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Simpkin AJ, Caballero I, McNicholas S, Stevenson K, Jiménez E, Sánchez Rodríguez F, Fando M, Uski V, Ballard C, Chojnowski G, Lebedev A, Krissinel E, Usón I, Rigden DJ, Keegan RM. Predicted models and CCP4. Acta Crystallogr D Struct Biol 2023; 79:806-819. [PMID: 37594303 PMCID: PMC10478639 DOI: 10.1107/s2059798323006289] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 07/19/2023] [Indexed: 08/19/2023] Open
Abstract
In late 2020, the results of CASP14, the 14th event in a series of competitions to assess the latest developments in computational protein structure-prediction methodology, revealed the giant leap forward that had been made by Google's Deepmind in tackling the prediction problem. The level of accuracy in their predictions was the first instance of a competitor achieving a global distance test score of better than 90 across all categories of difficulty. This achievement represents both a challenge and an opportunity for the field of experimental structural biology. For structure determination by macromolecular X-ray crystallography, access to highly accurate structure predictions is of great benefit, particularly when it comes to solving the phase problem. Here, details of new utilities and enhanced applications in the CCP4 suite, designed to allow users to exploit predicted models in determining macromolecular structures from X-ray diffraction data, are presented. The focus is mainly on applications that can be used to solve the phase problem through molecular replacement.
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Affiliation(s)
- Adam J. Simpkin
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Iracema Caballero
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona, Spain
| | - Stuart McNicholas
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, United Kingdom
| | - Kyle Stevenson
- UKRI–STFC, Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot OX11 0FA, United Kingdom
| | - Elisabet Jiménez
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona, Spain
| | - Filomeno Sánchez Rodríguez
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, United Kingdom
| | - Maria Fando
- UKRI–STFC, Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot OX11 0FA, United Kingdom
| | - Ville Uski
- UKRI–STFC, Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot OX11 0FA, United Kingdom
| | - Charles Ballard
- UKRI–STFC, Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot OX11 0FA, United Kingdom
| | - Grzegorz Chojnowski
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607 Hamburg, Germany
| | - Andrey Lebedev
- UKRI–STFC, Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot OX11 0FA, United Kingdom
| | - Eugene Krissinel
- UKRI–STFC, Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot OX11 0FA, United Kingdom
| | - Isabel Usón
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona, Spain
- ICREA, Institució Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys 23, 08003 Barcelona, Spain
| | - Daniel J. Rigden
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Ronan M. Keegan
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
- UKRI–STFC, Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot OX11 0FA, United Kingdom
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Krissinel E, Lebedev AA, Uski V, Ballard CB, Keegan RM, Kovalevskiy O, Nicholls RA, Pannu NS, Skubák P, Berrisford J, Fando M, Lohkamp B, Wojdyr M, Simpkin AJ, Thomas JMH, Oliver C, Vonrhein C, Chojnowski G, Basle A, Purkiss A, Isupov MN, McNicholas S, Lowe E, Triviño J, Cowtan K, Agirre J, Rigden DJ, Uson I, Lamzin V, Tews I, Bricogne G, Leslie AGW, Brown DG. CCP4 Cloud for structure determination and project management in macromolecular crystallography. Acta Crystallogr D Struct Biol 2022; 78:1079-1089. [PMID: 36048148 PMCID: PMC9435598 DOI: 10.1107/s2059798322007987] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/08/2022] [Indexed: 11/10/2022] Open
Abstract
Nowadays, progress in the determination of three-dimensional macromolecular structures from diffraction images is achieved partly at the cost of increasing data volumes. This is due to the deployment of modern high-speed, high-resolution detectors, the increased complexity and variety of crystallographic software, the use of extensive databases and high-performance computing. This limits what can be accomplished with personal, offline, computing equipment in terms of both productivity and maintainability. There is also an issue of long-term data maintenance and availability of structure-solution projects as the links between experimental observations and the final results deposited in the PDB. In this article, CCP4 Cloud, a new front-end of the CCP4 software suite, is presented which mitigates these effects by providing an online, cloud-based environment for crystallographic computation. CCP4 Cloud was developed for the efficient delivery of computing power, database services and seamless integration with web resources. It provides a rich graphical user interface that allows project sharing and long-term storage for structure-solution projects, and can be linked to data-producing facilities. The system is distributed with the CCP4 software suite version 7.1 and higher, and an online publicly available instance of CCP4 Cloud is provided by CCP4.
