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Article ; Online: Advanced exploitation of unmerged reflection data during processing and refinement with autoPROC and BUSTER.

Vonrhein, Clemens / Flensburg, Claus / Keller, Peter / Fogh, Rasmus / Sharff, Andrew / Tickle, Ian J / Bricogne, Gérard

Acta crystallographica. Section D, Structural biology

2024 Volume 80, Issue Pt 3, Page(s) 148–158

Abstract: The validation of structural models obtained by macromolecular X-ray crystallography against experimental diffraction data, whether before deposition into the PDB or after, is typically carried out exclusively against the merged data that are eventually ... ...

Abstract	The validation of structural models obtained by macromolecular X-ray crystallography against experimental diffraction data, whether before deposition into the PDB or after, is typically carried out exclusively against the merged data that are eventually archived along with the atomic coordinates. It is shown here that the availability of unmerged reflection data enables valuable additional analyses to be performed that yield improvements in the final models, and tools are presented to implement them, together with examples of the results to which they give access. The first example is the automatic identification and removal of image ranges affected by loss of crystal centering or by excessive decay of the diffraction pattern as a result of radiation damage. The second example is the `reflection-auditing' process, whereby individual merged data items showing especially poor agreement with model predictions during refinement are investigated thanks to the specific metadata (such as image number and detector position) that are available for the corresponding unmerged data, potentially revealing previously undiagnosed instrumental, experimental or processing problems. The third example is the calculation of so-called F(early) - F(late) maps from carefully selected subsets of unmerged amplitude data, which can not only highlight the location and extent of radiation damage but can also provide guidance towards suitable fine-grained parametrizations to model the localized effects of such damage.
MeSH term(s)	Crystallography, X-Ray ; Macromolecular Substances/chemistry
Chemical Substances	Macromolecular Substances
Language	English
Publishing date	2024-02-27
Publishing country	United States
Document type	Journal Article
ZDB-ID	2968623-4
ISSN	2059-7983 ; 0907-4449
ISSN (online)	2059-7983
ISSN	0907-4449
DOI	10.1107/S2059798324001487
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Article ; Online: Statistical quality indicators for electron-density maps.

Tickle, Ian J

Acta crystallographica. Section D, Biological crystallography

2012 Volume 68, Issue Pt 4, Page(s) 454–467

Abstract: The commonly used validation metrics for the local agreement of a structure model with the observed electron density, namely the real-space R (RSR) and the real-space correlation coefficient (RSCC), are reviewed. It is argued that the primary goal of all ...

Abstract	The commonly used validation metrics for the local agreement of a structure model with the observed electron density, namely the real-space R (RSR) and the real-space correlation coefficient (RSCC), are reviewed. It is argued that the primary goal of all validation techniques is to verify the accuracy of the model, since precision is an inherent property of the crystal and the data. It is demonstrated that the principal weakness of both of the above metrics is their inability to distinguish the accuracy of the model from its precision. Furthermore, neither of these metrics in their usual implementation indicate the statistical significance of the result. The statistical properties of electron-density maps are reviewed and an improved alternative likelihood-based metric is suggested. This leads naturally to a χ(2) significance test of the difference density using the real-space difference density Z score (RSZD). This is a metric purely of the local model accuracy, as required for effective model validation and structure optimization by practising crystallographers prior to submission of a structure model to the PDB. A new real-space observed density Z score (RSZO) is also proposed; this is a metric purely of the model precision, as a substitute for other precision metrics such as the B factor.
MeSH term(s)	Crystallography, X-Ray/methods ; Electrons ; Models, Molecular
Language	English
Publishing date	2012-03-16
Publishing country	United States
Document type	Journal Article
ZDB-ID	2020492-9
ISSN	1399-0047 ; 0907-4449
ISSN (online)	1399-0047
ISSN	0907-4449
DOI	10.1107/S0907444911035918
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Article: Experimental determination of optimal root-mean-square deviations of macromolecular bond lengths and angles from their restrained ideal values.

