A Novel Approach to Data Collection for Difficult Structures: Data Management for Large Numbers of Crystals with the BLEND Software

Mylona, Anastasia; Carr, S.B.; Aller, Pierre; Moraes, Isabel; Treisman, Richard; Evans, Gwyndaf; Foadi, James

doi:10.3390/cryst7080242

Cited by 6 publications

(4 citation statements)

References 42 publications

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“…DIALS is able to natively process data obtained at X-ray free-electron laser (XFEL) facilities (Ginn et al, 2015;Uervirojnangkoorn et al, 2015) and supports multi-crystal scaling (Beilsten-Edmands et al, 2020) and analysis via xia2.multiplex (Gildea et al, 2022), serial crystallography (Brewster et al, 2018;Parkhurst, 2020) and electron diffraction such as that obtained with standard field emission gun (FEG) cryo-microscopes (Clabbers et al, 2018). Data from multiple crystals may be scaled and merged together with BLEND (Mylona et al, 2017). Ice rings and further pathologies in measured data can be identified by a separate standalone tool named AUSPEX, which provides visual and automatic diagnostics based on statistics (Thorn et al, 2017) and, more recently, machine learning (Nolte et al, 2022).…”

Section: Data Processingmentioning

confidence: 99%

The CCP4 suite: integrative software for macromolecular crystallography

Agirre¹,

Atanasova²,

Bagdonas³

et al. 2023

Acta Crystallogr D Struct Biol

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202

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The Collaborative Computational Project No. 4 (CCP4) is a UK-led international collective with a mission to develop, test, distribute and promote software for macromolecular crystallography. The CCP4 suite is a multiplatform collection of programs brought together by familiar execution routines, a set of common libraries and graphical interfaces. The CCP4 suite has experienced several considerable changes since its last reference article, involving new infrastructure, original programs and graphical interfaces. This article, which is intended as a general literature citation for the use of the CCP4 software suite in structure determination, will guide the reader through such transformations, offering a general overview of the new features and outlining future developments. As such, it aims to highlight the individual programs that comprise the suite and to provide the latest references to them for perusal by crystallographers around the world.

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Section: Data Processingmentioning

confidence: 99%

The CCP4 suite: integrative software for macromolecular crystallography

Agirre¹,

Atanasova²,

Bagdonas³

et al. 2023

Acta Crystallogr D Struct Biol

Self Cite

202

View full text Add to dashboard Cite

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“…Many of these same packages can create and refine experimental parameter models, index reflections and integrate reflection intensities. Programs such as KAMO [87] and Blend [88] facilitate the identification of consistent unit cells and evaluate the capacity of data subsets to be merged. Their algorithms rely on the relationships between cell parameters or intensity correlations to select suitable merge sets.…”

Section: Toward Real-time Processingmentioning

confidence: 99%

Data-driven challenges and opportunities in crystallography

Glynn

Rodríguez

2019

Emerging Topics in Life Sciences

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Structural biology is in the midst of a revolution fueled by faster and more powerful instruments capable of delivering orders of magnitude more data than their predecessors. This increased pace in data gathering introduces new experimental and computational challenges, frustrating real-time processing and interpretation of data and requiring long-term solutions for data archival and retrieval. This combination of challenges and opportunities is driving the exploration of new areas of structural biology, including studies of macromolecular dynamics and the investigation of molecular ensembles in search of a better understanding of conformational landscapes. The next generation of instruments promises to yield even greater data rates, requiring a concerted effort by institutions, centers and individuals to extract meaning from every bit and make data accessible to the community at large, facilitating data mining efforts by individuals or groups as analysis tools improve.

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“…The MPL was established in 2007 and has supported MP research projects, which have led to 29 depositions in the PDB (Table 1). Further work by scientists at the MPL has advanced MP production, crystallography and data processing [10][11][12][13][14][15][16]. During the last decade, there has been a shift towards solving structures of eukaryotic, mainly human, MPs.…”

Section: Introductionmentioning

confidence: 99%

Changes in Membrane Protein Structural Biology

Birch

Cheruvara

Gamage

et al. 2020

Biology

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Membrane proteins are essential components of many biochemical processes and are important pharmaceutical targets. Membrane protein structural biology provides the molecular rationale for these biochemical process as well as being a highly useful tool for drug discovery. Unfortunately, membrane protein structural biology is a difficult area of study due to low protein yields and high levels of instability especially when membrane proteins are removed from their native environments. Despite this instability, membrane protein structural biology has made great leaps over the last fifteen years. Today, the landscape is almost unrecognisable. The numbers of available atomic resolution structures have increased 10-fold though advances in crystallography and more recently by cryo-electron microscopy. These advances in structural biology were achieved through the efforts of many researchers around the world as well as initiatives such as the Membrane Protein Laboratory (MPL) at Diamond Light Source. The MPL has helped, provided access to and contributed to advances in protein production, sample preparation and data collection. Together, these advances have enabled higher resolution structures, from less material, at a greater rate, from a more diverse range of membrane protein targets. Despite this success, significant challenges remain. Here, we review the progress made and highlight current and future challenges that will be overcome.

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A Novel Approach to Data Collection for Difficult Structures: Data Management for Large Numbers of Crystals with the BLEND Software

Cited by 6 publications

References 42 publications

The CCP4 suite: integrative software for macromolecular crystallography

The CCP4 suite: integrative software for macromolecular crystallography

Data-driven challenges and opportunities in crystallography

Changes in Membrane Protein Structural Biology

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