Dissociation Process of a MDM2/p53 Complex Investigated by Parallel Cascade Selection Molecular Dynamics and the Markov State Model von Tran, Duy Phuoc, Kitao, Akio

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Kinetic Selection and Relaxation of the Intrinsically Disordered Region of a Protein upon Binding von Tran, Duy Phuoc, Kitao, Akio

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Vibrational Energy Transfer from Heme through Atomic Contacts in Proteins von Yamashita, Satoshi, Mizuno, Misao, Tran, Duy Phuoc, Dokainish, Hisham, Kitao, Akio, Mizutani, Yasuhisa

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Using molecular dynamics simulations to prioritize and understand AI-generated cell penetrating peptides von Tran, Duy Phuoc, Tada, Seiichi, Yumoto, Akiko, Kitao, Akio, Ito, Yoshihiro, Uzawa, Takanori, Tsuda, Koji

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Binding free energy of protein/ligand complexes calculated using dissociation Parallel Cascade Selection Molecular Dynamics and Markov state model von Hata, Hiroaki, Tran, Duy Phuoc, Sobeh, Mohamed Marzouk, Kitao, Akio

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Inhibition of the hexamerization of SARS-CoV-2 endoribonuclease and modeling of RNA structures bound to the hexamer von Tran, Duy Phuoc, Taira, Yuta, Ogawa, Takumi, Misu, Ryoga, Miyazawa, Yoshiki, Kitao, Akio

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Edge expansion parallel cascade selection molecular dynamics simulation for investigating large-amplitude collective motions of proteins von Takaba, Kenichiro, Tran, Duy Phuoc, Kitao, Akio

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Generating Ampicillin-Level Antimicrobial Peptides with Activity-Aware Generative Adversarial Networks von Tucs, Andrejs, Tran, Duy Phuoc, Yumoto, Akiko, Ito, Yoshihiro, Uzawa, Takanori, Tsuda, Koji

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Parallel cascade selection molecular dynamics for efficient conformational sampling and free energy calculation of proteins von Kitao, Akio, Harada, Ryuhei, Nishihara, Yasutaka, Tran, Duy Phuoc

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In silico study of Bombyx mori fibroin enhancement by graphene in acidic environment von Tran, Duy Phuoc, Lam, Vi Toan, Tran, Tan Lien, Nguyen, Thuy Nhu Son, Thi Tran, Hanh Thu

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Calculation of Binding Free Energy and Kinetic Rates with Flexible Protein Docking von TRAN, Duy Phuoc, KITAO, Akio

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Obtaining Binding Free Energy from a Path Sampling without Force Bias von Phuoc Tran, Duy, Kitao, Akio

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GOMoDo: A GPCRs online modeling and docking webserver von Sandal, Massimo, Duy, Tran Phuoc, Cona, Matteo, Zung, Hoang, Carloni, Paolo, Musiani, Francesco, Giorgetti, Alejandro

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Melting of Mesoscale Lennard-Jones Crystals with Free Surfaces von Hoang, Vo Van, Duy, Tran Phuoc

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Atomic mechanism of homogeneous melting of bcc Fe at the limit of superheating von Phuoc Duy, Tran, Van Hoang, Vo

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Engineering of an in-cell protein crystal for fastening a metastable conformation of a target miniprotein von Kojima, Mariko, Abe, Satoshi, Furuta, Tadaomi, Tran, Duy Phuoc, Hirata, Kunio, Yamashita, Keitaro, Hishikawa, Yuki, Kitao, Akio, Ueno, Takafumi

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Delineating the conformational landscape of the adenosine A2A receptor during G protein coupling von Huang, Shuya Kate, Pandey, Aditya, Tran, Duy Phuoc, Villanueva, Nicolas L., Kitao, Akio, Sunahara, Roger K., Sljoka, Adnan, Prosser, R. Scott

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Ligand binding to anti-cancer target CD44 investigated by molecular simulations von Nguyen, Tin Trung, Tran, Duy Phuoc, Pham Dinh Quoc Huy, Hoang, Zung, Carloni, Paolo, Van Pham, Phuc, Nguyen, Chuong, Li, Mai Suan

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Structural properties of simulated liquid GanAsm von THU HANH, Tran Thi, VAN HOANG, Vo, PHUOC DUY, Tran

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Erratum: “Edge expansion parallel cascade selection molecular dynamics simulation for investigating large-amplitude collective motions of proteins” [J. Chem. Phys. 152, 225101 (202... von Takaba, Kenichiro, Tran, Duy Phuoc, Kitao, Akio

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