Activation pathway of Src kinase reveals intermediate states as targets for drug design
Shukla, Diwakar, Meng, Yilin, Roux, Benoît, Pande, Vijay S.·2014·Nature Communications
Cited by (338)
Items 201–300 of 338
- Exploring Protein Kinase Conformation Using Swarm-Enhanced Sampling Molecular DynamicsAlessio Atzori, Neil J. Bruce, Kepa Koldo Burusco, Berthold Wroblowski, Pascal Bonnet, Richard A. Bryce · 2014 · Journal of Chemical Information and Modeling
- Molecular Mechanism of Processive 3′ to 5′ RNA Translocation in the Active Subunit of the RNA Exosome ComplexLela Vuković, Christophe J. Chipot, Débora L. Makino, Elena Conti, Klaus J. Schulten · 2016 · Journal of the American Chemical Society
- Structural Consequences of Multisite Phosphorylation in the BAK1 Kinase DomainAlexander S. Moffett, Diwakar Shukla · 2020 · Biophysical Journal
- Sodium-induced population shift drives activation of thrombinUrsula Kahler, Anna Sophia Kamenik, Johannes Kraml, Klaus Roman Liedl · 2020 · Scientific Reports
- Dynamical Interaction Analysis of Proteins by a Random Forest-Fragment Molecular Orbital (RF-FMO) Method and Application to Src Tyrosine KinaseYuta Yamamoto, Shogo Nakano, Yasuteru Shigeta · 2022 · Bulletin of the Chemical Society of Japan
- Phosphorylation-Induced Conformational Dynamics and Inhibition of Janus Kinase 1 by Suppressors of Cytokine Signaling 1Md Fulbabu Sk, Nisha Amarnath Jonniya, Rajarshi Roy, Parimal Kar · 2022 · The Journal of Physical Chemistry B
- Population Shuffling of Protein ConformationsColin A. Smith, David Ban, Supriya Pratihar, Karin Giller, Claudia Schwiegk, Bert L. de Groot, Stefan Becker, Christian Griesinger, Donghan Lee · 2014 · Angewandte Chemie
- Computational study of the W 260 A activating mutant of S rc tyrosine kinaseYilin Meng, Benoı̂t Roux · 2015 · Protein Science
- Structural Features and Energetics of the Periplasmic Entrance Opening of the Outer Membrane Channel TolC Revealed by Molecular Dynamics Simulation and Markov State Model AnalysisJingwei Weng, Wenning Wang · 2019 · Journal of Chemical Information and Modeling
- Computer Simulations Predict High Structural Heterogeneity of Functional State of NMDA ReceptorsAnton V. Sinitskiy, Vijay S. Pande · 2018 · Biophysical Journal
- Computational Investigation of the Covalent Inhibition Mechanism of Bruton’s Tyrosine Kinase by IbrutinibAngela M. Barragan, Kyle Ghaby, Matthew P. Pond, Benoı̂t Roux · 2024 · Journal of Chemical Information and Modeling
- MEF-AlloSite: an accurate and robust Multimodel Ensemble Feature selection for the Allosteric Site identification modelSadettin Y. Ugurlu, David McDonald, Shan He · 2024 · Journal of Cheminformatics
- Computational study of non-catalytic T-loop pocket on CDK proteins for drug developmentHuiwen Wang, Kaili Wang, Zeyu Guan, Yiren Jian, Ya Jia, Fatah Kashanchi, Chen Zeng, Yunjie Zhao · 2017 · Chinese Physics B
- A Network of Conformational Transitions in the Apo Form of NDM-1 Enzyme Revealed by MD Simulation and a Markov State ModelKaifu Gao, Yunjie Zhao · 2017 · The Journal of Physical Chemistry B
- Kinetics analysis of ubiquitin local fluctuations with Markov state modeling of the LE4PD normal modesEric R. Beyerle, Marina Guenza · 2019 · The Journal of Chemical Physics
- Enhanced metastable state models of TAM kinase binding to cabozantinib explains the dynamic nature of receptor tyrosine kinasesGatta K. R. S. Naresh, Lalitha Guruprasad · 2020 · Journal of Biomolecular Structure and Dynamics
- Increasing the Sampling Efficiency of Protein Conformational Change by Combining a Modified Replica Exchange Molecular Dynamics and Normal Mode Analysis.Cheng Peng, Ji-Nan Wang, Yu-Long Shi, Zhi-Jian Xu, Wei-Liang Zhu · 2020 · Journal of Chemical Theory and Computation