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Staunton S, Rajendran D, Maher P, McCann J, McNicholas S, Feeney E, O’Broin C, Savinelli S, Mallon P, Watson A, Waqas S. Discharge-delaying factors for patients suitable for outpatient parenteral antimicrobial therapy (OPAT) in an Irish tertiary hospital during COVID-19. JAC Antimicrob Resist 2021; 3:dlab163. [PMID: 34661108 PMCID: PMC8516592 DOI: 10.1093/jacamr/dlab163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- S Staunton
- Department of Medicine, St Vincent’s University Hospital, Elm Park, Dublin 4, Ireland
| | - D Rajendran
- Department of Infectious Diseases, St Vincent’s University Hospital, Elm Park, Dublin 4, Ireland
| | - P Maher
- Department of Radiology, St Vincent’s University Hospital, Elm Park, Dublin 4, Ireland
| | - J McCann
- Department of Radiology, St Vincent’s University Hospital, Elm Park, Dublin 4, Ireland
| | - S McNicholas
- Department of Microbiology, St Vincent’s University Hospital, Elm Park, Dublin 4, Ireland
| | - E Feeney
- Department of Infectious Diseases, St Vincent’s University Hospital, Elm Park, Dublin 4, Ireland
| | - C O’Broin
- Department of Infectious Diseases, St Vincent’s University Hospital, Elm Park, Dublin 4, Ireland
| | - S Savinelli
- Department of Infectious Diseases, St Vincent’s University Hospital, Elm Park, Dublin 4, Ireland
| | - P Mallon
- Department of Infectious Diseases, St Vincent’s University Hospital, Elm Park, Dublin 4, Ireland
| | - A Watson
- Department of Medicine, St Vincent’s University Hospital, Elm Park, Dublin 4, Ireland
| | - S Waqas
- Department of Infectious Diseases, St Vincent’s University Hospital, Elm Park, Dublin 4, Ireland
- UCD School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
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Ho NX, Clarke L, Collins PM, Fitzgerald S, Sheehan S, Paul T, Treacy G, McNicholas S. 1080 An Audit on Compliance with Recommended Duration of Surgical Antimicrobial Prophylaxis in St. Vincent’s University Hospital, Dublin, Ireland. Br J Surg 2021. [DOI: 10.1093/bjs/znab259.120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Aim
Surgical site infection (SSI) is a common healthcare-associated infection, and a frequent cause of post-operative morbidity. SSI comprises any infection of the operative incision, cavity or involved organ, that occurs within the 30-day post-operative period. Antimicrobial prophylaxis is critical in reducing SSIs. Our aim was to assess adherence to the recommended surgical antimicrobial prophylaxis guidelines in St. Vincent’s University Hospital (SVUH), as part of the hospital antimicrobial stewardship programme. Compliance of surgical services was measured against the recommended regimens described in the SVUH Antimicrobial Guidelines.
Method
Data on duration and choice of prophylaxis were prospectively gathered on inpatients undergoing elective surgery during a three-week period between August-September 2020. Patients undergoing transplant procedures, inpatients in the intensive care unit, and patients who moved off-site postoperatively were excluded.
Results
Eighty-one patients were included. Sixty-four (79%) were compliant with prophylaxis duration, while seventeen (21%) were not. Reasons for extended prophylaxis included three (18%) cases where there were intra-operative complications and five (29%) cases of routine prescribing of an additional 24-hour coverage. Nine (53%) did not document the reason for extended cover.
