ArticleScientific reports2015
Cloud computing approaches for prediction of ligand binding poses and pathways.
Article in Scientific reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
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- Incorporating Prior Knowledge in the Seeds of Adaptive Sampling Molecular Dynamics Simulations of Ligand Transport in Enzymes with Buried Active Sites.Journal of chemical theory and computation · 2024Article
- Tutorial on how to build non-Markovian dynamic models from molecular dynamics simulations for studying protein conformational changes.The Journal of chemical physics · 2024Article
- Integrative generalized master equation: A method to study long-timescale biomolecular dynamics via the integrals of memory kernels.The Journal of chemical physics · 2023Article
- An Efficient Path Classification Algorithm Based on Variational Autoencoder to Identify Metastable Path Channels for Complex Conformational Changes.Journal of chemical theory and computation · 2023Article
- Sequence controlled secondary structure is important for the site-selectivity of lanthipeptide cyclization.Chemical science · 2023Article
- Exploring ligand binding pathways on proteins using hypersound-accelerated molecular dynamics.Nature communications · 2021Article
- Role of bacterial RNA polymerase gate opening dynamics in DNA loading and antibiotics inhibition elucidated by quasi-Markov State Model.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- De Novo Prediction of Binders and Nonbinders for T4 Lysozyme by gREST Simulations.Journal of chemical information and modeling · 2019Article
- Massive-Scale Binding Free Energy Simulations of HIV Integrase Complexes Using Asynchronous Replica Exchange Framework Implemented on the IBM WCG Distributed Network.Journal of chemical information and modeling · 2019Article
- How Effectively Can Adaptive Sampling Methods Capture Spontaneous Ligand Binding?Journal of chemical theory and computation · 2019Article
- Conformational investigation of the structure-activity relationship of GdFFD and its analogues on an achatin-like neuropeptide receptor of Aplysia californica involved in the feeding circuit.Physical chemistry chemical physics : PCCP · 2018Article
- An in silico high-throughput screen identifies potential selective inhibitors for the non-receptor tyrosine kinase Pyk2.Drug design, development and therapy · 2017Article
- Conformational heterogeneity of the calmodulin binding interface.Nature communications · 2016Article
- A network of molecular switches controls the activation of the two-component response regulator NtrC.Nature communications · 2015Article
- A comprehensive mechanism for 5-carboxylcytosine-induced transcriptional pausing revealed by Markov state models.The Journal of biological chemistryArticle
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
We describe an innovative protocol for ab initio prediction of ligand crystallographic binding poses and highly effective analysis of large datasets generated for protein-ligand dynamics. We include a procedure for setup and performance of distributed molecular dynamics simulations on cloud computing architectures, a model for efficient analysis of simulation data, and a metric for evaluation of model convergence. We give accurate binding pose predictions for five ligands ranging in affinity from 7 nM to > 200 μM for the immunophilin protein FKBP12, for expedited results in cases where experimental structures are difficult to produce. Our approach goes beyond single, low energy ligand poses to give quantitative kinetic information that can inform protein engineering and ligand design.
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