Publications by authors named "Nicola Richmond"

18 Publications

  • Page 1 of 1

Threshold concept acquisition in occupational therapy: A mixed methods study of students and clinicians.

Aust Occup Ther J 2019 10 17;66(5):568-580. Epub 2019 Jul 17.

Biostatics Unit, Faculty of Health, Deakin University, Geelong, Australia.

Background/aim: Demand for occupational therapy graduates able to work in complex and diverse workplaces is increasing. The threshold concepts framework has emerged as one pathway to assist in the development of work-ready graduates. A previous Australian study identified 10 threshold concepts for occupational therapy; the aim of this study was to explore the acquisition of these.

Method: A mixed-methods study using observational, cross sectional design and a triangulation design convergence model was undertaken. A survey using Likert scales and open response questions was developed by the authors. Seventy-three surveys were completed by 13 first and 20 final year Victorian occupational therapy students. Twenty recent graduates and 20 experienced clinicians from across Australia also participated. Seven first and 10 final year occupational therapy students, 10 recent graduates and 10 experienced clinicians also took part in in-depth interviews. Likert scales were used by participants to rate confidence that they had acquired the threshold concepts, they also answered open-response questions (via survey or interview) asking them to provide examples of how they would use threshold concepts in practice.

Results: Fourth year students were statistically significantly less confident than experienced clinicians for the threshold concepts Understanding the models and theories of occupational therapy and Applying clinical reasoning (P < 0.05). When whole group data were analysed, participants were most confident for Occupation and Client centred practice (P < 0.05). These results resonated with the qualitative findings which demonstrated a shift from surface to deep knowledge with increased experience. Fourth year students reported responses that suggested some threshold concepts were still in development, while experienced clinicians used a web of threshold concepts.

Conclusion: This exploratory study provides provisional data to suggest that students appear to still be acquiring some threshold concepts at graduation and experienced clinicians make use of a web of threshold concepts in their clinical practice.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/1440-1630.12595DOI Listing
October 2019

Market segmentation tools provide insights into demographic variations in bowel cancer screening uptake.

J Epidemiol Community Health 2019 08 25;73(8):778-785. Epub 2019 May 25.

Public Health, Derby City Council, Derby, UK.

Background: The National Health Service Bowel Cancer Screening Programme (NHS BCSP) aims to detect individuals who have precancerous polyps or early stage cancer, when it is easier to treat. To be effective, a screening uptake of at least 52% is required. Variations in uptake by demographic characteristic are reported and the aim of this study was to better understand who participates in the NHS BCSP, to inform action to address inequalities in screening uptake.

Methods: Invitation-level data for the Derbyshire population were supplied by the NHS BCSP Eastern Hub for the period 1 April 2014 to 31 March 2016. Data were linked by postal code to the Mosaic Public Sector Segmentation tool. Descriptive analysis using 14 groups and 61 types within Mosaic was undertaken to offer insight into the demographic, lifestyle and behavioural traits of people living in small geographies against their screening uptake, with a particular focus on identifying population groups with an uptake below 52% and so at risk of health inequalities.

Results: 180 176 screening invitations were dispatched with an overall uptake of 60.55%. Six Mosaic groups have an uptake below the 52% acceptable level: urban cohesion, rental hubs, transient renters, family basics, vintage value and municipal tenants. These groups are characterised by high levels of social-rented accommodation, multicultural urban communities and transient populations.

Conclusion: Segmentation tools offer an effective way to generate novel insights into bowel cancer screening uptake and develop tailored strategies for working with identified communities to increase participation.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1136/jech-2018-211085DOI Listing
August 2019

Economic evaluation of simulated and traditional clinical placements in occupational therapy education.

Aust Occup Ther J 2019 06 25;66(3):369-379. Epub 2019 Jan 25.

Centre for Health Economics, Monash Business School, Monash University, Clayton, VIC, Australia.

Introduction: This economic evaluation complements results of the randomised controlled trial that established non-inferiority of the learning outcomes of a one-week simulated clinical placement (SCP) in occupational therapy qualifying degrees in comparison to an equivalent traditional clinical placement (TCP). This companion study presents detailed cost analyses of two placement alternatives and a cost-benefit study to assess the value for money of SCP. An economic evaluation of simulated versus traditional placements has not previously been conducted in Australia.