Tickle, Ian J

Acta crystallographica. Section D, Biological crystallography

2007 Volume 63, Issue Pt 12, Page(s) 1274–81; author reply 1282–3

Abstract: ... in this area [Tickle et al. (1998), Acta Cryst. D54, 243-252] and indeed appear to be based ...

Abstract	A number of inconsistencies are apparent in the recent research paper by Jaskolski et al. [(2007), Acta Cryst. D63, 611-620] concerning their recommendations for the values of the magnitude and resolution-dependence of the root-mean-square deviations (RMSDs) of bond lengths and angles from their restrained ideal values in macromolecular refinement, as well as their suggestions for the use of variable standard uncertainties dependent on atomic displacement parameters (ADPs) and occupancies. Whilst many of the comments and suggestions in the paper regarding updates for the ideal geometry values proposed by Engh and Huber are entirely reasonable and supported by the experimental evidence, the recommendations concerning the optimal values of RMSDs appear to be in conflict with previous experimental and theoretical work in this area [Tickle et al. (1998), Acta Cryst. D54, 243-252] and indeed appear to be based on a misunderstanding of the distinction between RMSD and standard uncertainty (SU). In contrast, it is proposed here that the optimal values of all desired weighting parameters, in particular the weighting parameters for the ADP differences and for the diffraction terms, be estimated by the purely objective procedure of maximizing the experiment-based log(free likelihood). In principle, this allows all weighting parameters that are not known accurately a priori to be scaled globally, relative to those that are known accurately, for an optimal refinement. The RMS Z score (RMSZ) is recommended as a more satisfactory statistic than the RMSD to assess the extent to which the geometry deviates from the ideal values and a theoretical rationale for the results obtained is presented in which the optimal RMSZ is identified as the calculated versus true Z-score correlation coefficient, the latter being a monotonic function of the resolution cutoff of the data. Regarding the proposal to use variable standard uncertainties, it is suggested that any departure from the current practice of using fixed weights for geometric restraints based on experimental values of standard uncertainties be subject to the same experiment-based validation.
MeSH term(s)	Data Interpretation, Statistical ; Least-Squares Analysis ; Likelihood Functions ; Models, Molecular ; Molecular Structure ; Multiprotein Complexes/chemistry ; Uncertainty ; X-Ray Diffraction
Chemical Substances	Multiprotein Complexes
Language	English
Publishing date	2007-12
Publishing country	United States
Document type	Comment ; Letter
ZDB-ID	2020492-9
ISSN	2059-7983 ; 1399-0047 ; 0907-4449
ISSN (online)	2059-7983 ; 1399-0047
ISSN	0907-4449
DOI	10.1107/S0907444907050196
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Article: Fragment screening using X-ray crystallography.

Davies, Thomas G / Tickle, Ian J

Topics in current chemistry

2012 Volume 317, Page(s) 33–59

Abstract: The fragment-based approach is now well established as an important component of modern drug discovery. A key part in establishing its position as a viable technique has been the development of a range of biophysical methodologies with sufficient ... ...

Abstract	The fragment-based approach is now well established as an important component of modern drug discovery. A key part in establishing its position as a viable technique has been the development of a range of biophysical methodologies with sufficient sensitivity to detect the binding of very weakly binding molecules. X-ray crystallography was one of the first techniques demonstrated to be capable of detecting such weak binding, but historically its potential for screening was under-appreciated and impractical due to its relatively low throughput. In this chapter we discuss the various benefits associated with fragment-screening by X-ray crystallography, and describe the technical developments we have implemented to allow its routine use in drug discovery. We emphasize how this approach has allowed a much greater exploitation of crystallography than has traditionally been the case within the pharmaceutical industry, with the rapid and timely provision of structural information having maximum impact on project direction.
MeSH term(s)	Crystallography, X-Ray ; Drug Discovery/methods ; High-Throughput Screening Assays/methods ; Models, Molecular ; Small Molecule Libraries/analysis ; Small Molecule Libraries/chemistry
Chemical Substances	Small Molecule Libraries
Language	English
Publishing date	2012
Publishing country	Germany
Document type	Journal Article ; Review
ISSN	0340-1022
ISSN	0340-1022
DOI	10.1007/128_2011_179
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Article: 'Schizophrenia is a dirty word': service users' experiences of receiving a diagnosis of schizophrenia.

