing the Martini 3 protein model: A review of its path and potential
Luís Borges-Araújo, Gilberto P. Pereira, Mariana Valério, et al.
Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics (2024) Vol. 1872, Iss. 4, pp. 141014-141014
Closed Access | Times Cited: 11
Luís Borges-Araújo, Gilberto P. Pereira, Mariana Valério, et al.
Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics (2024) Vol. 1872, Iss. 4, pp. 141014-141014
Closed Access | Times Cited: 11
A coarse-grained model for disordered and multi-domain proteins
Fan Cao, Sören von Bülow, Giulio Tesei, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2024)
Open Access | Times Cited: 10
Fan Cao, Sören von Bülow, Giulio Tesei, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2024)
Open Access | Times Cited: 10
Computational Methods for Modeling Lipid-Mediated Active Pharmaceutical Ingredient Delivery
Markéta Paloncýová, Mariana Valério, Ricardo Nascimento dos Santos, et al.
Molecular Pharmaceutics (2025)
Open Access | Times Cited: 1
Markéta Paloncýová, Mariana Valério, Ricardo Nascimento dos Santos, et al.
Molecular Pharmaceutics (2025)
Open Access | Times Cited: 1
A Practical Guide to All-Atom and Coarse-Grained Molecular Dynamics Simulations Using Amber and Gromacs: A Case Study of Disulfide-Bond Impact on the Intrinsically Disordered Amyloid Beta
Pamela Smardz, Midhun Mohan Anila, R.E. Pawel, et al.
International Journal of Molecular Sciences (2024) Vol. 25, Iss. 12, pp. 6698-6698
Open Access | Times Cited: 5
Pamela Smardz, Midhun Mohan Anila, R.E. Pawel, et al.
International Journal of Molecular Sciences (2024) Vol. 25, Iss. 12, pp. 6698-6698
Open Access | Times Cited: 5
Multi-GPU UNRES for scalable coarse-grained simulations of very large protein systems
Krzysztof M. Ocetkiewicz, Cezary Czaplewski, Henryk Krawczyk, et al.
Computer Physics Communications (2024) Vol. 298, pp. 109112-109112
Open Access | Times Cited: 4
Krzysztof M. Ocetkiewicz, Cezary Czaplewski, Henryk Krawczyk, et al.
Computer Physics Communications (2024) Vol. 298, pp. 109112-109112
Open Access | Times Cited: 4
All-Atom Biomolecular Simulation in the Exascale Era
Thomas L. Beck, Paolo Carloni, D. Asthagiri
Journal of Chemical Theory and Computation (2024) Vol. 20, Iss. 5, pp. 1777-1782
Closed Access | Times Cited: 4
Thomas L. Beck, Paolo Carloni, D. Asthagiri
Journal of Chemical Theory and Computation (2024) Vol. 20, Iss. 5, pp. 1777-1782
Closed Access | Times Cited: 4
A Neural-Network-Based Mapping and Optimization Framework for High-Precision Coarse-Grained Simulation
Zhixuan Zhong, Lifeng Xu, Jian Jiang
Journal of Chemical Theory and Computation (2025)
Open Access
Zhixuan Zhong, Lifeng Xu, Jian Jiang
Journal of Chemical Theory and Computation (2025)
Open Access
UNRES web server: extensions to nucleic acids, prediction of peptide aggregation, and new types of restrained calculations
Rafał Ślusarz, Adam K. Sieradzan, Artur Giełdoń, et al.
Journal of Molecular Biology (2025), pp. 168968-168968
Closed Access
Rafał Ślusarz, Adam K. Sieradzan, Artur Giełdoń, et al.
Journal of Molecular Biology (2025), pp. 168968-168968
Closed Access
Unveiling nucleosome dynamics: A comparative study using all-atom and coarse-grained simulations enhanced by principal component analysis
Abhik Ghosh Moulick, Rutika Patel, Augustine C. Onyema, et al.
The Journal of Chemical Physics (2025) Vol. 162, Iss. 6
Open Access
Abhik Ghosh Moulick, Rutika Patel, Augustine C. Onyema, et al.