Conclusions
Compliance with recommended duration of prophylaxis improved in comparison to prior audits. Among patients receiving extended prophylaxis, documentation of the indication was poor. Patients with evidence of post-operative infection may be better served with targeted antimicrobial therapy rather than extended prophylaxis. One reason for extended prophylaxis may be due to difficulty accessing guidelines on recommended prophylaxis duration, hence a targeted smartphone application was introduced to improve accessibility.
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Affiliation(s)
- N X Ho
- St Vincent's University Hospital, Dublin, Ireland
| | - L Clarke
- St Vincent's University Hospital, Dublin, Ireland
| | - P M Collins
- St Vincent's University Hospital, Dublin, Ireland
| | - S Fitzgerald
- St Vincent's University Hospital, Dublin, Ireland
| | - S Sheehan
- St Vincent's University Hospital, Dublin, Ireland
| | - T Paul
- St Vincent's University Hospital, Dublin, Ireland
| | - G Treacy
- St Vincent's University Hospital, Dublin, Ireland
| | - S McNicholas
- St Vincent's University Hospital, Dublin, Ireland
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Farias LP, Vance GM, Coulson PS, Vitoriano-Souza J, Neto APDS, Wangwiwatsin A, Neves LX, Castro-Borges W, McNicholas S, Wilson KS, Leite LCC, Wilson RA. Epitope Mapping of Exposed Tegument and Alimentary Tract Proteins Identifies Putative Antigenic Targets of the Attenuated Schistosome Vaccine. Front Immunol 2021; 11:624613. [PMID: 33763055 PMCID: PMC7982949 DOI: 10.3389/fimmu.2020.624613] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 12/14/2020] [Indexed: 02/03/2023] Open
Abstract
The radiation-attenuated cercarial vaccine remains the gold standard for the induction of protective immunity against Schistosoma mansoni. Furthermore, the protection can be passively transferred to naïve recipient mice from multiply vaccinated donors, especially IFNgR KO mice. We have used such sera versus day 28 infection serum, to screen peptide arrays and identify likely epitopes that mediate the protection. The arrays encompassed 55 secreted or exposed proteins from the alimentary tract and tegument, the principal interfaces with the host bloodstream. The proteins were printed onto glass slides as overlapping 15mer peptides, reacted with primary and secondary antibodies, and reactive regions detected using an Agilent array scanner. Pep Slide Analyzer software provided a numerical value above background for each peptide from which an aggregate score could be derived for a putative epitope. The reactive regions of 26 proteins were mapped onto crystal structures using the CCP4 molecular graphics, to aid selection of peptides with the greatest accessibility and reactivity, prioritizing vaccine over infection serum. A further eight MEG proteins were mapped to regions conserved between family members. The result is a list of priority peptides from 44 proteins for further investigation in multiepitope vaccine constructs and as targets of monoclonal antibodies.
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Affiliation(s)
- Leonardo P. Farias
- Laboratório de Desenvolvimento de Vacinas, Instituto Butantan, São Paulo, Brazil
| | - Gillian M. Vance
- York Biomedical Research Institute, University of York, York, United Kingdom
| | - Patricia S. Coulson
- York Biomedical Research Institute, University of York, York, United Kingdom
| | | | - Almiro Pires da Silva Neto
- Laboratório de Inflamação e Biomarcadores, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
| | - Arporn Wangwiwatsin
- Parasite Genomics, Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Leandro Xavier Neves
- Instituto de Ciẽncias Exatas e Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
| | - William Castro-Borges
- Instituto de Ciẽncias Exatas e Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
| | - Stuart McNicholas
- York Structural Biology Laboratory, University of York, York, United Kingdom
| | - Keith S. Wilson
- York Structural Biology Laboratory, University of York, York, United Kingdom
| | - Luciana C. C. Leite
- Laboratório de Desenvolvimento de Vacinas, Instituto Butantan, São Paulo, Brazil
| | - R. Alan Wilson
- York Biomedical Research Institute, University of York, York, United Kingdom
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Lebedev A, Vagin A, McNicholas S, Thomas J, Uski V, Rigden D, Keegan R. Molecular replacement model preparation and its automation in MoRDa and MrBUMP. Acta Crystallogr A Found Adv 2019. [DOI: 10.1107/s2053273319093987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023] Open