Howe, Lorna / Tickle, Anna / Brown, Ian

Psychiatric bulletin (2014)

2014 Volume 38, Issue 4, Page(s) 154–158

Abstract: Aims and method To explore service users' experiences of receiving a diagnosis of schizophrenia and the stigma associated with the diagnostic label. Seven participants were interviewed about their perceptions of these experiences. Interviews were ... ...

Abstract	Aims and method To explore service users' experiences of receiving a diagnosis of schizophrenia and the stigma associated with the diagnostic label. Seven participants were interviewed about their perceptions of these experiences. Interviews were analysed using interpretative phenomenological analysis. Results Five superordinate themes resulted from the analysis: (1) avoidance of the diagnosis of schizophrenia; (2) stigma and diagnostic labels; (3) lack of understanding of schizophrenia; (4) managing stigma to maintain normality; (5) being 'schizophrenic'. These, together with their subthemes, highlighted avoidance of the term schizophrenia by participants and use of alternative terms by professionals, which limited opportunities for understanding the label and challenging associated stigma. Participants strived to maintain normality despite potential stigma. Clinical implications There is a need to address the process of giving a diagnosis as a phenomenon of consequence within its own terms. Implications relate to how professionals deliver and discuss the diagnosis of schizophrenia.
Language	English
Publishing date	2014-09-01
Publishing country	England
Document type	Journal Article
ZDB-ID	2766700-5
ISSN	2053-4876 ; 2053-4868
ISSN (online)	2053-4876
ISSN	2053-4868
DOI	10.1192/pb.bp.113.045179
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Article ; Online: XModeScore: a novel method for accurate protonation/tautomer-state determination using quantum-mechanically driven macromolecular X-ray crystallographic refinement.

Borbulevych, Oleg / Martin, Roger I / Tickle, Ian J / Westerhoff, Lance M

Acta crystallographica. Section D, Structural biology

2016 Volume 72, Issue Pt 4, Page(s) 586–598

Abstract: Gaining an understanding of the protein-ligand complex structure along with the proper protonation and explicit solvent effects can be important in obtaining meaningful results in structure-guided drug discovery and structure-based drug discovery. ... ...