- Molecular Dynamics and Machine Learning Give Insights on the Flexibility–Activity Relationships in Tyrosine KinomeSarmistha Majumdar, Francesco Di Palma, Francesca Spyrakis, Sergio Decherchi, Andrea Cavalli · 2023 · Journal of Chemical Information and Modeling
- Nucleosome condensate and linker DNA alter chromatin folding pathways and ratesQiu, Yunrui, Liu, Shuming, Lin, Xingcheng, Unarta, Ilona Christy, Huang, Xuhui, Zhang, Bin · 2026 · Biophysical Journal
- Combined approaches from physics, statistics, and computer science for ab initio protein structure prediction: ex unitate vires (unity is strength)?Marc H. Delarue, Patrice Koehl · 2018 · F1000Research
- Resolving Protein Conformational Plasticity and Substrate Binding via Machine Learning.N. Ahalawat, Mohammad Sahil, Jagannath Mondal · 2023 · Journal of Chemical Theory and Computation
- Focused conformational sampling in proteinsMarco Bacci, Cassiano Langini, Jiří Vymětal, Amedeo Caflisch, Andreas Vitalis · 2017 · The Journal of Chemical Physics
- FingerprintContacts: Predicting Alternative Conformations of Proteins from CoevolutionJiangyan Feng, Diwakar Shukla · 2020 · The Journal of Physical Chemistry B
- Constructing Kinetic Network Models to Elucidate Mechanisms of Functional Conformational Changes of Enzymes and Their Recognition with LigandsLu Zhang, Hanlun Jiang, Fu Kit Sheong, Fátima Pardo‐Ávila, Peter Pak‐Hang Cheung, Xuhui Huang · 2016 · Methods in enzymology on CD-ROM/Methods in enzymology
- Conformational landscape adaptations enable processive phosphorylation by Src family kinasesYixin Cui, Rustam Ali, Mary C. Clay, Paolo Rossi, Aizhuo Liu A, Darong Yang, Nancy R. Gough, Terrence L. Geiger, Charalampos G. Kalodimos · 2025 · Science
- Integrating pharmacophore mapping, virtual screening, density functional theory, molecular simulation towards the discovery of novel apolipoprotein (apoE ε4) inhibitorsSurabhi Johari, Ashwani Kumar Sharma, Subrata Sinha, Aparoop Das · 2019 · Computational Biology and Chemistry
- A Dynamic Switch in Inactive p38γ Leads to an Excited State on the Pathway to an Active KinasePhillip C. Aoto, Robyn L. Stanfield, Ian A. Wilson, H. Jane Dyson, Peter E. Wright · 2019 · Biochemistry
- Computational studies of anaplastic lymphoma kinase mutations reveal common mechanisms of oncogenic activationKeshav Patil, E. Joseph Jordan, Jin H. Park, Krishna Suresh, Courtney Michelle Smith, Abigail A. Lemmon, Yaël P. Mossé, Mark A. Lemmon, Ravi Radhakrishnan · 2021 · Proceedings of the National Academy of Sciences
- Catalytic Domains of Phosphodiesterase 5, 6, and 5/6 Chimera Display Differential Dynamics and Ligand Dissociation Energy BarriersJason G. Pattis, Shaan Kamal, Boyang Li, Eric R. May · 2019 · The Journal of Physical Chemistry B
- Kinetics and energetics of chemical reactions through intermediate statesA. Arango-Restrepo, J. M. Rubı́, Daniel A. Barragán R. · 2018 · Physica A Statistical Mechanics and its Applications
- Efficient and Accurate Modeling of Conformational Transitions in Proteins: The Case of c-Src KinaseEdoardo Milanetti, Alexandra G. Trandafir, Josephine Alba, Domenico Raimondo, Marco D’Abramo · 2018 · The Journal of Physical Chemistry B
- Identifying the structural and kinetic elements in protein large-amplitude conformational motionsJhih‐Wei Chu, Haw Yang · 2017 · International Reviews in Physical Chemistry
- Theoretical restrictions on longest implicit time scales in Markov state models of biomolecular dynamicsAnton V. Sinitskiy, Vijay S. Pande · 2018 · The Journal of Chemical Physics
- Multiscale Approach for Computing Gated Ligand Binding from Molecular Dynamics and Brownian Dynamics SimulationsSadiq, S. Kashif, Muñiz Chicharro, Abraham, Friedrich, Patrick, Wade, Rebecca C. · 2021 · Journal of Chemical Theory and Computation
