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Publication search results
found 771 matches
- 2024
- Hossein Nikravesh Matin, Saeed Setayeshi:
A computational tumor growth model experience based on molecular dynamics point of view using deep cellular automata. Artif. Intell. Medicine 148: 102752 (2024) - Fangfang Guo, Hengzheng Yang, Shihong Li, Yongxin Jiang, Xue Bai, Chengxiang Hu, Wannan Li, Weiwei Han:
Using Gaussian accelerated molecular dynamics combined with Markov state models to explore the mechanism of action of new oral inhibitors on Complex I. Comput. Biol. Medicine 177: 108598 (2024) - Qianqian Wang, Mingyu Zhang, Aohan Li, Xiaojun Yao, Yingqing Chen:
Unraveling the allosteric inhibition mechanism of PARP-1 CAT and the D766/770A mutation effects via Gaussian accelerated molecular dynamics and Markov state model. Comput. Biol. Medicine 168: 107682 (2024) - Deyan I. Mihaylov, S. X. Hu, Valentin V. Karasiev:
Dragon: A multi-GPU orbital-free density functional theory molecular dynamics simulation package for modeling of warm dense matter. Comput. Phys. Commun. 294: 108931 (2024) - Peter Ogrin, Cristiano L. Dias, Tomaz Urbic:
Code for molecular dynamics simulation of two dimensional Mercedes-Benz water model. Comput. Phys. Commun. 303: 109267 (2024) - Sebastian Anila, Sergey A. Samsonov:
Benchmarking Water Models in Molecular Dynamics of Protein-Glycosaminoglycan Complexes. J. Chem. Inf. Model. 64(5): 1691-1703 (2024) - Felipe Bravo-Moraga, Mauricio Bedoya, Ariela Vergara Jaque, Jans H. Alzate-Morales:
Understanding the Differences of Danusertib's Residence Time in Aurora Kinases A/B: Dissociation Paths and Key Residues Identified using Conventional and Enhanced Molecular Dynamics Simulations. J. Chem. Inf. Model. 64(12): 4759-4772 (2024) - Matic Broz, Chris Oostenbrink, Urban Bren:
The Effect of Microwaves on Protein Structure: Molecular Dynamics Approach. J. Chem. Inf. Model. 64(6): 2077-2083 (2024) - Manuel Carrer, Henrique M. Cezar, Sigbjørn Løland Bore, Morten Ledum, Michele Cascella:
Learning Force Field Parameters from Differentiable Particle-Field Molecular Dynamics. J. Chem. Inf. Model. 64(14): 5510-5520 (2024) - Zakaria L. Dahmani, Ana Ligia Scott, Catherine Vénien-Bryan, David Perahia, Mauricio G. S. Costa:
MDFF_NM: Improved Molecular Dynamics Flexible Fitting into Cryo-EM Density Maps with a Multireplica Normal Mode-Based Search. J. Chem. Inf. Model. 64(13): 5151-5160 (2024) - Yanjun Feng, Changda Gong, Jieyu Zhu, Guixia Liu, Yun Tang, Weihua Li:
Unraveling the Ligand-Binding Sites of CYP3A4 by Molecular Dynamics Simulations with Solvent Probes. J. Chem. Inf. Model. 64(8): 3451-3464 (2024) - Jingwei Gao, Cong Zhang, Hangyu Xu, Tianshu Zhang, Hongshuang Wang, Yibo Wang, Xiaohui Wang:
Dissecting the Role of the Hydroxyl Moiety at C14 in (+)-Opioid-Based TLR4 Antagonists via Wet-Lab Experiments and Molecular Dynamics Simulations. J. Chem. Inf. Model. 64(13): 5273-5284 (2024) - Fengjuan Huang, Jiahui Huang, Jiajia Yan, Yuying Liu, Jiangfang Lian, Qinxue Sun, Feng Ding, Yunxiang Sun:
Molecular Insights into the Effects of F16L and F19L Substitutions on the Conformation and Aggregation Dynamics of Human Calcitonin. J. Chem. Inf. Model. 64(11): 4500-4510 (2024) - Anton Jansen, Noora Aho, Gerrit Groenhof, Pavel Buslaev, Berk Hess:
phbuilder: A Tool for Efficiently Setting up Constant pH Molecular Dynamics Simulations in GROMACS. J. Chem. Inf. Model. 64(3): 567-574 (2024) - Petra Kührová, Vojtech Mlýnský, Michal Otyepka, Jirí Sponer, Pavel Banás:
Correction to "Sensitivity of the RNA Structure to Ion Conditions as Probed by Molecular Dynamics Simulations of Common Canonical RNA Duplexes". J. Chem. Inf. Model. 64(13): 5356 (2024) - Sonia Kumari, Masilamani Elizabeth Sobhia:
Targeting an Old Foe for Cancer: A Molecular Dynamics Perspective to Unravel the Specific Binding Nature of 2-Methoxy Estradiol to Human β-Tubulin Isotypes. J. Chem. Inf. Model. 64(10): 4121-4133 (2024) - Midhun K. Madhu, Kunal Shewani, Rajesh K. Murarka:
Biased Signaling in Mutated Variants of β2-Adrenergic Receptor: Insights from Molecular Dynamics Simulations. J. Chem. Inf. Model. 64(2): 449-469 (2024) - Yasir Mamun, Yuk-Ching Tse-Dinh, Prem Chapagain:
Insights into the DNA and RNA Interactions of Human Topoisomerase III Beta Using Molecular Dynamics Simulations. J. Chem. Inf. Model. 64(15): 6062-6071 (2024) - Nishita Mandal, Bartlomiej Surpeta, Jan Brezovsky:
Reinforcing Tunnel Network Exploration in Proteins Using Gaussian Accelerated Molecular Dynamics. J. Chem. Inf. Model. 64(16): 6623-6635 (2024) - Gabriel F. Martins, Nuno Galamba:
Wild-Type α-Synuclein Structure and Aggregation: A Comprehensive Coarse-Grained and All-Atom Molecular Dynamics Study. J. Chem. Inf. Model. 64(15): 6115-6131 (2024) - Yunhao Mei, Yong Shen:
Cation-π Interactions Greatly Influence Ion Transportability of the Light-Driven Sodium Pump KR2: A Molecular Dynamics Study. J. Chem. Inf. Model. 64(3): 974-982 (2024) - Pawan Panwar, Quanpeng Yang, Ashlie Martini:
Temperature-Dependent Density and Viscosity Prediction for Hydrocarbons: Machine Learning and Molecular Dynamics Simulations. J. Chem. Inf. Model. 64(7): 2760-2774 (2024) - Rutika Patel, Augustine Onyema, Phu K. Tang, Sharon M. Loverde:
Conformational Dynamics of the Nucleosomal Histone H2B Tails Revealed by Molecular Dynamics Simulations. J. Chem. Inf. Model. 64(12): 4709-4726 (2024) - Anupom Roy, Mikko Karttunen:
A Molecular Dynamics Simulation Study of the Effects of βGln114 Mutation on the Dynamic Behavior of the Catalytic Site of the Tryptophan Synthase. J. Chem. Inf. Model. 64(3): 983-1003 (2024) - Mateusz Rzycki, Dominik Drabik:
Multifaceted Activity of Fabimycin: Insights from Molecular Dynamics Studies on Bacterial Membrane Models. J. Chem. Inf. Model. 64(10): 4204-4217 (2024) - Mehdi Sahihi, Pierre Fayon, Lionel Nauton, Florent Goujon, Julien Devémy, Alain Dequidt, Patrice Hauret, Patrice Malfreyt:
Probing Enzymatic PET Degradation: Molecular Dynamics Analysis of Cutinase Adsorption and Stability. J. Chem. Inf. Model. 64(10): 4112-4120 (2024) - Anna P. Tolstova, Alexander A. Makarov, Alexei A. Adzhubei:
Structure Comparison of Beta Amyloid Peptide Aβ 1-42 Isoforms. Molecular Dynamics Modeling. J. Chem. Inf. Model. 64(3): 918-932 (2024) - Mingqiong Tong, Peng Liu, Chaoqun Li, Zhongyu Zhang, Wan Sun, Pingxuan Dong, Na Fan, Xiaoyue Wang, Jing Liu, Chao Lv, Zanxia Cao, Yan Wang:
Interaction of Asn297-Linked Glycan Ligands with the Fc Fragment of the Immunoglobulin Class G1: A Molecular Dynamics Simulation Study. J. Chem. Inf. Model. 64(3): 785-798 (2024) - José Luis Velázquez-Libera, Julio Caballero, Jans H. Alzate-Morales, Jose Javier Ruiz-Pernía, Iñaki Tuñón:
Understanding the Interactions of Ubiquitin-Specific Protease 7 with Its Substrates through Molecular Dynamics Simulations: Insights into the Role of Its C-Terminal Domains in Substrate Recognition. J. Chem. Inf. Model. 64(10): 4134-4148 (2024) - Christopher Vorreiter, Dina Robaa, Wolfgang Sippl:
Exploring Aromatic Cage Flexibility Using Cosolvent Molecular Dynamics Simulations─An In-Silico Case Study of Tudor Domains. J. Chem. Inf. Model. 64(11): 4553-4569 (2024)
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