Methods: Nine SCP/TCP rounds were conducted by six Australian universities. Costs were collected using study-specific instruments. Public health sector costs were sourced from available literature. Willingness-to-pay for SCP/TCP was estimated using both a Discrete Choice Experiment and a Contingent Valuation method. These methods were employed to assess a comparative 'value' of SCP/TCP from the perspective of heads of occupational therapy departments (N = 28), who were asked to put a monetary value on the broader range of benefits associated with SCP/TCP.

Results: From the universities' perspective the average cost per student ranged from AUD$460 to AUD$1511 for simulated and AUD$144 to AUD$1112 for traditional placement. From the health care sector perspective, the difference in costs favoured simulated placements for four implementations and traditional placements for five. In the Discrete Choice Experiment respondents preferred traditional rather than simulated placement and would pay additional AUD$533. The estimated monetary value of simulated placements from a contingent valuation ranged from AUD$200 to AUD$1600.

Conclusions: For universities that procure TCPs predominately at public health care facilities and sustain high administrative overheads, the SCP program could be a cost-saving alternative. From a broader value-for-money perspective, respondents favoured TCP over SCP, yet placed importance on placement availability and opportunity to demonstrate competence for students during the placement. Results should be interpreted with caution and further research with larger sample sizes is required.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/1440-1630.12563DOI Listing
June 2019

Simulated versus traditional occupational therapy placements: A randomised controlled trial.

Aust Occup Ther J 2018 12 31;65(6):556-564. Epub 2018 Aug 31.

Sydney School of Public Health, The University of Sydney, Lidcombe, New South Wales, Australia.

Background/aim: Professional practise placements in occupational therapy education are critical to ensuring graduate competence. Australian occupational therapy accreditation standards allow up to 200 of a mandated 1000 placement hours to include simulation-based learning. There is, however, minimal evidence about the effectiveness of simulation-based placements compared to traditional placements in occupational therapy. We evaluated whether occupational therapy students completing a 40 hour (one week block) Simulated Clinical Placement (SCP) attained non-inferior learning outcomes to students attending a 40 hour Traditional Clinical Placement (TCP).

Methods: A pragmatic, non-inferiority, assessor-blinded, multicentre, randomised controlled trial involving students from six Australian universities was conducted. Statistical power analysis estimated a required sample of 425. Concealed random allocation was undertaken with a 1:1 ratio within each university. Students were assigned to SCP or TCP in one of three settings: vocational rehabilitation, mental health or physical rehabilitation. SCP materials were developed, manualised and staff training provided. TCPs were in equivalent practice areas. Outcomes were assessed using a standardised examination, unit grades, the Student Practice Evaluation Form-Revised and student confidence survey. A generalised estimating equation approach was used to assess non-inferiority of the SCP to the TCP.

Results: Of 570 randomised students (84% female), 275 attended the SCP and 265 the TCP (n = 540, 94.7% retention). There were no significant differences between the TCP and SCP on (i) examination results (marginal mean difference 1.85, 95% CI: 0.46-3.24; P = 0.087); (ii) unit score (mean (SD) SCP: 71.9 (8.8), TCP: 70.34 (9.1); P = 0.066); or (iii) placement fail rate, assessed using the Student Practice Evaluation Form-Revised (100% passed both groups).

Conclusion: Students can achieve equivalent learning outcomes in a 40 hour simulated placement to those achieved in a 40 hour traditional placement. These findings provide assurance to students, educators and professional accreditation bodies that simulation can be embedded in occupational therapy education with good effect.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/1440-1630.12513DOI Listing
December 2018

Effectiveness and cost-effectiveness of embedded simulation in occupational therapy clinical practice education: study protocol for a randomised controlled trial.

Trials 2017 07 21;18(1):345. Epub 2017 Jul 21.

Australian Catholic University, 17-29 Young Street, Fitzroy, 3065, Australia.

