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Julia M. Montgomery, Justin A. Lemkul

Mostafa Javaheri Moghadam, Rebecca Mulder, Stijn De Baerdemacker

Sarah Naomi Bolz, Philipp Schake, Celina Stitz, Michael Schroeder

Laura I. Gil Pineda, Candace J. Miller, Alexander D. MacKerell, Justin A. Lemkul

Katrine Bugge, Andrea Sottini, Miloš T. Ivanović, Freia S. Buus, Daniel Saar, Catarina B. Fernandes, Fabienne Kocher, Jacob H. Martinsen, Benjamin Schuler, Robert B. Best, Birthe B. Kragelund

Zahra Hosseinzadeh, Raman Ghassemi, Saba Darbandi, Radman Alizadeh, Hossein Faramarzi, Shohreh Mashayekhan

Jules Marien, Julie Puyo-Fourtine, Chantal Prévost, Sophie Sacquin-Mora, Elise Duboué-Dijon

Sangram Prusty, Rafael Brüschweiler, Qiang Cui

Nikolett Péczka, Ivan Ranđelović, Zoltán Orgován, Noémi Csorba, Attila Egyed, László Petri, Péter Ábrányi-Balogh, Márton Gadanecz, András Perczel, József Tóvári, Gitta Schlosser, Tamás Takács, Levente M. Mihalovits, György G. Ferenczy, László Buday, György M. Keserű

Xiping Gong, Yumeng Zhang, Jianhan Chen

Shohreh Ariaeenejad, Javad Gharechahi, Mehdi Foroozandeh Shahraki, Fereshteh Fallah Atanaki, Jian-Lin Han, Xue-Zhi Ding, Falk Hildebrand, Mohammad Bahram, Kaveh Kavousi, Ghasem Hosseini Salekdeh

Darcy S. Davidson, Justin A. Lemkul

Isidora Diakogiannaki, Michail Papadourakis, Vasileia Spyridaki, Zoe Cournia, Andreas Koutselos

Alina Volkova, Pavel Semenyuk

Birte Schmitz, Benedikt Frieg, Nadine Homeyer, Gisela Jessen, Holger Gohlke

Craig A. Peeples, Ruibin Liu, Jana Shen

Thomas Ehret, Tim Heißenberg, Svenja de Buhr, Camilo Aponte-Santamaría, Claudia Steinem, Frauke Gräter

Elena Papaleo, Matteo Tiberti, Matteo Arnaudi, Chiara Pecorari, Fiorella Faienza, Lisa Cantwell, Kristine Degn, Francesca Pacello, Andrea Battistoni, Matteo Lambrughi, Giuseppe Filomeni

Jeremy Lapierre, Jochen S. Hub

Corentin Villot, Ka Un Lao

Sabyasachi Chakraborty, Kalyaneswar Mandal, Raghunathan Ramakrishnan

Javier Abellon-Ruiz, Kalyanashis Jana, Augustinas Silale, Andrew M. Frey, Arnaud Baslé, Matthias Trost, Ulrich Kleinekathöfer, Bert van den Berg

Tatsuo Akaki, Shinya Nakamura, Keiji Nishiwaki, Isao Nakanishi

Robert A. Becker, Jochen S. Hub

Till El Harrar, Holger Gohlke

Semen Yesylevskyy, Hector Martinez-Seara, Pavel Jungwirth

Masamitsu Nakayama, Shinichi Goto, Shinya Goto

Alessandra Luchini, Frederik Grønbæk Tidemand, Raul Araya-Secchi, Mario Campana, Marité Cárdenas, Lise Arleth

Kelsie M. King, Amanda K. Sharp, Darcy S. Davidson, Anne M. Brown, Justin A. Lemkul

Han Liu, Haohao Fu, Christophe Chipot, Xueguang Shao, Wensheng Cai

Jiahua Deng, Qiang Cui

Suvankar Ghosh, Sunanda Chatterjee, Priyadarshi Satpati

Mangesh Damre, Ashan Dayananda, Rohith Anand Varikoti, George Stan, Ruxandra I. Dima

Chao Lu, Chuanjie Wu, Delaram Ghoreishi, Wei Chen, Lingle Wang, Wolfgang Damm, Gregory A. Ross, Markus K. Dahlgren, Ellery Russell, Christopher D. Von Bargen, Robert Abel, Richard A. Friesner, Edward D. Harder

