scholarly journals Guidelines for reporting protein modelling studies

2021 ◽  
Author(s):  
Mauno Vihinen
Keyword(s):  
Computational Modelling ◽  
Structural Models ◽  
Protein Modelling ◽  
Modelling Procedure ◽  
Modelling Studies ◽  
Supplementary Material ◽  
Modelling Process

Computational modelling tools are widely used, however, articles describing modelling studies frequently do not contain sufficient details to allow the reader to comprehend the modelling procedure, quality of the produced model and validity of interpretations and predictions made based on the model. Here, guidelines were developed for items that have to be included when reporting studies and results based on protein modelling. A brief and concise checklist of required data items was compiled. These guidelines are simple to follow and apply, but require meticulous description of details, many of which can be placed to supplementary material. Authors have to pay attention to details when reporting modelling process. The generated structural models should be made publicly available, preferably by submitting to one of the existing repositories.

Pollutants in Organic Chemistry and Medicinal Chemistry Education Laboratory. Experimental and Machine Learning Studies

2020 ◽  
Vol 20 (9) ◽  
pp. 720-730
Author(s):  
Iker Montes-Bageneta ◽  
Urtzi Akesolo ◽  
Sara López ◽  
Maria Merino ◽  
Eneritz Anakabe ◽  
...  
Keyword(s):  
Organic Chemistry ◽  
Machine Learning ◽  
Chemistry Education ◽  
Organic Waste ◽  
Computational Modelling ◽  
University Education ◽  
Academic Factors ◽  
Academic Year ◽  
Statistical Analysis Software

Aims: Computational modelling may help us to detect the more important factors governing this process in order to optimize it. Background: The generation of hazardous organic waste in teaching and research laboratories poses a big problem that universities have to manage. Methods: In this work, we report on the experimental measurement of waste generation on the chemical education laboratories within our department. We measured the waste generated in the teaching laboratories of the Organic Chemistry Department II (UPV/EHU), in the second semester of the 2017/2018 academic year. Likewise, to know the anthropogenic and social factors related to the generation of waste, a questionnaire has been utilized. We focused on all students of Experimentation in Organic Chemistry (EOC) and Organic Chemistry II (OC2) subjects. It helped us to know their prior knowledge about waste, awareness of the problem of separate organic waste and the correct use of the containers. These results, together with the volumetric data, have been analyzed with statistical analysis software. We obtained two Perturbation-Theory Machine Learning (PTML) models including chemical, operational, and academic factors. The dataset analyzed included 6050 cases of laboratory practices vs. practices of reference. Results: These models predict the values of acetone waste with R2 = 0.88 and non-halogenated waste with R2 = 0.91. Conclusion: This work opens a new gate to the implementation of more sustainable techniques and a circular economy with the aim of improving the quality of university education processes.

scholarly journals Adult and fetal haemoglobin J-Sardegna [α50(CE8)His→Asp]: functional and molecular modelling studies

2000 ◽  
Vol 346 (1) ◽  
pp. 193-199 ◽  
Author(s):  
Marcella CORDA ◽  
Maria C. DE ROSA ◽  
Maria G. PELLEGRINI ◽  
Maria T. SANNA ◽  
Alessandra OLIANAS ◽  
...  
Keyword(s):  
Functional Properties ◽  
Computational Modelling ◽  
Oxygen Affinity ◽  
Oxygen Binding ◽  
Structural Level ◽  
Fetal Haemoglobin ◽  
Significant Difference ◽  
Molecular Modelling Studies ◽  
Modelling Studies ◽  
2,3 Dpg

