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2025	Application of Anomaly Detection to Identify Important Features of Protein Dynamics ACS Omega Yu Yamamori, Kentaro Tomii
2025	Encyclopedia of Bioinformatics and Computational Biology Jan Brezovsky, Aaftaab Sethi, Bartłomiej Surpeta
2025	Unravelling the role of key amino acid residues of the parainfluenza fusion peptide in membrane fusion RSC Chemical Biology Mariana Valério, Carolina C. Buga, Diogo A. Mendonça, Miguel A. R. B. Castanho, Manuel N. Melo, Cláudio M. Soares, Diana Lousa, Ana Salomé Veiga
2024	Using residue interaction networks to understand protein function and evolution and to engineer new proteins Current Opinion in Structural Biology Dariia Yehorova, Bruno Di Geronimo, Michael Robinson, Peter M. Kasson, Shina C.L. Kamerlin
2024	Structural and functional premise of transport protein transthyretin in the sight of silver and zinc oxide nanoparticles through atomistic simulations Inorganica Chimica Acta Zaved Hazarika, Anupam Nath Jha
2024	Effect of Direct and Water-Mediated Interactions on the Identification of Hotspots in Biomolecular Complexes with Multiple Subsystems Journal of Chemical Information and Modeling Vladimir Sladek, Polina V. Artiushenko, Dmitri G. Fedorov
2024	The Power of Molecular Dynamics Simulations and Their Applications to Discover Cysteine Protease Inhibitors Mini-Reviews in Medicinal Chemistry Igor José dos Santos Nascimento, Joilly Nilce Santana Gomes, Jéssika de Oliveira Viana, Yvnni Maria Sales de Medeiros e Silva, Euzébio Guimarães Barbosa, Ricardo Olimpio de Moura
2024	Elucidation of bezlotoxumab binding specificity to toxin B in Clostridioides difficile Journal of Biomolecular Structure and Dynamics Kun Karnchanapandh, Chonnikan Hanpaibool, Kamonpan Sanachai, Thanyada Rungrotmongkol
2023	Protein and Peptide‐Based Nanotechnology for Enhancing Stability, Bioactivity, and Delivery of Anthocyanins Advanced Healthcare Materials Lei Zhang, Liang Yao, Feng Zhao, Alice Yu, Yueru Zhou, Qingmei Wen, Jun Wang, Tao Zheng, Pu Chen
2023	Targeting protein-protein interactions with low molecular weight and short peptide modulators: insights on disease pathways and starting points for drug discovery Expert Opinion on Drug Discovery Daniela Trisciuzzi, Bruno O. Villoutreix, Lydia Siragusa, Massimo Baroni, Gabriele Cruciani, Orazio Nicolotti
2023	Rinmaker: a fast, versatile and reliable tool to determine residue interaction networks in proteins BMC Bioinformatics Alvise Spanò, Lorenzo Fanton, Davide Pizzolato, Jacopo Moi, Francesco Vinci, Alberto Pesce, Cedrix J. Dongmo Foumthuim, Achille Giacometti, Marta Simeoni
2023	PyInteraph2 and PyInKnife2 to Analyze Networks in Protein Structural Ensembles Journal of Chemical Information and Modeling Valentina Sora, Matteo Tiberti, Ludovica Beltrame, Deniz Dogan, Shahriyar Mahdi Robbani, Joshua Rubin, Elena Papaleo
2023	Effects of Cell-Adhesive Ligand Presentation on Pentapeptide Supramolecular Assembly and Gelation: Simulations and Experiments Cells Tissues Organs Andrew T. Thede, James D. Tang, Clare E. Cocker, Liza J. Harold, Connor D. Amelung, Anna R. Kittel, Phillip A. Taylor, Kyle J. Lampe
2023	KIF—Key Interactions Finder: A program to identify the key molecular interactions that regulate protein conformational changes The Journal of Chemical Physics Rory M. Crean, Joanna S. G. Slusky, Peter M. Kasson, Shina Caroline Lynn Kamerlin
2023	Insights into structure and activity relationship of clinically mutated PER1 and PER2 class A β-lactamase enzymes Journal of Biomolecular Structure and Dynamics Vidhu Agarwal, Tara Chand Yadav, Akhilesh Tiwari, Pritish Kumar Varadwaj
2022	SenseNet, a tool for analysis of protein structure networks obtained from molecular dynamics simulations PLOS ONE Markus Schneider, Iris Antes
2022	SARS-CoV-2 variants impact RBD conformational dynamics and ACE2 accessibility Frontiers in Medical Technology Mariana Valério, Luís Borges-Araújo, Manuel N. Melo, Diana Lousa, Cláudio M. Soares
2022	Dynamics and energetics of water transport through aquaporin mutants causing nephrogenic diabetes insipidus (NDI): A molecular dynamics study Journal of Biomolecular Structure and Dynamics Hooman Hadidi, Reza Kamali, Alireza Binesh
2022	Highly Similar Sequence and Structure Yet Different Biophysical Behavior: A Computational Study of Two Triosephosphate Isomerases Journal of Chemical Information and Modeling Cecilia Chávez-García, Mikko Karttunen