- Insights into Fluctuations of Structure of Proteins: Significance of Intermediary States in Regulating Biological FunctionsZahoor Ahmad Parray, Mohammad Shahid, Asimul Islam · 2022 · Polymers
- p38α Kinase Auto-Activation through Its Conformational Transition Induced by Tyr323 PhosphorylationYongjian Zang, He Wang, Dongxiao Hao, Ying Ru Kang, Jianwen Zhang, Xuhua Li, Lei Zhang, Zhiwei Yang, Shengli Zhang · 2022 · Journal of Chemical Information and Modeling
- All-atom adaptively biased path optimization of Src kinase conformational inactivation: Switched electrostatic network in the concerted motion of αC helix and the activation loop.Heng Wu, He Huang, C. Post · 2020 · Journal of Chemical Physics
- Excited States of apo-Guanidine-III Riboswitch Contribute to Guanidinium Binding through Both Conformational and Induced-Fit MechanismsKushal Singh, Govardhan Reddy · 2023 · Journal of Chemical Theory and Computation
- Free energy profile of the substrate‐induced occlusion of the human serotonin transporterLeticia Alves da Silva, Erika Lazzarin, Ralph Gradisch, Amy Clarke, T. Stockner · 2024 · Journal of Neurochemistry
- Analyzing the Long Time-Scale Dynamics of Uremic Toxins Bound to Sudlow Site II in Human Serum AlbuminJames Ludwig, Josh K. Smith, Jim Pfaendtner · 2021 · The Journal of Physical Chemistry B
- Phospho-Priming Confers Functionally Relevant Specificities for Rad53 Kinase AutophosphorylationEric Sheng-Wen Chen, Jui‐Hung Weng, Yu‐Hou Chen, Shunchang Wang, Xiaoxia Liu, Wei‐Cheng Huang, Tsutomu Matsui, Yoshiaki Kawano, Jiahn‐Haur Liao, Liang-Hin Lim et al. · 2017 · Biochemistry
- Hierarchical Markov State Model Building to Describe Molecular ProcessesDavid K. Wolfe, Joseph R. Persichetti, Ajeet K. Sharma, Phillip S. Hudson, H. Lee Woodcock, Edward P. O’Brien · 2020 · Journal of Chemical Theory and Computation
- Mechanical force can enhance c-Src kinase activity by impairing autoinhibitionCsaba Daday, Svenja de Buhr, Davide Mercadante, Frauke Gräter · 2022 · Biophysical Journal
- Maximizing Kinetic Information Gain of Markov State Models for Optimal Design of Spectroscopy ExperimentsShriyaa Mittal, Diwakar Shukla · 2018 · The Journal of Physical Chemistry B
- The αC-β4 loop controls the allosteric cooperativity between nucleotide and substrate in the catalytic subunit of protein kinase AC. Olivieri, Yingjie Wang, Caitlin Walker, M. V. Subrahmanian, Kim N. Ha, D. Bernlohr, Jia-Li Gao, C. Camilloni, M. Vendruscolo, S. Taylor et al. · 2023 · bioRxiv
- Molecular basis for differential recognition of an allosteric inhibitor by receptor tyrosine kinasesJyoti Verma, Harish Vashisth · 2024 · Proteins Structure Function and Bioinformatics
- The αC-β4 loop controls the allosteric cooperativity between nucleotide and substrate in the catalytic subunit of protein kinase ACristina Olivieri, Yingjie Wang, Caitlin Walker, Manu Veliparambil Subrahmanian, Kim N. Ha, David Bernlohr, Jiali Gao, Carlo Camilloni, Michele Vendruscolo, Susan Serota Taylor et al. · 2024 · eLife
- Exploiting Computationally Derived Out-Of-The-Box Protein Conformations for Drug DesignFabiana Caporuscio, Giulio Rastelli · 2016 · Future Medicinal Chemistry
- Glycine substitution in SH3-SH2 connector of Hck tyrosine kinase causes population shift from assembled to disassembled stateLei Huang, Michelle H. Wright, Sichun Yang, Lydia Blachowicz, Lee Makowski, Benoı̂t Roux · 2020 · Biochimica et Biophysica Acta (BBA) - General Subjects