The Journal of Chemical Physics (2025) Vol. 162, Iss. 6
Open Access
Unraveling internal friction in a coarse-grained protein model
Carlos Monago, J. A. de la Torre, Rafael Delgado‐Buscalioni, et al.
The Journal of Chemical Physics (2025) Vol. 162, Iss. 11
Closed Access
Carlos Monago, J. A. de la Torre, Rafael Delgado‐Buscalioni, et al.
The Journal of Chemical Physics (2025) Vol. 162, Iss. 11
Closed Access
Challenges in simulating whole virus particles and how to fix them with the SIRAH force field
Lucianna Helene Santos, Sergio Pantano
Biophysical Reviews (2025)
Closed Access
Lucianna Helene Santos, Sergio Pantano
Biophysical Reviews (2025)
Closed Access
CGsmiles: A Versatile Line Notation for Molecular Representations across Multiple Resolutions
Fabian Grünewald, Leif Seute, Riccardo Alessandri, et al.
Journal of Chemical Information and Modeling (2025)
Closed Access
Fabian Grünewald, Leif Seute, Riccardo Alessandri, et al.
Journal of Chemical Information and Modeling (2025)
Closed Access
MartiniGlass: a Tool for Enabling Visualization of Coarse-Grained Martini Topologies
Christopher Brasnett, Siewert J. Marrink
Journal of Chemical Information and Modeling (2025)
Open Access
Christopher Brasnett, Siewert J. Marrink
Journal of Chemical Information and Modeling (2025)
Open Access
Characterizing the Sequence Landscape of Peptide Fibrillization with a Bottom-Up Coarse-Grained Model
Evan Pretti, M. Scott Shell
The Journal of Physical Chemistry B (2025)
Closed Access
Evan Pretti, M. Scott Shell
The Journal of Physical Chemistry B (2025)
Closed Access
The tubular cavity of tobacco mosaic virus shields mechanical stress and regulates disassembly
Alejandro Díez-Martínez, Pablo Ibáñez‐Freire, Rafael Delgado‐Buscalioni, et al.
Acta Biomaterialia (2025)
Closed Access
Alejandro Díez-Martínez, Pablo Ibáñez‐Freire, Rafael Delgado‐Buscalioni, et al.
Acta Biomaterialia (2025)
Closed Access
Accurate coarse grained models for protein association and recognition
Agustí Emperador, E. Guàrdia
Advances in protein chemistry and structural biology (2025)
Closed Access
Agustí Emperador, E. Guàrdia
Advances in protein chemistry and structural biology (2025)
Closed Access
Building complex membranes with Martini 3
Tuğba N. Öztürk, Melanie König, Timothy S. Carpenter, et al.
Methods in enzymology on CD-ROM/Methods in enzymology (2024), pp. 237-285
Closed Access | Times Cited: 3
Tuğba N. Öztürk, Melanie König, Timothy S. Carpenter, et al.
Methods in enzymology on CD-ROM/Methods in enzymology (2024), pp. 237-285
Closed Access | Times Cited: 3
OLIVES: A Go-like Model for Stabilizing Protein Structure via Hydrogen Bonding Native Contacts in the Martini 3 Coarse-Grained Force Field
Kasper B. Pedersen, Luís Borges-Araújo, Amanda D. Stange, et al.
(2023)
Open Access | Times Cited: 7
Kasper B. Pedersen, Luís Borges-Araújo, Amanda D. Stange, et al.
(2023)
Open Access | Times Cited: 7
SIRAH Late Harvest: Coarse-Grained Models for Protein Glycosylation
Pablo Garay, Matías Machado, Hugo Verli, et al.
Journal of Chemical Theory and Computation (2024) Vol. 20, Iss. 2, pp. 963-976
Open Access | Times Cited: 2
Pablo Garay, Matías Machado, Hugo Verli, et al.
Journal of Chemical Theory and Computation (2024) Vol. 20, Iss. 2, pp. 963-976
Open Access | Times Cited: 2