Abdullah F. U. H. Saeed, Chun Chan, Hongxin Guan, Bing Gong, Peixuan Guo, Xiaolin Cheng, Songying Ouyang

Kevin C. Song, Andrew V. Molina, Ruofan Chen, Isabelle A. Gagnon, Young Hoon Koh, Benoît Roux, Tobin R. Sosnick

Ayşegül Özen, Emanuele Perola, Natasja Brooijmans, Joseph Kim

Mert Golcuk, Aysima Hacisuleyman, Burak Erman, Ahmet Yildiz, Mert Gur

Diego E. Escalante, David M. Ferguson

Ellen Rieloff, Marie Skepö

Jia-Jie Feng, Jia-Nan Chen, Wei Kang, Yun-Dong Wu

Ellen Rieloff, Marie Skepö

Matías R. Machado, Sergio Pantano

E. Duboué-Dijon, M. Javanainen, P. Delcroix, P. Jungwirth, H. Martinez-Seara

Mukesh Kumar, Elena Papaleo

Dmitry Suplatov, Yana Sharapova, Vytas Švedas

Iva Sučec, Yong Wang, Ons Dakhlaoui, Katharina Weinhäupl, Tobias Jores, Doriane Costa, Audrey Hessel, Martha Brennich, Doron Rapaport, Kresten Lindorff-Larsen, Beate Bersch, Paul Schanda

Stefano Piana, Paul Robustelli, Dazhi Tan, Songela Chen, David E. Shaw

Matthew Batchelor, Marcin Wolny, Emily G. Baker, Emanuele Paci, Arnout P. Kalverda, Michelle Peckham

Mikkel Christensen, Birgit Schiøtt

Yamina El Hamdaoui, Xiaosa Wu, Richard J. Clark, Julien Giribaldi, Raveendra Anangi, David J. Craik, Glenn F. King, Sebastien Dutertre, Quentin Kaas, Volker Herzig, Annette Nicke

