Synchrotron radiation as a tool for macromolecular X-Ray Crystallography: A XXI century perspective

Grabowski, M.; Cooper, David R.; Brzeziński, Dariusz; Macnar, Joanna M.; Shabalin, I.G.; Cymborowski, M.; Otwinowski, Zbyszek; Minor, Władek

doi:10.1016/j.nimb.2020.12.016

Cited by 4 publications

(2 citation statements)

References 63 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…By using a 3.5 T superB magnet, the photon energy of the storage ring is extended to the hard X-ray region. The fourth-generation light sources will exceed the performance of previous sources by one or more orders of magnitude in terms of the important parameters such as brightness, coherence and shortness of pulse duration (Grabowski et al, 2021). The high degree of coherence will allow efficient focusing of the synchrotron beams to the nanometre range.…”

Section: Introductionmentioning

confidence: 99%

A distributed data processing scheme based on Hadoop for synchrotron radiation experiments

Zhang,

Dai,

Sun

et al. 2024

J Synchrotron Radiat

View full text Add to dashboard Cite

With the development of synchrotron radiation sources and high-frame-rate detectors, the amount of experimental data collected at synchrotron radiation beamlines has increased exponentially. As a result, data processing for synchrotron radiation experiments has entered the era of big data. It is becoming increasingly important for beamlines to have the capability to process large-scale data in parallel to keep up with the rapid growth of data. Currently, there is no set of data processing solutions based on the big data technology framework for beamlines. Apache Hadoop is a widely used distributed system architecture for solving the problem of massive data storage and computation. This paper presents a set of distributed data processing schemes for beamlines with experimental data using Hadoop. The Hadoop Distributed File System is utilized as the distributed file storage system, and Hadoop YARN serves as the resource scheduler for the distributed computing cluster. A distributed data processing pipeline that can carry out massively parallel computation is designed and developed using Hadoop Spark. The entire data processing platform adopts a distributed microservice architecture, which makes the system easy to expand, reduces module coupling and improves reliability.

show abstract

Section: Introductionmentioning

confidence: 99%

A distributed data processing scheme based on Hadoop for synchrotron radiation experiments

Zhang,

Dai,

Sun

et al. 2024

J Synchrotron Radiat

View full text Add to dashboard Cite

show abstract

“…The three primary techniques used for structural studies are X-ray crystallography (PX), cryogenic electron microscopy (cryoEM), 1 and nuclear magnetic resonance (NMR). Despite advances in hardware, software, databases, and experimental protocols, which resulted in very high-quality macromolecular models for all three techniques, macromolecular crystallography remains the dominant technique for studying complexes between macromolecules and small molecule ligands, 2 because it provides very accurate and reliable models of interactions for complexes that cannot be analyzed with cryoEM.…”

Section: Introductionmentioning

confidence: 99%

Optimal structure determination from sub‐optimal diffraction data

et al. 2021

Self Cite

View full text Add to dashboard Cite

Herein we present the newest version of the HKL-3000 system that integrates data collection, data reduction, phasing, model building, refinement, and validation. The system significantly accelerates the process of structure determination and has proven its high value for the determination of very high-quality structures. The heuristic for choosing the best approach for every step of structure determination for various quality samples and diffraction data has been optimized. The latest modifications increase the likelihood of a successful structure determination with challenging data. The HKL-3000 is a successor of HKL and HKL-2000 programs. The use of the HKL family of programs has been reported for over 73,000 PDB deposits, that is, almost 50% of macromolecular structures determined with X-ray diffraction.

show abstract

References

2023

Radioactivity

View full text Add to dashboard Cite

Synchrotron radiation as a tool for macromolecular X-Ray Crystallography: A XXI century perspective

Cited by 4 publications

References 63 publications

A distributed data processing scheme based on Hadoop for synchrotron radiation experiments

A distributed data processing scheme based on Hadoop for synchrotron radiation experiments

Optimal structure determination from sub‐optimal diffraction data

References

Contact Info

Product

Resources

About