2020
DOI: 10.1002/pro.3995
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Using Integrative Modeling Platform to compute, validate, and archive a model of a protein complex structure

Abstract: Biology is advanced by producing structural models of biological systems, such as protein complexes. Some systems are recalcitrant to traditional structure determination methods. In such cases, it may still be possible to produce useful models by integrative structure determination that depends on simultaneous use of multiple types of data. An ensemble of models that are sufficiently consistent with the data is produced by a structural sampling method guided by a data-dependent scoring function. The variation … Show more

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Cited by 43 publications
(89 citation statements)
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“…Sufficient sampling, as opposed to optimization, is especially required for analyzing a Bayesian posterior model density [70]. If a sufficient model sample is in hand, the J o u r n a l P r e -p r o o f uncertainty of a model can be directly estimated based on the variability in the sample [9]. Thus, efficient structural sampling algorithms and computing hardware are needed.…”
Section: Bayesian Scoring Functionmentioning
confidence: 99%
“…Sufficient sampling, as opposed to optimization, is especially required for analyzing a Bayesian posterior model density [70]. If a sufficient model sample is in hand, the J o u r n a l P r e -p r o o f uncertainty of a model can be directly estimated based on the variability in the sample [9]. Thus, efficient structural sampling algorithms and computing hardware are needed.…”
Section: Bayesian Scoring Functionmentioning
confidence: 99%
“…Integrative structural modeling proceeded through the standard four-stage protocol ( Kim et al, 2018 ; Rout and Sali, 2019 ; Russel et al, 2012 ; Saltzberg et al, 2021 ), which was scripted using the Python Modeling Interface package, a library for modeling macromolecular complexes based on the Integrative Modeling Platform software ( Russel et al, 2012 ), version develop-31a0ad09b4 ( https://integrativemodeling.org ). The RBD, spanning amino acids R319-F541 was represented using the crystal structure of the co-complex of ACE2 bound RBD (PDB ID: 6M0J ( Lan et al, 2020 )).…”
Section: Methodsmentioning
confidence: 99%
“…With the RBD fixed in space, 2,500,000 alternate docked nanobody models were produced through 50 runs of replica exchange Gibbs sampling based on the Metropolis Monte Carlo algorithm, where each Monte Carlo step consisted of a series of random rotations and translations of rigid nanobodies. The initial set of models was filtered to select an ensemble of 26,400 good scoring models through a model validation pipeline as detailed ( Rout and Sali, 2019 ; Saltzberg et al, 2021 ; Viswanath et al, 2017 ). This ensemble satisfied all of the 27 crosslinks (for S1–1, S1–23 and S1-RBD-15) used for modeling, i.e.…”
Section: Methodsmentioning
confidence: 99%
“…Integrative structure determination of Smc5/6-Nse2/5/6 complex. Integrative structure modeling proceeded through the standard four-stage protocol (33)(34)(35)(36)(37), which was scripted using the Python Modeling Interface package, a library for modeling macromolecular complexes based…”
Section: Methodsmentioning
confidence: 99%
“…We omitted Nse-1-3-4 due to insufficient data to determine their juxtaposition in the complex. We used an integrative approach (33)(34)(35)(36)(37) to generate a structure of the five-subunit complex composed of Smc5, 6, and Nse2, 5, and 6 (designated Smc5/6-Nse2/5/6; Fig. 4A).…”
Section: Integrative Structure Modeling Of a Five-subunit Smc5/6 Complexmentioning
confidence: 99%