2019
DOI: 10.1101/839597
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GPCRmd uncovers the dynamics of the 3D-GPCRome

Abstract: G protein-coupled receptors (GPCRs) are involved in numerous physiological processes and the most frequent targets of approved drugs. The striking explosion in the number of new 3D molecular structures of GPCRs (3D-GPCRome) during the last decade has greatly advanced the mechanistic understanding and drug design opportunities for this protein family. While experimentally-resolved structures undoubtedly provide valuable snapshots of specific GPCR conformational states, they give only limited information on thei… Show more

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Cited by 15 publications
(25 citation statements)
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References 54 publications
(46 reference statements)
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“…and Ext. 9.42 ± 0.08 E-1 4.68 ± 0.00 E-1 Datasets Datasets used in this work are atomistic simulation trajectories of drug-target proteins reported in [19] and [20]. The two main datasets from [19] used are simulations of proteins in presence of FDA approved or underinvestigation molecules, as we aim to test the performance of ProGAE on capturing drug-induced structural variations.…”
Section: Training Loss S Protein Hace2mentioning
confidence: 99%
See 1 more Smart Citation
“…and Ext. 9.42 ± 0.08 E-1 4.68 ± 0.00 E-1 Datasets Datasets used in this work are atomistic simulation trajectories of drug-target proteins reported in [19] and [20]. The two main datasets from [19] used are simulations of proteins in presence of FDA approved or underinvestigation molecules, as we aim to test the performance of ProGAE on capturing drug-induced structural variations.…”
Section: Training Loss S Protein Hace2mentioning
confidence: 99%
“…To show that a single ProGAE model can be trained on multiple different proteins, we also utilize simulations of 38 different G protein-coupled receptors from the GPCRmd dataset [20]. More information on these datasets is included in Appendix A.4.…”
Section: Training Loss S Protein Hace2mentioning
confidence: 99%
“…Finally, large collections of molecular dynamics (MD) trajectories [161,162] may be exploited toward protein flexibility learning. However, today unbiased MD simulations are still too short (and likely too inaccurate) to sample large conformational changes.…”
Section: Protein Disorder Flexibility and Dynamicsmentioning
confidence: 99%
“…By these means, GPCRmd promotes transparency, consistency, and reproducibility in the field of GPCR dynamics and also facilitates data exchange between GPCR scientists from different disciplines. 24 Well before the official end of COST funding, the inclusiveness and influence of GLISTEN drove an intense community-wide desire to evolve a new COST Action. At the same time, developments in the field made clear that in order to meet current challenges, a wider perspective must be taken (explained in detail below).…”
Section: ■ Glisten and The Dawn Of Ernestmentioning
confidence: 99%