- Application of Congo red dye as a molecular probe to investigate the kinetics and thermodynamics of the formation processes of arachin and conarachin nanocomplexesJaqueline de Paula Rezende, Hauster Maximiler Campos de Paula, Talma Duarte Freitas, Yara Luíza Coelho, Luís Henrique Mendes da Silva, Ana Clarissa dos Santos Pires · 2022 · Food Chemistry
- TAB1 binding induced p38α conformation change: an accelerated molecular dynamics simulation studyYongjian Zang, He Wang, Ying Ru Kang, Jianwen Zhang, Xuhua Li, Lei Zhang, Zhiwei Yang, Shengli Zhang · 2022 · Physical Chemistry Chemical Physics
- Advances and challenges in drug repurposing in precision therapeutics of colorectal cancerXinning Yu, Hua-Tao Wu, Bingxuan Wu, Shu-Feng Zhi, Yang-Zheng Lan, Wen-Jia Chen, Jing Liu · 2025 · World Journal of Gastrointestinal Oncology
- Water-Based Pharmacophore Modeling in Kinase Inhibitor Design: A Case Study on Fyn and Lyn Protein KinasesMartin Ljubič, Marija Sollner Dolenc, Jure Borišek, Andrej Perdih · 2025 · Journal of Chemical Information and Modeling
- Allosteric Changes in the Conformational Landscape of Src Kinase upon Substrate Binding.Song-Ho Chong, Hiraku Oshima, Yuji Sugita · 2024 · Journal of Molecular Biology
- MARK4 protein can explore the active-like conformations in its non-phosphorylated stateSajjad Ahrari, Fatemeh Khosravi, Ali Osouli, Amirhossein Sakhteman, Alireza Nematollahi, Younes Ghasemi, Amir Savardashtaki · 2019 · Scientific Reports
- Identifying a Feasible Transition Pathway between Two Conformational States for a Protein.Yao Li, Hai-Peng Gong · 2022 · Journal of Chemical Theory and Computation
- Applying molecular hybridization to design a new class of pyrazolo[3,4-d]pyrimidines as Src inhibitors active in hepatocellular carcinomaSalvatore Di Maria, Raffaele Passannanti, Federica Poggialini, Chiara Vagaggini, Alessia Serafinelli, Elena Bianchi, Paolo Governa, Lorenzo Botta, Giovanni Maga, Emmanuele Crespan et al. · 2024 · European Journal of Medicinal Chemistry
- Chemical and Biophysical Approaches to Allosteric ModulationMonica Civera, Elisabetta Moroni, Luca Sorrentino, Francesca Vasile, Sara Sattin · 2021 · European Journal of Organic Chemistry
- Role of PDLIM4 and c-Src in breast cancer progressionDmitry Sergeevich Kravchenko, Elena Ivanovna Frolova, Julia E. Kravchenko, Stepan Petrovich Chumakov · 2016 · Molecular Biology
- Decoupling the dynamic mechanism revealed by FGFR2 mutation-induced population shiftYuxiang Zhang, Xiaolan Yin, Mingfei Ji, Yi Chen, Zong‐Tao Chai · 2023 · Journal of Biomolecular Structure and Dynamics
- Molecular Simulations of Conformational Transitions within the Insulin Receptor Kinase Reveal Consensus Features in a Multistep Activation PathwayKwangho Nam, Peng Tao, Victor Ovchinnikov · 2023 · The Journal of Physical Chemistry B
- Complete reconstruction of dasatinib unbinding pathway from c-Src kinase by supervised molecular dynamics simulation method; assessing efficiency and trustworthiness of the methodFarzin Sohraby, Mostafa Javaheri Moghadam, Masoud Aliyar, Hassan Aryapour · 2021 · Journal of Biomolecular Structure and Dynamics
- Molecular modeling study of the induced-fit effect on kinase inhibition: the case of fibroblast growth factor receptor 3 (FGFR3)Yan Li, Michel Delamar, Patricia Busca, Guillaume Prestat, Laurent Le Corre, Laurence Legeai‐Mallet, Rongjing Hu, Ruisheng Zhang, Florent Barbault · 2015 · Journal of Computer-Aided Molecular Design
- Global connectivity of hub residues in Oncoprotein structures encodes genetic factors dictating personalized drug response to targeted Cancer therapyVenky Soundararajan, Murali Aravamudan · 2014 · Scientific Reports
- Potential-Based Dynamical Reweighting for Markov State Models of Protein DynamicsJeffrey K. Weber, Vijay S. Pande · 2015 · Journal of Chemical Theory and Computation