Abstract	Gaining an understanding of the protein-ligand complex structure along with the proper protonation and explicit solvent effects can be important in obtaining meaningful results in structure-guided drug discovery and structure-based drug discovery. Unfortunately, protonation and tautomerism are difficult to establish with conventional methods because of difficulties in the experimental detection of H atoms owing to the well known limitations of X-ray crystallography. In the present work, it is demonstrated that semiempirical, quantum-mechanics-based macromolecular crystallographic refinement is sensitive to the choice of a protonation-state/tautomer form of ligands and residues, and can therefore be used to explore potential states. A novel scoring method, called XModeScore, is described which enumerates the possible protomeric/tautomeric modes, refines each mode against X-ray diffraction data with the semiempirical quantum-mechanics (PM6) Hamiltonian and scores each mode using a combination of energetic strain (or ligand strain) and rigorous statistical analysis of the difference electron-density distribution. It is shown that using XModeScore it is possible to consistently distinguish the correct bound protomeric/tautomeric modes based on routine X-ray data, even at lower resolutions of around 3 Å. These X-ray results are compared with the results obtained from much more expensive and laborious neutron diffraction studies for three different examples: tautomerism in the acetazolamide ligand of human carbonic anhydrase II (PDB entries 3hs4 and 4k0s), tautomerism in the 8HX ligand of urate oxidase (PDB entries 4n9s and 4n9m) and the protonation states of the catalytic aspartic acid found within the active site of an aspartic protease (PDB entry 2jjj). In each case, XModeScore applied to the X-ray diffraction data is able to determine the correct protonation state as defined by the neutron diffraction data. The impact of QM-based refinement versus conventional refinement on XModeScore is also discussed.
MeSH term(s)	Acetazolamide/chemistry ; Carbonic Anhydrase II/antagonists & inhibitors ; Carbonic Anhydrase II/chemistry ; Crystallography, X-Ray/methods ; Humans ; Software
Chemical Substances	Carbonic Anhydrase II (EC 4.2.1.-) ; Acetazolamide (O3FX965V0I)
Language	English
Publishing date	2016-03-30
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2020492-9
ISSN	2059-7983 ; 1399-0047 ; 0907-4449
ISSN (online)	2059-7983 ; 1399-0047
ISSN	0907-4449
DOI	10.1107/S2059798316002837
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Article ; Online: Rapid intraoperative molecular genetic classification of gliomas using Raman spectroscopy.

Livermore, Laurent James / Isabelle, Martin / Bell, Ian Mac / Scott, Connor / Walsby-Tickle, John / Gannon, Joan / Plaha, Puneet / Vallance, Claire / Ansorge, Olaf

Neuro-oncology advances

2019 Volume 1, Issue 1, Page(s) vdz008

Abstract: Background: The molecular genetic classification of gliomas, particularly the identification of isocitrate dehydrogenase (IDH) mutations, is critical for clinical and surgical decision-making. Raman spectroscopy probes the unique molecular vibrations of ...

Abstract	Background: The molecular genetic classification of gliomas, particularly the identification of isocitrate dehydrogenase (IDH) mutations, is critical for clinical and surgical decision-making. Raman spectroscopy probes the unique molecular vibrations of a sample to accurately characterize its molecular composition. No sample processing is required allowing for rapid analysis of tissue. The aim of this study was to evaluate the ability of Raman spectroscopy to rapidly identify the common molecular genetic subtypes of diffuse glioma in the neurosurgical setting using fresh biopsy tissue. In addition, classification models were built using cryosections, formalin-fixed paraffin-embedded (FFPE) sections and LN-18 (IDH-mutated and wild-type parental cell) glioma cell lines. Methods: Fresh tissue, straight from neurosurgical theatres, underwent Raman analysis and classification into astrocytoma, IDH-wild-type; astrocytoma, IDH-mutant; or oligodendroglioma. The genetic subtype was confirmed on a parallel section using immunohistochemistry and targeted genetic sequencing. Results: Fresh tissue samples from 62 patients were collected (36 astrocytoma, IDH-wild-type; 21 astrocytoma, IDH-mutated; 5 oligodendroglioma). A principal component analysis fed linear discriminant analysis classification model demonstrated 79%-94% sensitivity and 90%-100% specificity for predicting the 3 glioma genetic subtypes. For the prediction of IDH mutation alone, the model gave 91% sensitivity and 95% specificity. Seventy-nine cryosections, 120 FFPE samples, and LN18 cells were also successfully classified. Meantime for Raman data collection was 9.5 min in the fresh tissue samples, with the process from intraoperative biopsy to genetic classification taking under 15 min. Conclusion: These data demonstrate that Raman spectroscopy can be used for the rapid, intraoperative, classification of gliomas into common genetic subtypes.
Language	English
Publishing date	2019-05-28
Publishing country	England
Document type	Journal Article
ZDB-ID	3009682-0
ISSN	2632-2498 ; 2632-2498
ISSN (online)	2632-2498
ISSN	2632-2498
DOI	10.1093/noajnl/vdz008
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Article ; Online: Variants in

