Kwangho Nam

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 38

Top Topics

Structural Basis

Tyrosine Kinase

Crystal Structure

Molecular Dynamics

Top Venues

Journal of chemical information and modeling

Journal of chemical theory and computation

Science advances

The journal of physical chemistry. B

This page only lists publications with an associated author ORCID identifier.

Publications

Donghyuk Suh, Abdul Raafik Arattu Thodika, Seonghoon Kim, Kwangho Nam, Wonpil Im
CHARMM-GUI QM/MM Interfacer for a Quantum Mechanical and Molecular Mechanical (QM/MM) Simulation Setup: 1. Semiempirical Methods. Journal of chemical theory and computation 20 (12) (2024)
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, Magnus Wolf-Watz
Magnesium induced structural reorganization in the active site of adenylate kinase. Science advances 10 (32) (2024)
Donghyuk Suh, Abdul Raafik Arattu Thodika, Seonghoon Kim, Kwangho Nam, Wonpil Im
CHARMM-GUI QM/MM Interfacer for a Quantum Mechanical and Molecular Mechanical (QM/MM) Simulation Setup: 1. Semiempirical Methods. Journal of chemical theory and computation 20 (12) (2024)
Kwangho Nam, Yihan Shao, Dan T Major, Magnus Wolf-Watz
Perspectives on Computational Enzyme Modeling: From Mechanisms to Design and Drug Development. ACS omega 9 (7) (2024)
Kwangho Nam, Yihan Shao, Dan T Major, Magnus Wolf-Watz
Perspectives on Computational Enzyme Modeling: From Mechanisms to Design and Drug Development. ACS omega 9 (7) (2024)
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, Magnus Wolf-Watz
Magnesium induced structural reorganization in the active site of adenylate kinase. Science advances 10 (32) (2024)
Wonmuk Hwang, Steven L Austin, Arnaud Blondel, Eric D Boittier, Stefan Boresch, Matthias Buck, Joshua Buckner, Amedeo Caflisch, Hao-Ting Chang, Xi Cheng, Yeol Kyo Choi, Jhih-Wei Chu, Michael F Crowley, Qiang Cui, Ana Damjanovic, Yuqing Deng, Michael Devereux, Xinqiang Ding, Michael F Feig, Jiali Gao, David R Glowacki, James E Gonzales, Mehdi Bagerhi Hamaneh, Edward D Harder, Ryan L Hayes, Jing Huang, Yandong Huang, Phillip S Hudson, Wonpil Im, Shahidul M Islam, Wei Jiang, Michael R Jones, Silvan Käser, Fiona L Kearns, Nathan R Kern, Jeffery B Klauda, Themis Lazaridis, Jinhyuk Lee, Justin A Lemkul, Xiaorong Liu, Yun Lyna Luo, Alexander D MacKerell, Dan Thomas Major, Markus Meuwly, Kwangho Nam, Lennart Nilsson, Victor Ovchinnikov, Emanuele Paci, Soohyung Park, Richard W Pastor, Amanda R Pittman, Carol Beth Post, Samarjeet Prasad, Jingzhi Pu, John Z H Zhang, Thenmalarchelvi Rathinavelan, Daniel R Roe, Benoı T Roux, Christopher N Rowley, Jana Shen, Andrew C Simmonett, Alexander J Sodt, Kai Töpfer, Meenu Upadhyay, Arjan van der Vaart, Luis Itza Vazquez-Salazar, Richard M Venable, Luke C Warrensford, H Lee Woodcock, Yujin Wu, Charles L Brooks Iii, Bernard R Brooks, Martin Karplus
CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed. The journal of physical chemistry. B (2024)
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, Magnus Wolf-Watz
Magnesium induced structural reorganization in the active site of adenylate kinase. Science advances 10 (32) (2024)
Donghyuk Suh, Abdul Raafik Arattu Thodika, Seonghoon Kim, Kwangho Nam, Wonpil Im
CHARMM-GUI QM/MM Interfacer for a Quantum Mechanical and Molecular Mechanical (QM/MM) Simulation Setup: 1. Semiempirical Methods. Journal of chemical theory and computation (2024)
Donghyuk Suh, Abdul Raafik Arattu Thodika, Seonghoon Kim, Kwangho Nam, Wonpil Im