Yoshinori Matsuura, Yasumasa Joti, Bagautdin Bagautdinov, Katsuhide Yutani

Josef Melcr, Jean-Philip Piquemal

Pavel Semenyuk, Vladimir Muronetz

Frédéric Célerse, Louis Lagardère, Etienne Derat, Jean-Philip Piquemal

Pavlína Pokorná, Miroslav Krepl, Eva Bártová, Jiří Šponer

2026	Investigating the electrostatics underlying activation of the β 2 adrenergic receptor Biochimica et Biophysica Acta (BBA) - Biomembranes Julia M. Montgomery, Justin A. Lemkul
2026	Divide and correlate: mapping electronic correlations in proteins via local cut-wise reconstruction Chemical Communications Mostafa Javaheri Moghadam, Rebecca Mulder, Stijn De Baerdemacker
2025	The structural basis of drugs targeting protein–protein interactions uncovered with the protein–ligand interaction profiler PLIP Expert Opinion on Drug Discovery Sarah Naomi Bolz, Philipp Schake, Celina Stitz, Michael Schroeder
2025	Drude polarizable force field for phosphorylated polypeptides and proteins Biophysical Journal Laura I. Gil Pineda, Candace J. Miller, Alexander D. MacKerell, Justin A. Lemkul
2025	Role of charges in a dynamic disordered complex between an IDP and a folded domain Nature Communications Katrine Bugge, Andrea Sottini, Miloš T. Ivanović, Freia S. Buus, Daniel Saar, Catarina B. Fernandes, Fabienne Kocher, Jacob H. Martinsen, Benjamin Schuler, Robert B. Best, Birthe B. Kragelund
2025	Revolutionizing nanofiber engineering of peptide amphiphiles for advanced regenerative medicine Journal of Materials Science Zahra Hosseinzadeh, Raman Ghassemi, Saba Darbandi, Radman Alizadeh, Hossein Faramarzi, Shohreh Mashayekhan
2025	Sticky Salts: Overbinding of Monovalent Cations to Phosphorylations in All-Atom Force Fields Journal of Chemical Information and Modeling Jules Marien, Julie Puyo-Fourtine, Chantal Prévost, Sophie Sacquin-Mora, Elise Duboué-Dijon
2025	Comparative Analysis of Polarizable and Nonpolarizable CHARMM Family Force Fields for Proteins with Flexible Loops and High Charge Density Journal of Chemical Information and Modeling Sangram Prusty, Rafael Brüschweiler, Qiang Cui
2024	Contribution of Noncovalent Recognition and Reactivity to the Optimization of Covalent Inhibitors: A Case Study on KRasG12C ACS Chemical Biology Nikolett Péczka, Ivan Ranđelović, Zoltán Orgován, Noémi Csorba, Attila Egyed, László Petri, Péter Ábrányi-Balogh, Márton Gadanecz, András Perczel, József Tóvári, Gitta Schlosser, Tamás Takács, Levente M. Mihalovits, György G. Ferenczy, László Buday, György M. Keserű
2024	Likely Overstabilization of Charge–Charge Interactions in CHARMM36m(w): A Case for a99SB-disp Water The Journal of Physical Chemistry B Xiping Gong, Yumeng Zhang, Jianhan Chen
2024	Precision enzyme discovery through targeted mining of metagenomic data Natural Products and Bioprospecting Shohreh Ariaeenejad, Javad Gharechahi, Mehdi Foroozandeh Shahraki, Fereshteh Fallah Atanaki, Jian-Lin Han, Xue-Zhi Ding, Falk Hildebrand, Mohammad Bahram, Kaveh Kavousi, Ghasem Hosseini Salekdeh
2024	Pyroglutamylation modulates electronic properties and the conformational ensemble of the amyloid β‐peptide Proteins: Structure, Function, and Bioinformatics Darcy S. Davidson, Justin A. Lemkul
2024	Computational Investigation of BMAA and Its Carbamate Adducts as Potential GluR2 Modulators Journal of Chemical Information and Modeling Isidora Diakogiannaki, Michail Papadourakis, Vasileia Spyridaki, Zoe Cournia, Andreas Koutselos
2024	Tyrosine phosphorylation of recombinant hirudin increases affinity to thrombin and antithrombotic activity Proteins: Structure, Function, and Bioinformatics Alina Volkova, Pavel Semenyuk
2024	Extracting binding energies and binding modes from biomolecular simulations of fragment binding to endothiapepsin Archiv der Pharmazie Birte Schmitz, Benedikt Frieg, Nadine Homeyer, Gisela Jessen, Holger Gohlke
2024	Force Field Limitations of All-Atom Continuous Constant pH Molecular Dynamics The Journal of Physical Chemistry B Craig A. Peeples, Ruibin Liu, Jana Shen
2023	FERM domains recruit ample PI(4,5)P2s to form extensive protein-membrane attachments Biophysical Journal Thomas Ehret, Tim Heißenberg, Svenja de Buhr, Camilo Aponte-Santamaría, Claudia Steinem, Frauke Gräter