Zhu, Linyi / Kamalathevan, Pragash / Koneva, Lada A / Zarebska, Jadwiga Miotla / Chanalaris, Anastasios / Ismail, Heba / Wiberg, Akira / Ng, Michael / Muhammad, Hayat / Walsby-Tickle, John / McCullagh, James S O / Watt, Fiona E / Sansom, Stephen N / Furniss, Dominic / Gardiner, Matthew D / Vincent, Tonia L / Riley, Nick / Spiteri, Michelle / McNab, Ian /

Little, Christopher / Cogswell, Lucy / Critchley, Paul / Giele, Henk / Shirley, Rebecca

Science translational medicine

2022 Volume 14, Issue 676, Page(s) eabm4054

Abstract: More than 40% of individuals will develop osteoarthritis (OA) during their lifetime, yet there are currently no licensed disease-modifying treatments for this disabling condition. Common polymorphic variants ... ...

Abstract	More than 40% of individuals will develop osteoarthritis (OA) during their lifetime, yet there are currently no licensed disease-modifying treatments for this disabling condition. Common polymorphic variants in
MeSH term(s)	Mice ; Animals ; Tretinoin/pharmacology ; Tretinoin/therapeutic use ; Tretinoin/metabolism ; Osteoarthritis/drug therapy ; Osteoarthritis/genetics ; Osteoarthritis/metabolism ; Cartilage, Articular/metabolism ; Knee Joint ; Anti-Inflammatory Agents ; Chondrocytes/metabolism ; Aldehyde Dehydrogenase 1 Family/metabolism ; Retinal Dehydrogenase/metabolism
Chemical Substances	Tretinoin (5688UTC01R) ; Anti-Inflammatory Agents ; Aldh1a2 protein, mouse (EC 1.2.1.36) ; Aldehyde Dehydrogenase 1 Family (EC 1.2.1) ; Retinal Dehydrogenase (EC 1.2.1.36)
Language	English
Publishing date	2022-12-21
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2518854-9
ISSN	1946-6242 ; 1946-6234
ISSN (online)	1946-6242
ISSN	1946-6234
DOI	10.1126/scitranslmed.abm4054
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Article ; Online: Detection of secondary binding sites in proteins using fragment screening.

Ludlow, R Frederick / Verdonk, Marcel L / Saini, Harpreet K / Tickle, Ian J / Jhoti, Harren

Proceedings of the National Academy of Sciences of the United States of America

2015 Volume 112, Issue 52, Page(s) 15910–15915

Abstract: Proteins need to be tightly regulated as they control biological processes in most normal cellular functions. The precise mechanisms of regulation are rarely completely understood but can involve binding of endogenous ligands and/or partner proteins at ... ...

Abstract	Proteins need to be tightly regulated as they control biological processes in most normal cellular functions. The precise mechanisms of regulation are rarely completely understood but can involve binding of endogenous ligands and/or partner proteins at specific locations on a protein that can modulate function. Often, these additional secondary binding sites appear separate to the primary binding site, which, for example for an enzyme, may bind a substrate. In previous work, we have uncovered several examples in which secondary binding sites were discovered on proteins using fragment screening approaches. In each case, we were able to establish that the newly identified secondary binding site was biologically relevant as it was able to modulate function by the binding of a small molecule. In this study, we investigate how often secondary binding sites are located on proteins by analyzing 24 protein targets for which we have performed a fragment screen using X-ray crystallography. Our analysis shows that, surprisingly, the majority of proteins contain secondary binding sites based on their ability to bind fragments. Furthermore, sequence analysis of these previously unknown sites indicate high conservation, which suggests that they may have a biological function, perhaps via an allosteric mechanism. Comparing the physicochemical properties of the secondary sites with known primary ligand binding sites also shows broad similarities indicating that many of the secondary sites may be druggable in nature with small molecules that could provide new opportunities to modulate potential therapeutic targets.
MeSH term(s)	Algorithms ; Binding Sites ; Crystallography, X-Ray ; Humans ; Models, Molecular ; Protein Binding ; Protein Interaction Domains and Motifs ; Protein Interaction Mapping/methods ; Proteins/chemistry ; Proteins/metabolism
Chemical Substances	Proteins
Language	English
Publishing date	2015-12-29
Publishing country	United States
Document type	Journal Article
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.1518946112
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Article ; Online: Comparison of caries detection methods using varying numbers of intra-oral digital photographs with visual examination for epidemiology in children.