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Keegan R, Rigden D, McNicholas S, Krissinel E, Thomas J, Simpkin A, Simkovic F, Winn M, Wilson K. Ensembling for molecular replacement: making the most of your distant homologues. Acta Crystallogr A Found Adv 2018. [DOI: 10.1107/s2053273318092586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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McNicholas S, Croll T, Burnley T, Palmer CM, Hoh SW, Jenkins HT, Dodson E, Cowtan K, Agirre J. Automating tasks in protein structure determination with the clipper python module. Protein Sci 2018; 27:207-216. [PMID: 28901669 PMCID: PMC5734304 DOI: 10.1002/pro.3299] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 09/08/2017] [Accepted: 09/11/2017] [Indexed: 11/06/2022]
Abstract
Scripting programming languages provide the fastest means of prototyping complex functionality. Those with a syntax and grammar resembling human language also greatly enhance the maintainability of the produced source code. Furthermore, the combination of a powerful, machine-independent scripting language with binary libraries tailored for each computer architecture allows programs to break free from the tight boundaries of efficiency traditionally associated with scripts. In the present work, we describe how an efficient C++ crystallographic library such as Clipper can be wrapped, adapted and generalized for use in both crystallographic and electron cryo-microscopy applications, scripted with the Python language. We shall also place an emphasis on best practices in automation, illustrating how this can be achieved with this new Python module.
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Affiliation(s)
- Stuart McNicholas
- Department of Chemistry, York Structural Biology LaboratoryThe University of YorkYorkYO10 5DDUnited Kingdom
| | - Tristan Croll
- Department of Haematology, Cambridge Institute for Medical ResearchUniversity of CambridgeCambridgeCB2 0XYUnited Kingdom
| | - Tom Burnley
- STFC Rutherford Appleton Laboratory OX11 0QXCollaborative Computational Project for Electron cryo‐Microscopy (CCP‐EM)United Kingdom
| | - Colin M. Palmer
- STFC Rutherford Appleton Laboratory OX11 0QXCollaborative Computational Project for Electron cryo‐Microscopy (CCP‐EM)United Kingdom
| | - Soon Wen Hoh
- Department of Chemistry, York Structural Biology LaboratoryThe University of YorkYorkYO10 5DDUnited Kingdom
| | - Huw T. Jenkins
- Department of Chemistry, York Structural Biology LaboratoryThe University of YorkYorkYO10 5DDUnited Kingdom
| | - Eleanor Dodson
- Department of Chemistry, York Structural Biology LaboratoryThe University of YorkYorkYO10 5DDUnited Kingdom
| | - Kevin Cowtan
- Department of Chemistry, York Structural Biology LaboratoryThe University of YorkYorkYO10 5DDUnited Kingdom
| | - Jon Agirre
- Department of Chemistry, York Structural Biology LaboratoryThe University of YorkYorkYO10 5DDUnited Kingdom
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McNicholas S, Agirre J. Glycoblocks: a schematic three-dimensional representation for glycans and their interactions. Acta Crystallogr D Struct Biol 2017; 73:187-194. [PMID: 28177314 PMCID: PMC5297921 DOI: 10.1107/s2059798316013553] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 08/23/2016] [Indexed: 02/08/2023] Open
Abstract
The close-range interactions provided by covalently linked glycans are essential for the correct folding of glycoproteins and also play a pivotal role in recognition processes. Being able to visualise protein-glycan and glycan-glycan contacts in a clear way is thus of great importance for the understanding of these biological processes. In structural terms, glycosylation sugars glue the protein together via hydrogen bonds, whereas non-covalently bound glycans frequently harness additional stacking interactions. Finding an unobscured molecular view of these multipartite scenarios is usually far from trivial; in addition to the need to show the interacting protein residues, glycans may contain many branched sugars, each composed of more than ten non-H atoms and offering more than three potential bonding partners. With structural glycoscience finally gaining popularity and steadily increasing the deposition rate of three-dimensional structures of glycoproteins, the need for a clear way of depicting these interactions is more pressing than ever. Here a schematic representation, named Glycoblocks, is introduced which combines a simplified bonding-network depiction (covering hydrogen bonds and stacking interactions) with the familiar two-dimensional glycan notation used by the glycobiology community, brought into three dimensions by the CCP4 molecular graphics project (CCP4mg).