Background: Clinical placements are a critical component of the training for health professionals such as occupational therapists. However, with growing student enrolments in professional education courses and workload pressures on practitioners, it is increasingly difficult to find sufficient, suitable placements that satisfy program accreditation requirements. The professional accrediting body for occupational therapy in Australia allows up to 200 of the mandatory 1000 clinical placement hours to be completed via simulation activities, but evidence of effectiveness and efficiency for student learning outcomes is lacking. Increasingly placement providers charge a fee to host students, leading educators to consider whether providing an internal program might be a feasible alternative for a portion of placement hours. Economic analysis of the incremental costs and benefits of providing a traditional versus simulated placement is required to inform decision-making.

Methods/design: This study is a pragmatic, non-inferiority, single-blind, multicentre, two-group randomised controlled trial (RCT) with an embedded economic analysis. The RCT will compare a block of 40 hours of simulated placement (intervention) with a 40-hour block of traditional placement (comparator), with a focus on student learning outcomes and delivery costs. Six universities will instigate the educational intervention within their respective occupational therapy courses, randomly assigning their cohort of students (1:1 allocation) to the simulated or traditional clinical placements. The primary outcome is achievement of professional behaviours (e.g. communication, clinical reasoning) as assessed by a post-placement written examination. Secondary outcomes include proportions passing the placement assessed using the Student Practice Evaluation Form-Revised, changes in student confidence pre-/post-placement, student and educator evaluation of the placement experience and cost-effectiveness of simulated versus traditional clinical placements. Comprehensive cost data will be collected for both the simulated and traditional placement programs at each site for economic evaluation.

Discussion: Use of simulation in health-related fields like occupational therapy is common, but these activities usually relate to brief opportunities for isolated skill development. The simulated clinical placement evaluated in this trial is less common because it encapsulates a 5-day block of integrated activities, designed and delivered in a manner intended to emulate best-practice placement experiences. The planned study is rare due to inclusion of an economic analysis that aims to provide valuable information about the relationship between costs and outcomes across participating sites.

Trial Registration: Australian New Zealand Clinical Trials Registry, ACTRN12616001339448 . Registered 26 September 2016.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13063-017-2087-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5521130PMC
July 2017

Instructional practices for evidence-based practice with pre-registration allied health students: a review of recent research and developments.

Adv Health Sci Educ Theory Pract 2017 Oct 28;22(4):1031-1045. Epub 2016 Jul 28.

Deakin University, Waterfront Campus, 1 Gheringhap Street, Geelong, VIC, 3217, Australia.

The aim of this study is to update a previous review published in this journal on the effectiveness of teaching and assessment interventions for evidence based practice in health professions, and to determine the extent to which the five recommendations made from that review have been implemented. The Integrating Theory, Evidence and Action method was used to synthesise all published evidence from 2011 to 2015, which addressed instructional practices used for evidence based practice with pre-registration allied health students. Seventeen articles were found to meet the inclusion criteria, and were analysed for both their individual rigour and relationship to the five recommendations. The evidence reviewed in this study was diverse in both its geographical setting and the allied health disciplines represented. Most of the evidence used less rigorous methods, and the evidence base is generally exploratory in nature. To date, the five recommendations regarding instructional practices in this area have been implemented to varying degrees. Many current practices promote social negotiation, collaborative decision-making and collaborative learning, so the social constructivist approach is being adopted. However, the prior knowledge of students is not being assessed as a basis for scaffolding, communication of evidence based practice to varying audiences is rarely addressed and the role of clinicians in the learning of evidence based practice knowledge, skills, beliefs and attitudes remains limited.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s10459-016-9702-9DOI Listing
October 2017

Transformation from student to occupational therapist: Using the Delphi technique to identify the threshold concepts of occupational therapy.

Aust Occup Ther J 2016 Apr 29;63(2):95-104. Epub 2015 Dec 29.

School of Health and Social Development, Deakin University, Geelong, Victoria, Australia.

Background/aim: Understanding and facilitating the transformation from occupational therapy student to practitioner is central to the development of competent and work-ready graduates. However, the pivotal concepts and capabilities that need to be taught and learnt in occupational therapy are not necessarily explicit. The threshold concepts theory of teaching and learning proposes that every discipline has a set of transformational concepts that students must acquire in order to progress. As students acquire the threshold concepts, they develop a transformed way of understanding content related to their course of study which contributes to their developing expertise. The aim of this study was to identify the threshold concepts of occupational therapy.

