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Computational complexity, algorithmic scope, and evolution
Leonhard Sidl, Maximilian Faissner, Manuel Uhlir, Cristian A Velandia-Huerto, Maria Waldl, Hua-Ting Yao, Ivo L Hofacker and Peter F Stadler Journal of Physics: Complexity 6(1) 015013 (2025) https://doi.org/10.1088/2632-072X/adb928
Guilherme C. de Andrade, Michelle F. Mota, Dinarte N. Moreira-Ferreira, Jerson L. Silva, Guilherme A.P. de Oliveira and Mayra A. Marques 145 145 (2025) https://doi.org/10.1016/bs.apcsb.2024.09.010
Andrew T. Martens and Vincent J. Hilser (2025) https://doi.org/10.1101/2025.06.25.661590
How proteins manage to fold and how chaperones manage to assist the folding
Sergiy O. Garbuzynskiy, Victor V. Marchenkov, Natalia Y. Marchenko, Gennady V. Semisotnov and Alexei V. Finkelstein Physics of Life Reviews 52 66 (2025) https://doi.org/10.1016/j.plrev.2024.12.006
Predicting Protein Folding Pathways With Quadratic Constraints on Rates of Entropy Change: A Nonlinear Optimization-Based Control Approach
Protein structure prediction via deep learning: an in-depth review
Yajie Meng, Zhuang Zhang, Chang Zhou, Xianfang Tang, Xinrong Hu, Geng Tian, Jialiang Yang and Yuhua Yao Frontiers in Pharmacology 16 (2025) https://doi.org/10.3389/fphar.2025.1498662
Proteome-wide determinants of co-translational chaperone binding in bacteria
Carla Verónica Galmozzi, Frank Tippmann, Florian Wruck, Josef Johannes Auburger, Ilia Kats, Manuel Guennigmann, Katharina Till, Edward P. O´Brien, Sander J. Tans, Günter Kramer and Bernd Bukau Nature Communications 16(1) (2025) https://doi.org/10.1038/s41467-025-59067-9
Oded Agam and Erez Braun (2024) https://doi.org/10.1101/2024.05.06.592702
Base Pairing Promoted the Self-Organization of Genetic Coding, Catalysis, and Free-Energy Transduction
A Stochastic Landscape Approach for Protein Folding State Classification
Michael Faran, Dhiman Ray, Shubhadeep Nag, Umberto Raucci, Michele Parrinello and Gili Bisker Journal of Chemical Theory and Computation 20(13) 5428 (2024) https://doi.org/10.1021/acs.jctc.4c00464
Alessandra Lima da Silva, Diego Mariano, Mariana Parise, Angie L. A. Puelles, Tatiane Senna Bialves, Luana Luiza Bastos, Lucas Santos and Rafael Pereira Lemos 1 (2024) https://doi.org/10.4018/979-8-3693-3192-7.ch001
Opportunities and challenges in design and optimization of protein function
Dina Listov, Casper A. Goverde, Bruno E. Correia and Sarel Jacob Fleishman Nature Reviews Molecular Cell Biology 25(8) 639 (2024) https://doi.org/10.1038/s41580-024-00718-y
Charles W. Carter, Guo Qing Tang, Sourav Kumar Patra, Laurie Betts, Henry Dieckhaus, Brian Kuhlman, Jordan Douglas, Peter R. Wills, Remco Bouckaert, Milena Popovic and Mark Ditzler (2024) https://doi.org/10.1101/2024.12.17.628912
Entropy associated with conformational and solvent-density fluctuations in biomolecular solutions
Magnesium induced structural reorganization in the active site of adenylate kinase
Kwangho Nam, Abdul Raafik Arattu Thodika, Sonja Tischlik, Chanrith Phoeurk, Tamás Milán Nagy, Léon Schierholz, Jörgen Ådén, Per Rogne, Malte Drescher, A. Elisabeth Sauer-Eriksson and Magnus Wolf-Watz Science Advances 10(32) (2024) https://doi.org/10.1126/sciadv.ado5504
