molecular-dynamics based markov state models (Molecular Dynamics Inc)
90
Structured Review
Molecular Dynamics Inc
molecular-dynamics based markov state models
Molecular Dynamics Based Markov State Models, supplied by Molecular Dynamics Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/system+dynamics-based+model/molecular+dynamics+based+markov+state+models/pm40014017-641-21-21
Average 90 stars, based on 1 article reviews
Molecular Dynamics Based Markov State Models, supplied by Molecular Dynamics Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/system+dynamics-based+model/molecular+dynamics+based+markov+state+models/pm40014017-641-21-21
Average 90 stars, based on 1 article reviews
molecular-dynamics based markov state models - by Bioz Stars,
2026-10
90/100 stars
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other:Article Title: Targeting Bacterial RNA Polymerase: Harnessing Simulations and Machine Learning to Design Inhibitors for Drug-Resistant Pathogens. Article Snippet: The increase in antimicrobial resistance presents a major challenge in treating bacterial infections, underscoring the need for innovative drug discovery approaches and novel inhibitors.. Bacterial RNA polymerase (RNAP) has emerged as a crucial target for antibiotic development due to its essential role in transcription.. RNAP is a molecular motor, and its function relies heavily on the dynamic shifts between multiple conformational states. Article Title: Understanding the Fast-Triggering Unfolding Dynamics of FK-11 upon Photoexcitation of Azobenzene Article Snippet: 2018, 140 (7), 2386-2396. (20) Malmstrom, R. D.; Lee, C. T.; Article Title: Elucidation of the Dynamics of Transcription Elongation by RNA Polymerase II using Kinetic Network Models Article Snippet: 2008, 129, 064107. (23) Malmstrom, R. D.; Lee, C. T.; Article Title: Effect of Clustering Algorithm on Establishing Markov State Model for Molecular Dynamics Simulations. Article Snippet: Recently, the Markov state model has been applied for kinetic analysis of molecular dynamics simulations.. However, discretization of the conformational space remains a primary challenge in model building, and it is not clear how the space decomposition by distinct clustering strategies exerts influence on the model output.. In this work, different clustering algorithms are employed to partition the conformational space sampled in opening and closing of fatty acid binding protein 4 as well as inactivation and activation of the epidermal growth factor receptor. Article Title: An Efficient Path Classification Algorithm Based on Variational Autoencoder to Identify Metastable Path Channels for Complex Conformational Changes. Article Snippet: Conformational changes (i.e., dynamic transitions between pairs of conformational states) play important roles in many chemical and biological processes.. Constructing the Markov state model (MSM) from extensive molecular dynamics (MD) simulations is an effective approach to dissect the mechanism of conformational changes.. When combined with transition path theory (TPT), MSM can be applied to elucidate the ensemble of kinetic pathways connecting pairs of conformational states. Article Title: Markov State Models Provide Insights into Dynamic Modulation of Protein Function Article Snippet: 2014, 21, 626−632. (17) Malmstrom, R. D.; Lee, C. T.; Article Title: SARS-CoV-2 RNA-Dependent RNA Polymerase Follows Asynchronous Translocation Pathway for Viral Transcription and Replication. Article Snippet: Translocation is one essential step for the SARS-CoV-2 RNAdependent RNA polymerase (RdRp) to exert viral replication and transcription.. Although cryo-EM structures of SARS-CoV-2 RdRp are available, the molecular mechanisms of dynamic translocation remain elusive.. Herein, we constructed a Markov state model based on extensive molecular dynamics simulations to elucidate the translocation dynamics of the SARS-CoV-2 RdRp. Article Title: Design of ?-amyloid aggregation inhibitors from a predicted structural motif Article Snippet: Towards this end, we have previously reported the results of a |