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Affiliation(s)
- Stuart McNicholas
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England
| | - Jon Agirre
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England
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Agirre J, Ariza A, Offen WA, Turkenburg JP, Roberts SM, McNicholas S, Harris PV, McBrayer B, Dohnalek J, Cowtan KD, Davies GJ, Wilson KS. Three-dimensional structures of two heavily N-glycosylated Aspergillus sp. family GH3 β-D-glucosidases. Acta Crystallogr D Struct Biol 2016; 72:254-65. [PMID: 26894673 PMCID: PMC4756609 DOI: 10.1107/s2059798315024237] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 12/16/2015] [Indexed: 01/25/2023] Open
Abstract
The industrial conversion of cellulosic plant biomass into useful products such as biofuels is a major societal goal. These technologies harness diverse plant degrading enzymes, classical exo- and endo-acting cellulases and, increasingly, cellulose-active lytic polysaccharide monooxygenases, to deconstruct the recalcitrant β-D-linked polysaccharide. A major drawback with this process is that the exo-acting cellobiohydrolases suffer from severe inhibition from their cellobiose product. β-D-Glucosidases are therefore important for liberating glucose from cellobiose and thereby relieving limiting product inhibition. Here, the three-dimensional structures of two industrially important family GH3 β-D-glucosidases from Aspergillus fumigatus and A. oryzae, solved by molecular replacement and refined at 1.95 Å resolution, are reported. Both enzymes, which share 78% sequence identity, display a three-domain structure with the catalytic domain at the interface, as originally shown for barley β-D-glucan exohydrolase, the first three-dimensional structure solved from glycoside hydrolase family GH3. Both enzymes show extensive N-glycosylation, with only a few external sites being truncated to a single GlcNAc molecule. Those glycans N-linked to the core of the structure are identified purely as high-mannose trees, and establish multiple hydrogen bonds between their sugar components and adjacent protein side chains. The extensive glycans pose special problems for crystallographic refinement, and new techniques and protocols were developed especially for this work. These protocols ensured that all of the D-pyranosides in the glycosylation trees were modelled in the preferred minimum-energy (4)C1 chair conformation and should be of general application to refinements of other crystal structures containing O- or N-glycosylation. The Aspergillus GH3 structures, in light of other recent three-dimensional structures, provide insight into fungal β-D-glucosidases and provide a platform on which to inform and inspire new generations of variant enzymes for industrial application.
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Affiliation(s)
- Jon Agirre
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England
| | - Antonio Ariza
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England
| | - Wendy A. Offen
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England
| | - Johan P. Turkenburg
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England
| | - Shirley M. Roberts
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England
| | - Stuart McNicholas
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England
| | | | | | - Jan Dohnalek
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England
| | - Kevin D. Cowtan
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England
| | - Gideon J. Davies
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England
| | - Keith S. Wilson
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England
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Nicholls RA, Fischer M, McNicholas S, Murshudov GN. Conformation-independent structural comparison of macromolecules with ProSMART. Acta Crystallogr D Biol Crystallogr 2014; 70:2487-99. [PMID: 25195761 PMCID: PMC4157452 DOI: 10.1107/s1399004714016241] [Citation(s) in RCA: 139] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Accepted: 07/12/2014] [Indexed: 12/05/2023]
Abstract
The identification and exploration of (dis)similarities between macromolecular structures can help to gain biological insight, for instance when visualizing or quantifying the response of a protein to ligand binding. Obtaining a residue alignment between compared structures is often a prerequisite for such comparative analysis. If the conformational change of the protein is dramatic, conventional alignment methods may struggle to provide an intuitive solution for straightforward analysis. To make such analyses more accessible, the Procrustes Structural Matching Alignment and Restraints Tool (ProSMART) has been developed, which achieves a conformation-independent structural alignment, as well as providing such additional functionalities as the generation of restraints for use in the refinement of macromolecular models. Sensible comparison of protein (or DNA/RNA) structures in the presence of conformational changes is achieved by enforcing neither chain nor domain rigidity. The visualization of results is facilitated by popular molecular-graphics software such as CCP4mg and PyMOL, providing intuitive feedback regarding structural conservation and subtle dissimilarities between close homologues that can otherwise be hard to identify. Automatically generated colour schemes corresponding to various residue-based scores are provided, which allow the assessment of the conservation of backbone and side-chain conformations relative to the local coordinate frame. Structural comparison tools such as ProSMART can help to break the complexity that accompanies the constantly growing pool of structural data into a more readily accessible form, potentially offering biological insight or influencing subsequent experiments.