Method: The Delphi technique, a data collection method that aims to demonstrate consensus in relation to important questions, was used with three groups comprising final year occupational therapy students (n = 11), occupational therapy clinicians (n = 21) and academics teaching occupational therapy (n = 10) in Victoria, Australia.

Results: Participants reached consensus regarding 10 threshold concepts for the occupational therapy discipline. These are: understanding and applying the models and theories of occupational therapy; occupation; evidence-based practice; clinical reasoning; discipline specific skills and knowledge; practising in context; a client-centred approach; the occupational therapist role; reflective practice and; a holistic approach.

Conclusion: The threshold concepts identified provide valuable information for the discipline. They can potentially inform the development of competencies for occupational therapy and provide guidance for teaching and learning activities to facilitate the transformation to competent practitioner.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/1440-1630.12252DOI Listing
April 2016

Validity of ligand efficiency metrics.

ACS Med Chem Lett 2014 Jun 9;5(6):616-8. Epub 2014 May 9.

Medicines Research Centre, GlaxoSmithKline , Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K.

A recent viewpoint article (Improving the plausibility of success with inefficient metrics. ACS Med. Chem. Lett. 2014, 5, 2-5) argued that the standard definition of ligand efficiency (LE) is mathematically invalid. In this viewpoint, we address this criticism and show categorically that the definition of LE is mathematically valid. LE and other metrics such as lipophilic ligand efficiency (LLE) can be useful during the multiparameter optimization challenge faced by medicinal chemists.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1021/ml500146dDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4060940PMC
June 2014

Over expression of wild type or a catalytically dead mutant of Sirtuin 6 does not influence NFκB responses.

PLoS One 2012 6;7(7):e39847. Epub 2012 Jul 6.

Platform Technology Sciences, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire, United Kingdom.

SIRT6 is involved in inflammation, aging and metabolism potentially by modulating the functions of both NFκB and HIF1α. Since it is possible to make small molecule activators and inhibitors of Sirtuins we wished to establish biochemical and cellular assays both to assist in drug discovery efforts and to validate whether SIRT6 represents a valid drug target for these indications. We confirmed in cellular assays that SIRT6 can deacetylate acetylated-histone H3 lysine 9 (H3K9Ac), however this deacetylase activity is unusually low in biochemical assays. In an effort to develop alternative assay formats we observed that SIRT6 overexpression had no influence on TNFα induced nuclear translocation of NFκB, nor did it have an effect on nuclear mobility of RelA/p65. In an effort to identify a gene expression profile that could be used to identify a SIRT6 readout we conducted genome-wide expression studies. We observed that overexpression of SIRT6 had little influence on NFκB-dependent genes, but overexpression of the catalytically inactive mutant affected gene expression in developmental pathways.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0039847PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3391194PMC
March 2013

Influences on patient satisfaction survey results: is there a need for a rethink?

Qual Prim Care 2010 ;18(6):373-8

NHS Derbyshire County, Chesterfield S41 7PF, UK.

Background: Patient experience is a key principle of the NHS and is increasingly linked to payment of providers.

Aim: To establish if any correlation exists between patient satisfaction scores (as measured in the MORI survey) and practice list size or deprivation score.

Method: This was a retrospective correlation review using data for general practices in Derbyshire County Primary Care Trust extracted from existing publicly available sources. Correlation between satisfaction score and both deprivation index and practice list size was examined.

Results: Data from all 96 practices were reviewed. Overall satisfaction showed a statistically significant negative correlation with deprivation (r=-0.28, P=0.006). Neither question pertaining to QOF payment showed a correlation with deprivation, however, there was a statistically significant negative correlation with list size (Q5a r=-0.52, P <0.01. Q7 r=-0.43, P <0.01). Questions regarding satisfaction with the doctor showed weak but statistically significant negative correlations with deprivation, (r varying from -0.21 to -0.39, P <0.05). Satisfaction with nurses showed positive correlations with deprivation, with satisfaction increasing in line with deprivation (r varying from 0.24 to 0.36, P <0.05). Regarding list size, for nurse care the reverse was seen, with increased list size being linked to decreased satisfaction (r varying from -0.21 to -0.45, P <0.05).