Haemoglobin (Hb) J-Sardegna [α50(CE8)His → Asp] is a haemoglobin variant characteristic of subjects from the island of Sardinia. Here we report a study of the functional properties of both fetal and adult Hb J-Sardegna. The results indicate that adult Hb J-Sardegna displays an oxygen affinity that is higher than that of adult Hb only in the presence of 2,3-diphosphoglycerate (2,3-DPG). On the contrary, at 20 °C, the oxygen affinity of fetal Hb J-Sardegna is identical to that of normal fetal haemoglobin, both in the presence and in the absence of 2,3-DPG. A significant difference between these two systems (i.e. a higher oxygen affinity of fetal Hb J-Sardegna) shows up very clearly only when temperature is increased to 37 °C. Hence in fetal Hb, the main effect of the amino acid substitution is a decrease in the overall enthalpy change of oxygenation. The results outline the role of the α1-β1 interface in assessing the thermodynamics of oxygen binding. The functional properties of both adult and fetal Hb J-Sardegna have been interpreted at the structural level in light of the results obtained by a computational modelling approach performed in comparison with HbA and Hb Aichi, a variant characterized by a different mutation [α50(CE8)His → Arg] at the same position.

scholarly journals Developing WHO guidelines: Time to formally include evidence from mathematical modelling studies

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 1584 ◽  
Author(s):  
Matthias Egger ◽  
Leigh Johnson ◽  
Christian Althaus ◽  
Anna Schöni ◽  
Georgia Salanti ◽  
...  
Keyword(s):  
Mathematical Modelling ◽  
The Body ◽  
World Health ◽  
Who Guidelines ◽  
Problem Model ◽  
Assessment Development ◽  
Modelling Studies ◽  
Health Organization

In recent years, the number of mathematical modelling studies has increased steeply. Many of the questions addressed in these studies are relevant to the development of World Health Organization (WHO) guidelines, but modelling studies are rarely formally included as part of the body of evidence. An expert consultation hosted by WHO, a survey of modellers and users of modelling studies, and literature reviews informed the development of recommendations on when and how to incorporate the results of modelling studies into WHO guidelines. In this article, we argue that modelling studies should routinely be considered in the process of developing WHO guidelines, but particularly in the evaluation of public health programmes, long-term effectiveness or comparative effectiveness.  There should be a systematic and transparent approach to identifying relevant published models, and to commissioning new models.  We believe that the inclusion of evidence from modelling studies into the Grading of Recommendations Assessment, Development and Evaluation (GRADE) process is possible and desirable, with relatively few adaptations.  No single “one-size-fits-all” approach is appropriate to assess the quality of modelling studies. The concept of the ‘credibility’ of the model, which takes the conceptualization of the problem, model structure, input data, different dimensions of uncertainty, as well as transparency and validation into account, is more appropriate than ‘risk of bias’.

Consequences of climatic change for distributions

2019 ◽  
pp. 165-184
Author(s):  
Brian Huntley
Keyword(s):  
Genetic Variation ◽  
Gene Flow ◽  
Species Distributions ◽  
Climatic Changes ◽  
Adaptive Genetic Variation ◽  
Spatial Structuring ◽  
Modelling Studies ◽  
Population Sizes ◽  
Fossil Records

Species’ distributions, population sizes, and community composition are affected, directly and indirectly, by climatic changes, leading to changes in location, extent, and/or quality of distributions, range fragmentation or coalescence, and temporal discontinuities in suitable conditions. Quaternary fossil records document these responses, emphasizing individualism of species’ responses and impermanence of communities. Recent observations document similar changes attributable to recent climatic changes, including rapid decreases and increases in ranges and/or populations. Both also document extinctions associated with rapid climatic changes. Modelling studies predict substantial changes in species’ distributions, population sizes, and communities in response to future climatic changes. Implicit assumptions that genetic variation enabling adaptation is ubiquitous throughout species’ ranges, or that gene flow may be sufficiently rapid to allow adaptation, may be invalid. Work is needed to investigate spatial structuring of adaptive genetic variation and rates of gene flow, and to develop new models. Without this, species extinction risks may be severely underestimated.