2022	SINAPs: A Software Tool for Analysis and Visualization of Interaction Networks of Molecular Dynamics Simulations Journal of Chemical Information and Modeling Corentin Bedart, Nicolas Renault, Philippe Chavatte, Adeline Porcherie, Abderrahim Lachgar, Monique Capron, Amaury Farce
2022	In Silico Comparative Structural and Residue Interaction Network Analysis of MATE Efflux Proteins in P. aeruginosa and S. aureus Chemistry Africa Vandna Kumari, Shamsher S. Kanwar
2022	Siah-1-interacting protein regulates mutated huntingtin protein aggregation in Huntington’s disease models Cell & Bioscience Ewelina Latoszek, Małgorzata Wiweger, Jan Ludwiczak, Stanisław Dunin-Horkawicz, Jacek Kuznicki, Magdalena Czeredys
2021	Adjacent dimer epitope of envelope protein as an important region for Zika virus serum neutralization: a computational investigation Journal of Biomolecular Structure and Dynamics Carlos Alessandro Fuzo, Luiz Felipe Lemes de Araujo, Rafael de Souza Pontes, Patricia Martinez Évora, Rodrigo Guerino Stabeli
2021	Bcl-xL Dynamics under the Lens of Protein Structure Networks The Journal of Physical Chemistry B Valentina Sora, Dionisio Sanchez, Elena Papaleo
2021	pyProGA—A PyMOL plugin for protein residue network analysis PLOS ONE Vladimir Sladek, Yuta Yamamoto, Ryuhei Harada, Mitsuo Shoji, Yasuteru Shigeta, Vladimir Sladek
2021	MDM-TASK-web: MD-TASK and MODE-TASK web server for analyzing protein dynamics Computational and Structural Biotechnology Journal Olivier Sheik Amamuddy, Michael Glenister, Thulani Tshabalala, Özlem Tastan Bishop
2021	Investigation of the aquaporin‐2 gating mechanism with molecular dynamics simulations Proteins: Structure, Function, and Bioinformatics Hooman Hadidi, Reza Kamali, Alireza Binesh
2021	Molecular dynamics simulations and analysis for bioinformatics undergraduate students Biochemistry and Molecular Biology Education Gonçalo C. Justino, Catarina P. Nascimento, Marta C. Justino
2021	Exploring the dynamic mechanism of allosteric drug SHP099 inhibiting SHP2E69K Molecular Diversity Shan Du, Xin-hua Lu, Wei-Ya Li, Li-Peng Li, Yang-Chun Ma, Liang Zhou, Jing-Wei Wu, Ying Ma, Run-Ling Wang
2021	Molecular dynamics study of CDC25BR492L mutant causing the activity decrease of CDC25B Journal of Molecular Graphics and Modelling Hao-Xin Li, Wen-Yu Yang, Li-Peng Li, Hui Zhou, Wei-Ya Li, Ying Ma, Run-Ling Wang
2021	Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus PeerJ Mohini Yadav, Manabu Igarashi, Norifumi Yamamoto
2021	Impact of Mutation on the Structural Stability and the Conformational Landscape of Inhibitor-Resistant TEM β-Lactamase: A High-Performance Molecular Dynamics Simulation Study The Journal of Physical Chemistry B Sandip K. Mukherjee, Mandira Mukherjee, Padmaja P. Mishra
2020	In Silico Repurposing of J147 for Neonatal Encephalopathy Treatment: Exploring Molecular Mechanisms of Mutant Mitochondrial ATP Synthase Current Pharmaceutical Biotechnology Iwuchukwu A. Emmanuel, Fisayo A. Olotu, Clement Agoni, Mahmoud E.S. Soliman
2020	Integration of network models and evolutionary analysis into high-throughput modeling of protein dynamics and allosteric regulation: theory, tools and applications Briefings in Bioinformatics Zhongjie Liang, Gennady M Verkhivker, Guang Hu
2020	ANCA: A Web Server for Amino Acid Networks Construction and Analysis Frontiers in Molecular Biosciences Wenying Yan, Chunjiang Yu, Jiajia Chen, Jianhong Zhou, Bairong Shen
2020	Dynamics, a Powerful Component of Current and Future in Silico Approaches for Protein Design and Engineering International Journal of Molecular Sciences Bartłomiej Surpeta, Carlos Sequeiros-Borja, Jan Brezovsky
2020	Triple Mycobacterial ATP-synthase mutations impedes Bedaquiline binding: Atomistic and structural perspectives Computational Biology and Chemistry Elliasu Y. Salifu, Clement Agoni, Fisayo A. Olotu, Mahmoud E.S. Soliman
2019	Molecular modelling predicts that 2-methoxyestradiol disrupts HIF function by binding to the PAS-B domain Steroids Andrea Poch, Felipe Villanelo, Soledad Henriquez, Paulina Kohen, Alex Muñoz, Jerome F. Strauss, Luigi Devoto
2019	Visualizing Protein Folding and Unfolding Journal of Molecular Biology Jennifer Ferina, Valerie Daggett
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