- Generating conformational transition paths with low potential-energy barriers for proteinsMinh Khoa Nguyen, Léonard Jaillet, Stéphane Redon · 2018 · Journal of Computer-Aided Molecular Design
- Elucidating the conformational change of dengue envelope protein using the Markov state modelDwaipayan Chaudhuri, Satyabrata Majumder, Joyeeta Datta, Kalyan Giri · 2024 · Molecular Simulation
- Development of 5-Trifluoromethylpyrimidine Derivatives as Dual Inhibitors of EGFR and Src for Cancer TherapyLongjia Yan, Li Liu, Qin Lin Wang, N.G. Raghavendra Rao, Yi Le · 2022 · Heterocycles
- The αC-β4 loop controls the allosteric cooperativity between nucleotide and substrate in the catalytic subunit of protein kinase AC. Olivieri, Ying-Jie Wang, Caitlin Walker, M. V. Subrahmanian, Kim N. Ha, David A. Bernlohr, Jia-Li Gao, C. Camilloni, M. Vendruscolo, Susan S. Taylor et al. · 2024 · eLife
- Halloysite Nanotube-Based Delivery of Pyrazolo[3,4-d]pyrimidine Derivatives for Prostate and Bladder Cancer TreatmentMarina Massaro, Rebecca Ciani, Giancarlo Grossi, Gianfranco Cavallaro, Raquel de Melo Barbosa, Marta Falesiedi, Cosimo G. Fortuna, Anna Carbone, Silvia Schenone, Rita Sánchez‐Espejo et al. · 2024 · Pharmaceutics
- Predictive Gene Signature for Pyrazolopyrimidine Derivative c-Src Inhibitor 10a Sensitivity in Melanoma CellsBarış Küçükkaraduman, Can Türk, Anna Lucia Fallacara, Murat İşbilen, Kerem Mert Senses, Zeynep Özge Ayyıldız, Muhammad Waqas Akbar, Michal Lotem, Maurizio Botta, Ali Osmay Gure · 2020 · ACS Medicinal Chemistry Letters
- Efficient Interrogation of the Kinetic Barriers Demarcating Catalytic States of a Tyrosine Kinase with Optimal Physical Descriptors and Mixture ModelsPallab Dutta, Neelanjana Sengupta · 2022 · ChemPhysChem
- Dynamic conformational states of apo, ATP and cabozantinib bound TAM kinases to differentiate active-inactive kinetic modelsGatta K R S Naresh, L. Guruprasad · 2023 · Journal of Biomolecular Structure and Dynamics
- Mean field treatment of heterogeneous steady state kineticsNadav Geva, Valerie Vaissier Welborn, James J. Shepherd, Troy Van Voorhis · 2017 · Chemical Physics Letters
- Computational investigations on target-site searching and recognition mechanisms by thymine DNA glycosylase during DNA repair processLingyan Wang, Kaiyuan Song, Jin Hui Yu, Lin‐Tai Da · 2022 · Acta Biochimica et Biophysica Sinica
- Entropy-production-driven oscillators in simple nonequilibrium networksJeffrey K. Weber, Vijay S. Pande · 2015 · Physical Review E
- Receptor–Ligand Binding Free Energies from a Consecutive Histograms Monte Carlo Sampling MethodHao Liu, Jianpeng Deng, Zhou Luo, Yawei Lin, Kenneth M. Merz, Zheng Zheng · 2020 · Journal of Chemical Theory and Computation
- Markov State Models in Drug DesignBettina G. Keller, Stevan Aleksić, Luca Donati · 2018 · Methods and principles in medicinal chemistry
- Improved Estimates of Folding Stabilities and Kinetics with Multiensemble Markov Models.Si Zhang, Yun-Hui Ge, Vincent A. Voelz · 2024 · Biochemistry
- Markovian state models uncover casein kinase 1 dynamics that govern circadian periodRicci, Clarisse Gravina, Philpott, Jonathan M., Torgrimson, Megan R., Freeberg, Alfred M., Narasimamurthy, Rajesh, Pécora de Barros, Emilia, Amaro, Rommie, Virshup, David M., McCammon, J. Andrew, Partch, Carrie L. · 2025 · Biophysical Journal
- Elucidating Mechanisms of Molecular Recognition Between Human Argonaute and miRNA Using Computational ApproachesHanlun Jiang, Lizhe Zhu, Amélie Héliou, Xin Gao, Julie Bernauer, Xuhui Huang · 2016 · Methods in molecular biology
- Computational Exploration of Conformational Transitions in Protein Drug TargetsBenjamin P. Cossins, Alastair D. G. Lawson, Jiye Shi · 2018 · Methods in molecular biology