Modal Testing for Validation of Blade Models

2008 ◽  
Vol 32 (2) ◽  
pp. 91-102 ◽  
Author(s):  
D. Todd Griffith ◽  
Thomas G. Carne ◽  
Joshua A. Paquette
Keyword(s):  
Model Validation ◽  
Turbine Blades ◽  
Structural Models ◽  
Modal Testing ◽  
Wind Turbine Blades ◽  
Test Technique ◽  
Modal Test ◽  
Test Result ◽  
Made In

The focus of this paper is a test program designed for wind turbine blades. Model validation is a comprehensive undertaking which requires carefully designing and executing experiments, proposing appropriate physics-based models, and applying correlation techniques to improve these models based on the test data. Structural models are useful for making decisions when designing a new blade or assessing blade performance, and the process of model validation is needed to ensure the quality of these models. Blade modal testing is essential for validation of blade structural models, and this report discusses modal test techniques required to achieve validation. Choices made in the design of a modal test can significantly affect the final test result. This study aims to demonstrate the importance of the proper pre-test design and test technique for validating blade structural models.

scholarly journals Don't know, can't know: embracing deeper uncertainties when analysing risks

2011 ◽  
Vol 369 (1956) ◽  
pp. 4730-4750 ◽  
Author(s):  
David J. Spiegelhalter ◽  
Hauke Riesch
Keyword(s):  
Level Structure ◽  
Evidence Based ◽  
Formal Models ◽  
Intergovernmental Panel ◽  
Policy Makers ◽  
Risk Modelling ◽  
Based Medicine ◽  
Expression Of Uncertainty ◽  
Modelling Process

Numerous types of uncertainty arise when using formal models in the analysis of risks. Uncertainty is best seen as a relation, allowing a clear separation of the object, source and ‘owner’ of the uncertainty, and we argue that all expressions of uncertainty are constructed from judgements based on possibly inadequate assumptions, and are therefore contingent. We consider a five-level structure for assessing and communicating uncertainties, distinguishing three within-model levels—event, parameter and model uncertainty—and two extra-model levels concerning acknowledged and unknown inadequacies in the modelling process, including possible disagreements about the framing of the problem. We consider the forms of expression of uncertainty within the five levels, providing numerous examples of the way in which inadequacies in understanding are handled, and examining criticisms of the attempts taken by the Intergovernmental Panel on Climate Change to separate the likelihood of events from the confidence in the science. Expressing our confidence in the adequacy of the modelling process requires an assessment of the quality of the underlying evidence, and we draw on a scale that is widely used within evidence-based medicine. We conclude that the contingent nature of risk-modelling needs to be explicitly acknowledged in advice given to policy-makers, and that unconditional expressions of uncertainty remain an aspiration.

scholarly journals Developing WHO guidelines: Time to formally include evidence from mathematical modelling studies

F1000Research ◽  
2018 ◽  
Vol 6 ◽  
pp. 1584 ◽  
Author(s):  
Matthias Egger ◽  
Leigh Johnson ◽  
Christian Althaus ◽  
Anna Schöni ◽  
Georgia Salanti ◽  
...  
Keyword(s):  
Mathematical Modelling ◽  
The Body ◽  
World Health ◽  
Who Guidelines ◽  
Problem Model ◽  
Assessment Development ◽  
Modelling Studies ◽  
Health Organization

In recent years, the number of mathematical modelling studies has increased steeply. Many of the questions addressed in these studies are relevant to the development of World Health Organization (WHO) guidelines, but modelling studies are rarely formally included as part of the body of evidence. An expert consultation hosted by WHO, a survey of modellers and users of modelling studies, and literature reviews informed the development of recommendations on when and how to incorporate the results of modelling studies into WHO guidelines. In this article, we argue that modelling studies should routinely be considered in the process of developing WHO guidelines, but particularly in the evaluation of public health programmes, long-term effectiveness or comparative effectiveness.  There should be a systematic and transparent approach to identifying relevant published models, and to commissioning new models.  We believe that the inclusion of evidence from modelling studies into the Grading of Recommendations Assessment, Development and Evaluation (GRADE) process is possible and desirable, with relatively few adaptations.  No single “one-size-fits-all” approach is appropriate to assess the quality of modelling studies. The concept of the ‘credibility’ of the model, which takes the conceptualization of the problem, model structure, input data, different dimensions of uncertainty, as well as transparency and validation into account, is more appropriate than ‘risk of bias’.