2023	TRAP1 S-nitrosylation as a model of population-shift mechanism to study the effects of nitric oxide on redox-sensitive oncoproteins Cell Death & Disease Elena Papaleo, Matteo Tiberti, Matteo Arnaudi, Chiara Pecorari, Fiorella Faienza, Lisa Cantwell, Kristine Degn, Francesca Pacello, Andrea Battistoni, Matteo Lambrughi, Giuseppe Filomeni
2023	Converging PMF Calculations of Antibiotic Permeation across an Outer Membrane Porin with Subkilocalorie per Mole Accuracy Journal of Chemical Information and Modeling Jeremy Lapierre, Jochen S. Hub
2023	Electronic structure theory on modeling short-range noncovalent interactions between amino acids The Journal of Chemical Physics Corentin Villot, Ka Un Lao
2023	Understanding the Role of Intramolecular Ion-Pair Interactions in Conformational Stability Using an Ab Initio Thermodynamic Cycle The Journal of Physical Chemistry B Sabyasachi Chakraborty, Kalyaneswar Mandal, Raghunathan Ramakrishnan
2023	BtuB TonB-dependent transporters and BtuG surface lipoproteins form stable complexes for vitamin B12 uptake in gut Bacteroides Nature Communications Javier Abellon-Ruiz, Kalyanashis Jana, Augustinas Silale, Andrew M. Frey, Arnaud Baslé, Matthias Trost, Ulrich Kleinekathöfer, Bert van den Berg
2023	Fragment Molecular Orbital Based Affinity Prediction toward Pyruvate Dehydrogenase Kinases: Insights into the Charge Transfer in Hydrogen Bond Networks Chemical and Pharmaceutical Bulletin Tatsuo Akaki, Shinya Nakamura, Keiji Nishiwaki, Isao Nakanishi
2023	Molecular simulations of DEAH-box helicases reveal control of domain flexibility by ligands: RNA, ATP, ADP, and G-patch proteins Biological Chemistry Robert A. Becker, Jochen S. Hub
2023	Cumulative Millisecond-Long Sampling for a Comprehensive Energetic Evaluation of Aqueous Ionic Liquid Effects on Amino Acid Interactions Journal of Chemical Information and Modeling Till El Harrar, Holger Gohlke
2023	Curvature Matters: Modeling Calcium Binding to Neutral and Anionic Phospholipid Bilayers The Journal of Physical Chemistry B Semen Yesylevskyy, Hector Martinez-Seara, Pavel Jungwirth
2022	Physical Characteristics of von Willebrand Factor Binding with Platelet Glycoprotein Ibɑ Mutants at Residue 233 Causing Various Biological Functions TH Open Masamitsu Nakayama, Shinichi Goto, Shinya Goto
2022	Structural model of tissue factor (TF) and TF-factor VIIa complex in a lipid membrane: A combined experimental and computational study Journal of Colloid and Interface Science Alessandra Luchini, Frederik Grønbæk Tidemand, Raul Araya-Secchi, Mario Campana, Marité Cárdenas, Lise Arleth
2022	Impact of Electronic Polarization on Preformed, β-Strand Rich Homogenous and Heterogeneous Amyloid Oligomers Journal of Computational Biophysics and Chemistry Kelsie M. King, Amanda K. Sharp, Darcy S. Davidson, Anne M. Brown, Justin A. Lemkul
2022	Accurate Description of Solvent-Exposed Salt Bridges with a Non-polarizable Force Field Incorporating Solvent Effects Journal of Chemical Information and Modeling Han Liu, Haohao Fu, Christophe Chipot, Xueguang Shao, Wensheng Cai
2022	Electronic Polarization Is Essential for the Stabilization and Dynamics of Buried Ion Pairs in Staphylococcal Nuclease Mutants Journal of the American Chemical Society Jiahua Deng, Qiang Cui
2022	Effect of a monovalent salt on the energetics of an antimicrobial-peptide: micelle dissociation Physical Chemistry Chemical Physics Suvankar Ghosh, Sunanda Chatterjee, Priyadarshi Satpati
2021	Factors underlying asymmetric pore dynamics of disaggregase and microtubule-severing AAA+ machines Biophysical Journal Mangesh Damre, Ashan Dayananda, Rohith Anand Varikoti, George Stan, Ruxandra I. Dima
2021	OPLS4: Improving Force Field Accuracy on Challenging Regimes of Chemical Space Journal of Chemical Theory and Computation Chao Lu, Chuanjie Wu, Delaram Ghoreishi, Wei Chen, Lingle Wang, Wolfgang Damm, Gregory A. Ross, Markus K. Dahlgren, Ellery Russell, Christopher D. Von Bargen, Robert Abel, Richard A. Friesner, Edward D. Harder
2021	Structural Insights into gp16 ATPase in the Bacteriophage ϕ29 DNA Packaging Motor Biochemistry Abdullah F. U. H. Saeed, Chun Chan, Hongxin Guan, Bing Gong, Peixuan Guo, Xiaolin Cheng, Songying Ouyang
2021	Folding and misfolding of potassium channel monomers during assembly and tetramerization Proceedings of the National Academy of Sciences Kevin C. Song, Andrew V. Molina, Ruofan Chen, Isabelle A. Gagnon, Young Hoon Koh, Benoît Roux, Tobin R. Sosnick