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Affiliation(s)
- Robert A. Nicholls
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, England
| | - Marcus Fischer
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Stuart McNicholas
- Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, England
| | - Garib N. Murshudov
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, England
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Howard L, Flach C, Leese M, Byford S, Killaspy H, Cole L, Lawlor C, Betts J, Sharac J, Cutting P, McNicholas S, Johnson S. Effectiveness and cost-effectiveness of admissions to women's crisis houses compared with traditional psychiatric wards: pilot patient-preference randomised controlled trial. Br J Psychiatry 2014; 53:s32-40. [PMID: 20679277 DOI: 10.1192/bjp.bp.110.081083] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
BACKGROUND Women's crisis houses have been developed in the UK as a less stigmatising and less institutional alternative to traditional psychiatric wards. AIMS To examine the effectiveness and cost-effectiveness of women's crisis houses by first examining the feasibility of a pilot patient-preference randomised controlled trial (PP-RCT) design (ISRCTN20804014). METHOD We used a PP-RCT study design to investigate women presenting in crisis needing informal admission. The four study arms were the patient preference arms of women's crisis house or hospital admission, and randomised arms of women's crisis house or hospital admission. RESULTS Forty-one women entered the randomised arms of the trial (crisis house n = 19, wards n = 22) and 61 entered the patient-preference arms (crisis house n = 37, ward n = 24). There was no significant difference in outcomes (symptoms, functioning, perceived coercion, stigma, unmet needs or quality of life) or costs for any of the groups (randomised or preference arms), but women who obtained their preferred intervention were more satisfied with treatment. CONCLUSIONS Although the sample sizes were too small to allow definite conclusions, the results suggest that when services are able to provide interventions preferred by patients, those patients are more likely to be satisfied with treatment. This pilot study provides some evidence that women's crisis houses are as effective as traditional psychiatric wards, and may be more cost-effective.
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Affiliation(s)
- L Howard
- Health Service and Population Research Department, Institute of Psychiatry, Box PO29, De Crespigny Park, London SE5 8AF, UK.