scholarly journals Computational Modelling of the Interaction of Gold Nanoparticle with Lung Surfactant Monolayer

MRS Advances ◽  
2019 ◽  
Vol 4 (20) ◽  
pp. 1177-1185 ◽  
Author(s):  
Sheikh I. Hossain ◽  
Neha S. Gandhi ◽  
Zak E. Hughes ◽  
Suvash C. Saha
Keyword(s):  
Respiratory Diseases ◽  
Lung Surfactant ◽  
Computational Modelling ◽  
Fine Tuning ◽  
Coarse Grained ◽  
Normal Lung ◽  
Open Questions ◽  
Compression And Expansion ◽  
Modelling Studies ◽  
Dynamics Simulations

ABSTRACTLung surfactant (LS), a thin layer of phospholipids and proteins inside the alveolus of the lung is the first biological barrier to inhaled nanoparticles (NPs). LS stabilizes and protects the alveolus during its continuous compression and expansion by fine-tuning the surface tension at the air-water interface. Previous modelling studies have reported the biophysical function of LS monolayer and its role, but many open questions regarding the consequences and interactions of airborne nano-sized particles with LS monolayer remain. In spite of gold nanoparticles (AuNPs) having a paramount role in biomedical applications, the understanding of the interactions between bare AuNPs (as pollutants) and LS monolayer components still unresolved. Continuous inhalation of NPs increases the possibility of lung ageing, reducing the normal lung functioning and promoting lung malfunction, and may induce serious lung diseases such as asthma, lung cancer, acute respiratory distress syndrome, and more. Different medical studies have shown that AuNPs can disrupt the routine lung functions of gold miners and promote respiratory diseases. In this work, coarse-grained molecular dynamics simulations are performed to gain an understanding of the interactions between bare AuNPs and LS monolayer components at the nanoscale. Different surface tensions of the monolayer are used to mimic the biological process of breathing (inhalation and exhalation). It is found that the NP affects the structure and packing of the lipids by disordering lipid tails. Overall, the analysed results suggest that bare AuNPs impede the normal biophysical function of the lung, a finding that has beneficial consequences to the potential development of treatments of various respiratory diseases.

scholarly journals Catalysis: transition-state molecular recognition?

2010 ◽  
Vol 6 ◽  
pp. 1026-1034 ◽  
Author(s):  
Ian H Williams
Keyword(s):  
Free Energy ◽  
Molecular Recognition ◽  
Transition State ◽  
Computational Modelling ◽  
Catalytic Antibodies ◽  
Single Atom ◽  
Boat Conformation ◽  
Methyl Transferase ◽  
Modelling Studies ◽  
Dynamics Simulations

The key to understanding the fundamental processes of catalysis is the transition state (TS): indeed, catalysis is a transition-state molecular recognition event. Practical objectives, such as the design of TS analogues as potential drugs, or the design of synthetic catalysts (including catalytic antibodies), require prior knowledge of the TS structure to be mimicked. Examples, both old and new, of computational modelling studies are discussed, which illustrate this fundamental concept. It is shown that reactant binding is intrinsically inhibitory, and that attempts to design catalysts that focus simply upon attractive interactions in a binding site may fail. Free-energy changes along the reaction coordinate for SN2 methyl transfer catalysed by the enzyme catechol-O-methyl transferase are described and compared with those for a model reaction in water, as computed by hybrid quantum-mechanical/molecular-mechanical molecular dynamics simulations. The case is discussed of molecular recognition in a xylanase enzyme that stabilises its sugar substrate in a (normally unfavourable) boat conformation and in which a single-atom mutation affects the free-energy of activation dramatically.

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