Protein Design by Integrating Machine Learning and Quantum-Encoded Optimization
Protein Structure Prediction with High Degrees of Freedom in a Gate-Based Quantum Computer
Jaya Vasavi Pamidimukkala, Soham Bopardikar, Avinash Dakshinamoorthy, Ashwini Kannan, Kalyan Dasgupta and Sanjib Senapati Journal of Chemical Theory and Computation 20(22) 10223 (2024) https://doi.org/10.1021/acs.jctc.4c00848
In the Beginning: Let Hydration Be Coded in Proteins for Manifestation and Modulation by Salts and Adenosine Triphosphate
Aplicaciones de la teoría de nudos: quilaridad y la proteína p53
Jonathan Toledo-Toledo, Dalia Elizabeth García Sánchez, Nancy Márquez Lázaro and Adrián López Antonio REVISTA IPSUMTEC 6(4) 114 (2023) https://doi.org/10.61117/ipsumtec.v6i4.271
Protein Structure Prediction: Challenges, Advances, and the Shift of Research Paradigms
In silico
identification and characterization of potential druggable targets among hypothetical proteins of
Leptospira interrogans
serovar Copenhageni: a comprehensive bioinformatics approach
Quratulain Siddiqui, Mohd Shukuri Mohd Ali, Adam Thean Chor Leow, Siti Nurbaya Oslan and Fairolniza Mohd Shariff Journal of Biomolecular Structure and Dynamics 41(20) 10347 (2023) https://doi.org/10.1080/07391102.2022.2154845
How does a biopolymer (protein) fold into a unique 3D structure?
Protein folding quantum circuit quantum circuit for bio material modelling compression
M. O. Lisnchenko and S. I. Protasov Izvestiya Vysshikh Uchebnykh Zavedenii. Materialy Elektronnoi Tekhniki = Materials of Electronics Engineering 25(4) 305 (2023) https://doi.org/10.17073/1609-3577-2022-4-305-311
Advanced Spectroscopic Methods to Study Biomolecular Structure and Dynamics
Niharika Nag, Santanu Sasidharan, Prakash Saudagar and Timir Tripathi Advanced Spectroscopic Methods to Study Biomolecular Structure and Dynamics 1 (2023) https://doi.org/10.1016/B978-0-323-99127-8.00002-7
How Does a Biopolymer (Protein) Fold into a Unique 3D Structure?
Molecular basis of structural stability of Irisin: A combined molecular dynamics simulation and in vitro studies for Urea-induced denaturation
Rashid Waseem, Neetu Singh Yadav, Tanzeel Khan, Faizan Ahmad, Syed Naqui Kazim, Md Imtaiyaz Hassan, Amresh Prakash and Asimul Islam Journal of Molecular Liquids 372 121120 (2023) https://doi.org/10.1016/j.molliq.2022.121120
Richard Kerner’s Path Integral Approach Aims to Understand the Self-Organized Matter Agglomeration and Its Translation into the Energy Landscape Kinetics Paradigm
Hydrophobicity─A Single Parameter for the Accurate Prediction of Disordered Regions in Proteins
Nitin Kumar Singh, Pratyasha Bhardwaj and Mithun Radhakrishna Journal of Chemical Information and Modeling 63(16) 5375 (2023) https://doi.org/10.1021/acs.jcim.3c00592
Advanced Spectroscopic Methods to Study Biomolecular Structure and Dynamics
Kavya Prince, Santanu Sasidharan, Niharika Nag, Timir Tripathi and Prakash Saudagar Advanced Spectroscopic Methods to Study Biomolecular Structure and Dynamics 483 (2023) https://doi.org/10.1016/B978-0-323-99127-8.00018-0
Solvent-Induced Interactions and Forces in Protein Folding