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McNicholas S, McDermott H, Power L, Johnson EM, Moroney J, Humphreys H, Smyth EG. Sporobolomyces roseus in the cerebrospinal fluid of an immunocompetent patient – to treat or not to treat? J Med Microbiol 2012; 61:295-296. [DOI: 10.1099/jmm.0.036293-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Affiliation(s)
- S. McNicholas
- Department of Microbiology, Beaumont Hospital, Dublin 9, Ireland
- Department of Clinical Microbiology, Royal College of Surgeons in Ireland, Dublin 9, Ireland
| | - H. McDermott
- Department of Microbiology, Beaumont Hospital, Dublin 9, Ireland
| | - L. Power
- Department of Microbiology, Beaumont Hospital, Dublin 9, Ireland
| | - E. M. Johnson
- Mycology Reference Laboratory, Southwest HPA Laboratory, Myrtle Road, Kingsdown, Bristol, UK
| | - J. Moroney
- Department of Neurology, Beaumont Hospital, Dublin 9, Ireland
| | - H. Humphreys
- Department of Microbiology, Beaumont Hospital, Dublin 9, Ireland
- Department of Clinical Microbiology, Royal College of Surgeons in Ireland, Dublin 9, Ireland
| | - E. G. Smyth
- Department of Microbiology, Beaumont Hospital, Dublin 9, Ireland
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McNicholas S, McAdam B, Flynn M, Humphreys H. The challenges of implantable cardiac device infection due to Helcococcus kunzii. J Hosp Infect 2011; 78:337-8. [PMID: 21676496 DOI: 10.1016/j.jhin.2011.04.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Accepted: 04/13/2011] [Indexed: 11/30/2022]
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15
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McNicholas S, Potterton E, Wilson KS, Noble MEM. Presenting your structures: the CCP4mg molecular-graphics software. Acta Crystallogr D Biol Crystallogr 2011; 67:386-94. [PMID: 21460457 PMCID: PMC3069754 DOI: 10.1107/s0907444911007281] [Citation(s) in RCA: 1013] [Impact Index Per Article: 77.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Accepted: 02/25/2011] [Indexed: 11/25/2022]
Abstract
The CCP4 molecular-graphics program now uses the Qt framework to provide a modern look and feel. There are many new features including rendering for publication-quality images and sequence alignment. CCP4mg is a molecular-graphics program that is designed to give rapid access to both straightforward and complex static and dynamic representations of macromolecular structures. It has recently been updated with a new interface that provides more sophisticated atom-selection options and a wizard to facilitate the generation of complex scenes. These scenes may contain a mixture of coordinate-derived and abstract graphical objects, including text objects, arbitrary vectors, geometric objects and imported images, which can enhance a picture and eliminate the need for subsequent editing. Scene descriptions can be saved to file and transferred to other molecules. Here, the substantially enhanced version 2 of the program, with a new underlying GUI toolkit, is described. A built-in rendering module produces publication-quality images.
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Affiliation(s)
- S McNicholas
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, England.
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16
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McNicholas S, Andrews C, Boland K, Shields M, Doherty G, Murray F, Smyth E, Humphreys H, Fitzpatrick F. P06.05 A point prevalence study of healthcare-associated infection in patients with delayed discharge in an acute tertiary referral hospital. J Hosp Infect 2010. [DOI: 10.1016/s0195-6701(10)60060-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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17
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McNicholas S, Hanahoe B, Higgins F, McAnena O, Corbett-Feeney G, Cormican M. Linezolid resistant enterococcus faecium. Ir Med J 2008; 101:225-226. [PMID: 18810787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
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18
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McNicholas S, Barber A, Corbett-Feeney G, Cormican M. Linezolid audit: similarities and contrasts with published experience. J Antimicrob Chemother 2006; 57:1008-9. [PMID: 16549512 DOI: 10.1093/jac/dkl090] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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19
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Potterton L, McNicholas S, Krissinel E, Gruber J, Cowtan K, Emsley P, Murshudov GN, Cohen S, Perrakis A, Noble M. Developments in the CCP4 molecular-graphics project. Acta Crystallogr D Biol Crystallogr 2004; 60:2288-94. [PMID: 15572783 DOI: 10.1107/s0907444904023716] [Citation(s) in RCA: 492] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2004] [Accepted: 09/22/2004] [Indexed: 11/11/2022]
Abstract
Progress towards structure determination that is both high-throughput and high-value is dependent on the development of integrated and automatic tools for electron-density map interpretation and for the analysis of the resulting atomic models. Advances in map-interpretation algorithms are extending the resolution regime in which fully automatic tools can work reliably, but at present human intervention is required to interpret poor regions of macromolecular electron density, particularly where crystallographic data is only available to modest resolution [for example, I/sigma(I) < 2.0 for minimum resolution 2.5 A]. In such cases, a set of manual and semi-manual model-building molecular-graphics tools is needed. At the same time, converting the knowledge encapsulated in a molecular structure into understanding is dependent upon visualization tools, which must be able to communicate that understanding to others by means of both static and dynamic representations. CCP4 mg is a program designed to meet these needs in a way that is closely integrated with the ongoing development of CCP4 as a program suite suitable for both low- and high-intervention computational structural biology. As well as providing a carefully designed user interface to advanced algorithms of model building and analysis, CCP4 mg is intended to present a graphical toolkit to developers of novel algorithms in these fields.