CHARMM-GUI QM/MM Interfacer for a Quantum Mechanical and Molecular Mechanical (QM/MM) Simulation Setup: 1. Semiempirical Methods. Journal of chemical theory and computation 20 (12) (2024)
Beata Dulko-Smith, Pedro Ojeda-May, Jörgen Ådén, Magnus Wolf-Watz, Kwangho Nam
Mechanistic Basis for a Connection between the Catalytic Step and Slow Opening Dynamics of Adenylate Kinase. Journal of chemical information and modeling (2023)
Kwangho Nam, Abdul Raafik Arattu Thodika, Christin Grundström, Uwe H Sauer, Magnus Wolf-Watz
Elucidating Dynamics of Adenylate Kinase from Enzyme Opening to Ligand Release. Journal of chemical information and modeling 64 (1) (2023)
Kwangho Nam, Abdul Raafik Arattu Thodika, Christin Grundström, Uwe H Sauer, Magnus Wolf-Watz
Elucidating Dynamics of Adenylate Kinase from Enzyme Opening to Ligand Release. Journal of chemical information and modeling 64 (1) (2023)
Kwangho Nam, Magnus Wolf-Watz
Protein dynamics: The future is bright and complicated! Structural dynamics (Melville, N.Y.) 10 (1) (2023)
Kwangho Nam, Abdul Raafik Arattu Thodika, Christin Grundström, Uwe H Sauer, Magnus Wolf-Watz
Elucidating Dynamics of Adenylate Kinase from Enzyme Opening to Ligand Release. Journal of chemical information and modeling 64 (1) (2023)
Kwangho Nam, Abdul Raafik Arattu Thodika, Christin Grundström, Uwe H Sauer, Magnus Wolf-Watz
Elucidating Dynamics of Adenylate Kinase from Enzyme Opening to Ligand Release. Journal of chemical information and modeling 64 (1) (2023)
Beata Dulko-Smith, Pedro Ojeda-May, Jörgen Ådén, Magnus Wolf-Watz, Kwangho Nam
Mechanistic Basis for a Connection between the Catalytic Step and Slow Opening Dynamics of Adenylate Kinase. Journal of chemical information and modeling 63 (5) (2023)
Kwangho Nam, Abdul Raafik Arattu Thodika, Christin Grundström, Uwe H Sauer, Magnus Wolf-Watz
Elucidating Dynamics of Adenylate Kinase from Enzyme Opening to Ligand Release. Journal of chemical information and modeling (2023)
Xiaoliang Pan, Richard Van, Jingzhi Pu, Kwangho Nam, Yuezhi Mao, Yihan Shao
Free Energy Profile Decomposition Analysis for QM/MM Simulations of Enzymatic Reactions. Journal of chemical theory and computation (2023)
Kwangho Nam, Magnus Wolf-Watz
Protein dynamics: The future is bright and complicated! Structural dynamics (Melville, N.Y.) 10 (1) (2023)
Kwangho Nam, Abdul Raafik Arattu Thodika, Christin Grundström, Uwe H Sauer, Magnus Wolf-Watz
Elucidating Dynamics of Adenylate Kinase from Enzyme Opening to Ligand Release. Journal of chemical information and modeling 64 (1) (2023)
Kwangho Nam, Abdul Raafik Arattu Thodika, Christin Grundström, Uwe H Sauer, Magnus Wolf-Watz
Elucidating Dynamics of Adenylate Kinase from Enzyme Opening to Ligand Release. Journal of chemical information and modeling 64 (1) (2023)
Beata Dulko-Smith, Pedro Ojeda-May, Jörgen Ådén, Magnus Wolf-Watz, Kwangho Nam
Mechanistic Basis for a Connection between the Catalytic Step and Slow Opening Dynamics of Adenylate Kinase. Journal of chemical information and modeling 63 (5) (2023)
Kwangho Nam, Yunwen Tao, Victor Ovchinnikov
Molecular Simulations of Conformational Transitions within the Insulin Receptor Kinase Reveal Consensus Features in a Multistep Activation Pathway. The journal of physical chemistry. B (2023)
Kwangho Nam, Abdul Raafik Arattu Thodika, Christin Grundström, Uwe H Sauer, Magnus Wolf-Watz
Elucidating Dynamics of Adenylate Kinase from Enzyme Opening to Ligand Release. Journal of chemical information and modeling 64 (1) (2023)