Boye, Uriana / Pretty, Ian A / Tickle, Martin / Walsh, Tanya

BMC oral health

2013 Volume 13, Page(s) 6

Abstract: Background: This was a method comparison study. The aim of study was to compare caries information obtained from a full mouth visual examination using the method developed by the British Association for the Study of Community Dentistry (BASCD) for ... ...

Abstract	Background: This was a method comparison study. The aim of study was to compare caries information obtained from a full mouth visual examination using the method developed by the British Association for the Study of Community Dentistry (BASCD) for epidemiological surveys with caries data obtained from eight, six and four intra-oral digital photographs of index teeth in two groups of children aged 5 years and 10/11 years. Methods: Five trained and calibrated examiners visually examined the whole mouth of 240 5-year-olds and 250 10-/11-year-olds using the BASCD method. The children also had intra-oral digital photographs taken of index teeth. The same 5 examiners assessed the intra-oral digital photographs (in groups of 8, 6 and 4 intra-oral photographs) for caries using the BASCD criteria; dmft/DMFT were used to compute Weighted Kappa Statistic as a measure of intra-examiner reliability and intra-class correlation coefficients as a measure of inter-examiner reliability for each method. A method comparison analysis was performed to determine the 95% limits of agreement for all five examiners, comparing the visual examination method with the photographic assessment method using 8, 6 and 4 intra-oral photographs. Results: The intra-rater reliability for the visual examinations ranged from 0.81 to 0.94 in the 5-year-olds and 0.90 to 0.97 in the 10-/11-year-olds. Those for the photographic assessments in the 5-year-olds were for 8 intra-oral photographs, 0.86 to 0.94, for 6 intra-oral photographs, 0.85 to 0.98 and for 4 intra-oral photographs, 0.80 to 0.96; for the 10-/11-year-olds were for 8 intra-oral photographs 0.84 to 1.00, for 6 intra-oral photographs 0.82 to 1.00 and for 4 intra-oral photographs 0.72 to 0.98. The 95% limits of agreement were -1.997 to 1.967, -2.375 to 2.735 and -2.250 to 2.921 respectively for the 5-year-olds and -2.614 to 2.027, -2.179 to 3.887 and -2.594 to 2.163 respectively for the 10-/11-year-olds. Conclusions: The photographic assessment method, particularly assessment of 8 intra-oral digital photographs is comparable to the visual examination method in the primary dentition. With the additional benefits of archiving, remote scoring, allowing multiple scorers to score images and enabling longitudinal analysis, the photographic assessment method may be used as an alternative caries detection method in the primary dentition in situations where the visual examination method may not be applicable such as when examiner blinding is required and in practice based randomised controlled trials (RCTs).
MeSH term(s)	Child ; Child, Preschool ; Cross-Sectional Studies ; DMF Index ; Dental Caries/diagnosis ; Dental Caries/epidemiology ; Dental Caries Activity Tests ; England/epidemiology ; Humans ; Observer Variation ; Photography, Dental ; Reproducibility of Results
Language	English
Publishing date	2013-01-11
Publishing country	England
Document type	Comparative Study ; Journal Article
ZDB-ID	2091511-1
ISSN	1472-6831 ; 1472-6831
ISSN (online)	1472-6831
ISSN	1472-6831
DOI	10.1186/1472-6831-13-6
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