Conclusion: Although variables showed weak correlations, there were correlations between list size and deprivation in the results of the patient experience questionnaire. Linking this to payment has implications for primary care contracting.
View Article and Find Full Text PDF

Download full-text PDF

Source
April 2011

Lead optimization using matched molecular pairs: inclusion of contextual information for enhanced prediction of HERG inhibition, solubility, and lipophilicity.

J Chem Inf Model 2010 Oct;50(10):1872-86

Information School, University of Sheffield, Sheffield S1 4DP, UK.

Previous studies of the analysis of molecular matched pairs (MMPs) have often assumed that the effect of a substructural transformation on a molecular property is independent of the context (i.e., the local structural environment in which that transformation occurs). Experiments with large sets of hERG, solubility, and lipophilicity data demonstrate that the inclusion of contextual information can enhance the predictive power of MMP analyses, with significant trends (both positive and negative) being identified that are not apparent when using conventional, context-independent approaches.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1021/ci100258pDOI Listing
October 2010

A 27-year-old man presenting with acute chest pain and dyspnea.

Chest 2009 Jun;135(6):1684-1687

Department of Cardiothoracic Surgery Kingdom, Guys & St. Thomas Hospital, London, UK.

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1378/chest.08-2750DOI Listing
June 2009

Process validation and screen reproducibility in high-throughput screening.

J Biomol Screen 2009 Jan;14(1):66-76

GlaxoSmithKline R&D Pharmaceuticals, Screening and Compound Profiling, Tres Cantos, Spain.

The use of large-scale compound screening has become a key component of drug discovery projects in both the pharmaceutical and the biotechnological industries. More recently, these activities have also been embraced by the academic community as a major tool for chemical genomic activities. High-throughput screening (HTS) activities constitute a major step in the initial drug discovery efforts and involve the use of large quantities of biological reagents, hundreds of thousands to millions of compounds, and the utilization of expensive equipment. All these factors make it very important to evaluate in advance of the HTS campaign any potential issues related to reproducibility of the experimentation and the quality of the results obtained at the end of these very costly activities. In this article, the authors describe how GlaxoSmithKline (GSK) has addressed the need of a true validation of the HTS process before embarking in full HTS campaigns. They present 2 different aspects of the so-called validation process: (1) optimization of the HTS workflow and its validation as a quality process and (2) the statistical evaluation of the HTS, focusing on the reproducibility of results and the ability to distinguish active from nonactive compounds in a vast collection of samples. The authors describe a variety of reproducibility indexes that are either innovative or have been adapted from generic medical diagnostic screening strategies. In addition, they exemplify how these validation tools have been implemented in a number of case studies at GSK.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1177/1087057108326664DOI Listing
January 2009

GALAHAD: 1. pharmacophore identification by hypermolecular alignment of ligands in 3D.

J Comput Aided Mol Des 2006 Sep 19;20(9):567-87. Epub 2006 Oct 19.

Krebs Institute for Biomolecular Research, Department of Information Studies, University of Sheffield, 211 Portobello St., Sheffield, S7 4DP, UK.

Alignment of multiple ligands based on shared pharmacophoric and pharmacosteric features is a long-recognized challenge in drug discovery and development. This is particularly true when the spatial overlap between structures is incomplete, in which case no good template molecule is likely to exist. Pair-wise rigid ligand alignment based on linear assignment (the LAMDA algorithm) has the potential to address this problem (Richmond et al. in J Mol Graph Model 23:199-209, 2004). Here we present the version of LAMDA embodied in the GALAHAD program, which carries out multi-way alignments by iterative construction of hypermolecules that retain the aggregate as well as the individual attributes of the ligands. We have also generalized the cost function from being purely atom-based to being one that operates on ionic, hydrogen bonding, hydrophobic and steric features. Finally, we have added the ability to generate useful partial-match 3D search queries from the hypermolecules obtained. By running frozen conformations through the GALAHAD program, one can utilize the extended version of LAMDA to generate pharmacophores and pharmacosteres that agree well with crystal structure alignments for a range of literature datasets, with minor adjustments of the default parameters generating even better models. Allowing for inclusion of partial match constraints in the queries yields pharmacophores that are consistently a superset of full-match pharmacophores identified in previous analyses, with the additional features representing points of potentially beneficial interaction with the target.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s10822-006-9082-yDOI Listing
September 2006

Unsupervised 3D ring template searching as an ideas generator for scaffold hopping: use of the LAMDA, RigFit, and field-based similarity search (FBSS) methods.