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Affiliation(s)
- Liz Potterton
- Department of Chemistry, University of York, England.
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20
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Vagin AA, Steiner RA, Lebedev AA, Potterton L, McNicholas S, Long F, Murshudov GN. REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use. Acta Crystallogr D Biol Crystallogr 2004; 60:2184-95. [PMID: 15572771 DOI: 10.1107/s0907444904023510] [Citation(s) in RCA: 1084] [Impact Index Per Article: 54.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 04/19/2004] [Accepted: 09/22/2004] [Indexed: 11/11/2022]
Abstract
One of the most important aspects of macromolecular structure refinement is the use of prior chemical knowledge. Bond lengths, bond angles and other chemical properties are used in restrained refinement as subsidiary conditions. This contribution describes the organization and some aspects of the use of the flexible and human/machine-readable dictionary of prior chemical knowledge used by the maximum-likelihood macromolecular-refinement program REFMAC5. The dictionary stores information about monomers which represent the constitutive building blocks of biological macromolecules (amino acids, nucleic acids and saccharides) and about numerous organic/inorganic compounds commonly found in macromolecular crystallography. It also describes the modifications the building blocks undergo as a result of chemical reactions and the links required for polymer formation. More than 2000 monomer entries, 100 modification entries and 200 link entries are currently available. Algorithms and tools for updating and adding new entries to the dictionary have also been developed and are presented here. In many cases, the REFMAC5 dictionary allows entirely automatic generation of restraints within REFMAC5 refinement runs.
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Affiliation(s)
- Alexei A Vagin
- Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5YW, England
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21
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22
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Potterton E, McNicholas S, Krissinel E, Cowtan K, Noble M. The CCP4 molecular-graphics project. Acta Crystallogr D Biol Crystallogr 2002; 58:1955-7. [PMID: 12393928 DOI: 10.1107/s0907444902015391] [Citation(s) in RCA: 183] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2002] [Accepted: 08/28/2002] [Indexed: 11/10/2022]
Abstract
This new package will provide easy-to-use access to crystallographic structure solution, model building and structure analysis. It will be possible for any developer to integrate scientific software into the system.
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Affiliation(s)
- Elizabeth Potterton
- Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, England.
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23
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McNicholas S, Torabinejad M. Esotropia following posterior superior alveolar nerve block. J Calif Dent Assoc 1992; 20:33-4. [PMID: 1283884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Adequate use of local anesthetics is an important phase of modern dentistry. Regardless of the care used in administration of local anesthetics, unusual reactions can occur. A case is presented in which posterior superior alveolar administration of two percent Lidocaine 1/100,000 epinephrine resulted in medial rotation of the orbit (esotropia).
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Affiliation(s)
- S McNicholas
- Department of Endodontics, Loma Linda University School of Dentistry, California
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Abstract
Prostaglandins (PG) have been implicated in the genesis of periapical lesions. Periapical specimens from patients with clinical signs and symptoms of chronic and acute apical periodontitis were obtained and immediately frozen in liquid nitrogen. Periradicular tissues from unerupted third molars were frozen and used as controls. The concentration of PGE2 was determined by radioimmunoassay. Low levels of PGE2 were found in the control tissues as compared with those detected in chronic and acute lesions. Significantly higher levels of PGE2 were found in acute lesions than those found in chronic lesions. The results show that acute lesions have higher concentrations of PGE2 than chronic lesions and confirm the role of prostaglandins in the pathogenesis of human periapical lesions.
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Affiliation(s)
- S McNicholas
- Department of Endodontics, School of Dentistry, Loma Linda University
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