Apoorv Verma, Emma Åberg-Zingmark, Tobias Sparrman, Ameeq Ul Mushtaq, Per Rogne, Christin Grundström, Ronnie P-A Berntsson, Uwe H Sauer, Lars Backman, Kwangho Nam, A Elisabeth Sauer-Eriksson, Magnus Wolf-Watz
Insights into the evolution of enzymatic specificity and catalysis: From Asgard archaea to human adenylate kinases. Science advances 8 (44) (2022)
Xiaoliang Pan, Richard Van, Evgeny Epifanovsky, Jian Liu, Jingzhi Pu, Kwangho Nam, Yihan Shao
Accelerating Ab Initio Quantum Mechanical and Molecular Mechanical (QM/MM) Molecular Dynamics Simulations with Multiple Time Step Integration and a Recalibrated Semiempirical QM/MM Hamiltonian. The journal of physical chemistry. B (2022)
Pawan Thapa, Nicholas K Byrnes, Alena A Denisenko, James X Mao, Austin D McDonald, Charleston A Newhouse, Thanh T Vuong, Katherine Woodruff, Kwangho Nam, David R Nygren, Benjamin J P Jones, Frank W Foss
Demonstration of Selective Single-Barium Ion Detection with Dry Diazacrown Ether Naphthalimide Turn-on Chemosensors. ACS sensors 6 (1) (2021)
Xiaoliang Pan, Junjie Yang, Richard Van, Evgeny Epifanovsky, Junming Ho, Jing Huang, Jingzhi Pu, Ye Mei, Kwangho Nam, Yihan Shao
Machine-Learning-Assisted Free Energy Simulation of Solution-Phase and Enzyme Reactions. Journal of chemical theory and computation 17 (9) (2021)
Xiaoliang Pan, Kwangho Nam, Evgeny Epifanovsky, Andrew C Simmonett, Edina Rosta, Yihan Shao
A simplified charge projection scheme for long-range electrostatics in ab initio QM/MM calculations. The Journal of chemical physics 154 (2) (2021)
Pedro Ojeda-May, Ameeq Ui Mushtaq, Per Rogne, Apoorv Verma, Victor Ovchinnikov, Christin Grundström, Beata Dulko-Smith, Uwe H Sauer, Magnus Wolf-Watz, Kwangho Nam
Dynamic Connection between Enzymatic Catalysis and Collective Protein Motions. Biochemistry 60 (28) (2021)
Uddhav K Shigdel, Victor Ovchinnikov, Seung-Joo Lee, Jenny A Shih, Martin Karplus, Kwangho Nam, Gregory L Verdine
The trajectory of intrahelical lesion recognition and extrusion by the human 8-oxoguanine DNA glycosylase. Nature communications 11 (1) (2020)
Per Rogne, Beata Dulko-Smith, Jack Goodman, Marie Rosselin, Christin Grundström, Christian Hedberg, Kwangho Nam, A Elisabeth Sauer-Eriksson, Magnus Wolf-Watz
Structural Basis for GTP versus ATP Selectivity in the NMP Kinase AK3. Biochemistry 59 (38) (2020)
Yaozong Li, Kwangho Nam
Repulsive Soft-Core Potentials for Efficient Alchemical Free Energy Calculations. Journal of chemical theory and computation 16 (8) (2020)
Kwangho Nam, Martin Karplus
Insights into the origin of the high energy-conversion efficiency of F1-ATPase. Proceedings of the National Academy of Sciences of the United States of America 116 (32) (2019)
Susanta Das, Kwangho Nam, Dan Thomas Major
Rapid Convergence of Energy and Free Energy Profiles with Quantum Mechanical Size in Quantum Mechanical-Molecular Mechanical Simulations of Proton Transfer in DNA. Journal of chemical theory and computation 14 (3) (2018)
Pedro Ojeda-May, Kwangho Nam
Acceleration of Semiempirical QM/MM Methods through Message Passage Interface (MPI), Hybrid MPI/Open Multiprocessing, and Self-Consistent Field Accelerator Implementations. Journal of chemical theory and computation 13 (8) (2017)
Yaozong Li, Kwangho Nam
Dynamic, structural and thermodynamic basis of insulin-like growth factor 1 kinase allostery mediated by activation loop phosphorylation. Chemical science 8 (5) (2017)