J Chem Inf Model 2006 Sep-Oct;46(5):1882-90

Tripos GmbH, Martin-Kollar-Strasse 17, D-81829 Munich, Germany.

Crystal structures taken from the Cambridge Structural Database were used to build a ring scaffold database containing 19 050 3D structures, with each such scaffold then being used to generate a centroid connecting path (CCP) representation. The CCP is a novel object that connects ring centroids, ring linker atoms, and other important points on the connection path between ring centroids. Unsupervised searching in the scaffold and CCP data sets was carried out using the atom-based LAMDA and RigFit search methods and the field-based similarity search method. The performance of these methods was tested with three different ring scaffold queries. These searches demonstrated that unsupervised 3D scaffold searching methods can find not only the types of ring systems that might be retrieved in carefully defined pharmacophore searches (supervised approach) but also additional, structurally diverse ring systems that could form the starting point for lead discovery programs or other scaffold-hopping applications. Not only are the methods effective but some are sufficiently rapid to permit scaffold searching in large chemical databases on a routine basis.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1021/ci049657kDOI Listing
November 2006

Lack of effects of guanfacine on executive and memory functions in healthy male volunteers.

Psychopharmacology (Berl) 2005 Oct 19;182(2):205-13. Epub 2005 Oct 19.

Department of Experimental Psychology, University of Cambridge, Downing Street, Cambridge, CB2 3EB, UK.

Rationale: Guanfacine is an alpha2-adrenergic receptor agonist that has been shown to have beneficial effects on working memory and attentional functions in monkeys and in patients with attention deficit hyperactivity disorder.

Objectives: The aim of this study was to further investigate the cognitive-enhancing properties of guanfacine using an established battery of tasks measuring executive and memory functions.

Methods: Sixty healthy male volunteers were randomised into three groups. Cognitive testing was performed from +2 to +4 h after double-blind administration of a single oral dose of 1 or 2 mg of guanfacine or placebo.

Results: Systolic blood pressure was significantly reduced by both doses of guanfacine at the end of the testing session. There were no statistically significant effects on any of the cognitive measures. Two trend effects were observed with poorer performance on digit span backward and slower 'Go' reaction times after guanfacine.

Conclusion: This study found no improvement of prefrontal memory or executive functions after guanfacine. Negative effects on blood pressure and trend effects on digit span backward and go reaction time indicate a mild sedative effect of guanfacine at these doses, possibly via mechanisms of autoreceptor down-regulation.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00213-005-0078-4DOI Listing
October 2005

Alignment of three-dimensional molecules using an image recognition algorithm.

J Mol Graph Model 2004 Oct;23(2):199-209

Department of Information Studies, Krebs Institute for Biomolecular Research, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK.

This paper describes a novel approach, based on image recognition in two dimensions, for the atom-based alignment of two rigid molecules in three dimensions. The atoms are characterised by their partial charges and their positions relative to the remaining atoms in the molecule. Based on this information, a cost of matching a pair of atoms, one from each molecule, is assigned to all possible pairs. A preliminary set of intermolecular atom equivalences that minimises the total atom matching cost is then determined using an algorithm for solving the linear assignment problem. Several geometric heuristics are described that aim to reduce the number of atom equivalences that are inconsistent with the 3D structures. Those that remain are used to calculate an alignment transformation that achieves an optimal superposition of atoms that have a similar local geometry and partial charge. This alignment is then refined by calculating a new set of equivalences consisting of atom pairs that are approximately overlaid, irrespective of partial charge. A range of examples is provided to demonstrate the efficiency and effectiveness of the method.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jmgm.2004.04.004DOI Listing
October 2004