2021	ACS Symposium Series Ayşegül Özen, Emanuele Perola, Natasja Brooijmans, Joseph Kim
2021	Binding Mechanism of Neutralizing Nanobodies Targeting SARS-CoV-2 Spike Glycoprotein Journal of Chemical Information and Modeling Mert Golcuk, Aysima Hacisuleyman, Burak Erman, Ahmet Yildiz, Mert Gur
2021	Structural modeling and analysis of the SARS-CoV-2 cell entry inhibitor camostat bound to the trypsin-like protease TMPRSS2 Medicinal Chemistry Research Diego E. Escalante, David M. Ferguson
2021	Molecular Dynamics Simulations of Phosphorylated Intrinsically Disordered Proteins: A Force Field Comparison International Journal of Molecular Sciences Ellen Rieloff, Marie Skepö
2021	Accurate Structure Prediction for Protein Loops Based on Molecular Dynamics Simulations with RSFF2C Journal of Chemical Theory and Computation Jia-Jie Feng, Jia-Nan Chen, Wei Kang, Yun-Dong Wu
2021	The Effect of Multisite Phosphorylation on the Conformational Properties of Intrinsically Disordered Proteins International Journal of Molecular Sciences Ellen Rieloff, Marie Skepö
2020	Split the Charge Difference in Two! A Rule of Thumb for Adding Proper Amounts of Ions in MD Simulations Journal of Chemical Theory and Computation Matías R. Machado, Sergio Pantano
2020	Progress in Molecular Biology and Translational Science
2020	A practical guide to biologically relevant molecular simulations with charge scaling for electronic polarization The Journal of Chemical Physics E. Duboué-Dijon, M. Javanainen, P. Delcroix, P. Jungwirth, H. Martinez-Seara
2020	A pan-cancer assessment of alterations of the kinase domain of ULK1, an upstream regulator of autophagy Scientific Reports Mukesh Kumar, Elena Papaleo
2020	EasyAmber: A comprehensive toolbox to automate the molecular dynamics simulation of proteins Journal of Bioinformatics and Computational Biology Dmitry Suplatov, Yana Sharapova, Vytas Švedas
2020	Structural basis of client specificity in mitochondrial membrane-protein chaperones Science Advances Iva Sučec, Yong Wang, Ons Dakhlaoui, Katharina Weinhäupl, Tobias Jores, Doriane Costa, Audrey Hessel, Martha Brennich, Doron Rapaport, Kresten Lindorff-Larsen, Beate Bersch, Paul Schanda
2020	Development of a Force Field for the Simulation of Single-Chain Proteins and Protein–Protein Complexes Journal of Chemical Theory and Computation Stefano Piana, Paul Robustelli, Dazhi Tan, Songela Chen, David E. Shaw
2019	Methods in Molecular Biology Robert B. Best
2019	Dynamic ion pair behavior stabilizes single α-helices in proteins Journal of Biological Chemistry Matthew Batchelor, Marcin Wolny, Emily G. Baker, Emanuele Paci, Arnout P. Kalverda, Michelle Peckham
2019	Revealing a Dual Role of Ganglioside Lipids in the Aggregation of Membrane-Associated Islet Amyloid Polypeptide The Journal of Membrane Biology Mikkel Christensen, Birgit Schiøtt
2019	Periplasmic Expression of 4/7 α-Conotoxin TxIA Analogs in E. coli Favors Ribbon Isomer Formation – Suggestion of a Binding Mode at the α7 nAChR Frontiers in Pharmacology Yamina El Hamdaoui, Xiaosa Wu, Richard J. Clark, Julien Giribaldi, Raveendra Anangi, David J. Craik, Glenn F. King, Sebastien Dutertre, Quentin Kaas, Volker Herzig, Annette Nicke
2019	Evaluating the strengths of salt bridges in the CutA1 protein using molecular dynamic simulations: a comparison of different force fields FEBS Open Bio Yoshinori Matsuura, Yasumasa Joti, Bagautdin Bagautdinov, Katsuhide Yutani
2019	Accurate Biomolecular Simulations Account for Electronic Polarization Frontiers in Molecular Biosciences Josef Melcr, Jean-Philip Piquemal
2019	Protein Interaction with Charged Macromolecules: From Model Polymers to Unfolded Proteins and Post-Translational Modifications International Journal of Molecular Sciences Pavel Semenyuk, Vladimir Muronetz
2019	Massively Parallel Implementation of Steered Molecular Dynamics in Tinker-HP: Comparisons of Polarizable and Non-Polarizable Simulations of Realistic Systems Journal of Chemical Theory and Computation Frédéric Célerse, Louis Lagardère, Etienne Derat, Jean-Philip Piquemal
2019	Role of Fine Structural Dynamics in Recognition of Histone H3 by HP1γ(CSD) Dimer and Ability of Force Fields to Describe Their Interaction Network Journal of Chemical Theory and Computation Pavlína Pokorná, Miroslav Krepl, Eva Bártová, Jiří Šponer
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