- Markov State Models Underlying the N-Terminal Premodel of TOPK/PBK.He Wang, Xun Zhu, Yizhen Zhao, Y. Zang, Jianwen Zhang, Ying Kang, Zhiwei Yang, Peng Lin, Lei Zhang, Sheng-Li Zhang · 2022 · Journal of Physical Chemistry B
- Allosterically coupled conformational dynamics in solution prepare the sterol transfer protein StarD4 to release its cargo upon interaction with target membranesHeng-Yi Xie, Harel Weinstein · 2023 · bioRxiv
- Computational Analysis of Activation of Dimerized Epidermal Growth Factor Receptor Kinase Using the String Method and Markov State ModelMasao Inoue, Toru Ekimoto, Tsutomu Yamane, M. Ikeguchi · 2024 · Journal of Chemical Information and Modeling
- Methods Applied for the Allosteric Site RevelationDuan Ni, Shaoyong Lu, Jian Zhang · 2018 · Encyclopedia of Analytical Chemistry
- Metastatic function of METTL18 in breast cancer via actin methylation and SrcHan Gyung Kim, Ji Hye Kim, Woo Seok Yang, Jae Gwang Park, Yong Gyu Lee, Yo Han Hong, Eunji Kim, Minkyeong Jo, Chae Young Lee, Shi Hyung Kim et al. · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
- Design and Discovery of Kinase Inhibitors Using Docking StudiesTeodora Djikić, Žarko Gagić, Katarina M. Nikolic · 2021 · Elsevier eBooks
- Energetics of substrate transport in proton-dependent oligopeptide transportersBalaji Selvam, Nicole Chiang, Diwakar Shukla · 2024 · Communications Chemistry
- Molecular Dynamics Computer Simulations of Biological SystemsJames W. Carter, Anna Sofia Tascini, John M. Seddon, Fernando Bresme · 2017 · Royal Society of Chemistry eBooks
- How does evolution design functional free energy landscapes of proteins? A case study on the emergence of regulation in the Cyclin Dependent Kinase familyZ. Shamsi, D. Shukla · 2020 · Molecular Systems Design & Engineering
- Роль PDLIM4 и c-Src в развитии рака молочной железыDmitry Sergeevich Kravchenko, Е. И. Фролова, Ю.Е. Кравченко, Stepan Petrovich Chumakov, Elena Ivanovna Frolova, Julia E. Kravchenko · 2016 · Molecular Biology
- Entropy Transfer between Residue Pairs Shows that Allostery is an Intrinsic Property of Proteins: Quantifying Allosteric Communication in UbiquitinAysima Hacisuleyman, Burak Erman · 2016 · bioRxiv (Cold Spring Harbor Laboratory)
- Complete reconstruction of the unbinding pathway of an anticancer drug by conventional unbiased molecular dynamics simulationFarzin Sohraby, Mostafa Javaheri Moghadam, Masoud Aliyar, Hassan Aryapour · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
- The αC-β4 loop controls the allosteric cooperativity between nucleotide and substrate in the catalytic subunit of protein kinase ACristina Olivieri, Yingjie Wang, Caitlin Walker, Manu Veliparambil Subrahmanian, Kim N. Ha, David Bernlohr, Jiali Gao, Carlo Camilloni, Michele Vendruscolo, Susan Serota Taylor et al. · 2023 · eLife
- Building multiscale Markov state models by systematic mapping of temporal communitiesNir Nitskansky, Kessem Clein, Barak Raveh · 2025 · Bioinform.
- Synergistic antibody neutralization of SEB is driven by allosteric transfer entropyGanggang Bai, Yanhong Ge, Yuhong Su, Chuance Sun, Buyong Ma · 2026 · Biophysical Journal
- Mutation-Dependent Conformational Dynamics and Dual-Mode Afatinib Binding in EGFR Exon 19 VariantsK. Bhanja, Rajesh Ghosh, Niladri Patra · 2026 · The Journal of Physical Chemistry B
- Nanoscale Dynamics and Energetics of Proteins and Protein-Nucleic Acid Complexes in Classical Molecular Dynamics SimulationsSuresh Gorle, Lela Vuković · 2018 · Methods in molecular biology
- Prognostic Pathways Guide Drug Indications in Pan-CancersFanlin Meng, Kenan Zhang, Changlin Yang, Ke Zhang, Quan Xu, Ruifang Ren, Yiming Zhou, Yimin Sun, Yan Peng, Yanze Li et al. · 2022 · Frontiers in Oncology