Molecular electronic spectroscopy: from often neglected fundamental principles to limitations of state-of-the-art computational methods

2015 ◽  
Vol 131 (1) ◽  
pp. 9-26 ◽  
Author(s):  
Heinz Mustroph ◽  
Steffen Ernst ◽  
Bianca Senns ◽  
Andrew D. Towns
Keyword(s):  
Computational Methods ◽  
State Of The Art ◽  
Electronic Spectroscopy ◽  
Molecular Electronic

Identification, Prediction and Data Analysis of Noncoding RNAs: A Review

2019 ◽  
Vol 15 (3) ◽  
pp. 216-230 ◽  
Author(s):  
Abbasali Emamjomeh ◽  
Javad Zahiri ◽  
Mehrdad Asadian ◽  
Mehrdad Behmanesh ◽  
Barat A. Fakheri ◽  
...  
Keyword(s):  
Computational Methods ◽  
State Of The Art ◽  
Noncoding Rnas ◽  
Research Field ◽  
Design Strategies ◽  
Structural Prediction ◽  
Computational Costs ◽  
Cellular Processes ◽  
Laboratory Techniques ◽  
Fast Prediction

Background:Noncoding RNAs (ncRNAs) which play an important role in various cellular processes are important in medicine as well as in drug design strategies. Different studies have shown that ncRNAs are dis-regulated in cancer cells and play an important role in human tumorigenesis. Therefore, it is important to identify and predict such molecules by experimental and computational methods, respectively. However, to avoid expensive experimental methods, computational algorithms have been developed for accurately and fast prediction of ncRNAs.Objective:The aim of this review was to introduce the experimental and computational methods to identify and predict ncRNAs structure. Also, we explained the ncRNA’s roles in cellular processes and drugs design, briefly.Method:In this survey, we will introduce ncRNAs and their roles in biological and medicinal processes. Then, some important laboratory techniques will be studied to identify ncRNAs. Finally, the state-of-the-art models and algorithms will be introduced along with important tools and databases.Results:The results showed that the integration of experimental and computational approaches improves to identify ncRNAs. Moreover, the high accurate databases, algorithms and tools were compared to predict the ncRNAs.Conclusion:ncRNAs prediction is an exciting research field, but there are different difficulties. It requires accurate and reliable algorithms and tools. Also, it should be mentioned that computational costs of such algorithm including running time and usage memory are very important. Finally, some suggestions were presented to improve computational methods of ncRNAs gene and structural prediction.

Computational Methods and Tools for Decision Support in Biomedicine

2009 ◽  
pp. 1-17
Author(s):  
Ioannis Dimou ◽  
Michalis Zervakis ◽  
David Lowe ◽  
Manolis Tsiknakis
Keyword(s):  
Decision Making ◽  
Decision Support ◽  
Computational Methods ◽  
Pattern Analysis ◽  
State Of The Art ◽  
Biomedical Informatics ◽  
Feature Space ◽  
Diagnostic Tools ◽  
Methodological Issues ◽  
Medical Problems

The automation of diagnostic tools and the increasing availability of extensive medical datasets in the last decade have triggered the development of new analytical methodologies in the context of biomedical informatics. The aim is always to explore a problem’s feature space, extract useful information and support clinicians in their time, volume, and accuracy demanding decision making tasks. From simple summarizing statistics to state-of-the-art pattern analysis algorithms, the underlying principles that drive most medical problems show trends that can be identified and taken into account to improve the usefulness of computerized medicine to the field-clinicians and ultimately to the patient. This chapter presents a thorough review of this field and highlights the achievements and shortcomings of each family of methods. The authors’ effort has been focused on methodological issues as to generalize useful conclusions based on the large number of notable, yet case-specific developments presented in the field.

Network Cleansing

2009 ◽  
pp. 80-97 ◽  
Author(s):  
Paolo Marcatili ◽  
Anna Tramontano
Keyword(s):  
Experimental Data ◽  
Computational Methods ◽  
Gold Standard ◽  
State Of The Art ◽  
Experimental Studies ◽  
The State ◽  
Biological Information ◽  
Ppi Network

This chapter provides an overview of the current computational methods for PPI network cleansing. The authors first present the issue of identifying reliable PPIs from noisy and incomplete experimental data. Next, they address the questions of which are the expected results of the different experimental studies, of what can be defined as true interactions, of which kind of data are to be integrated in assigning reliability levels to PPIs and which gold standard should the authors use in training and testing PPI filtering methods. Finally, Marcatili and Tramontano describe the state of the art in the field, presenting the different classes of algorithms and comparing their results. The aim of the chapter is to guide the reader in the choice of the most convenient methods, experiments and integrative data and to underline the most common biases and errors to obtain a portrait of PINs which is not only reliable but as well able to correctly retrieve the biological information contained in such data.

scholarly journals Vibronic structure of photosynthetic pigments probed by polarized two-dimensional electronic spectroscopy andab initiocalculations

2019 ◽  
Vol 10 (35) ◽  
pp. 8143-8153 ◽  
Author(s):  
Yin Song ◽  
Alexander Schubert ◽  
Elizabeth Maret ◽  
Ryan K. Burdick ◽  
Barry D. Dunietz ◽  
...  
Keyword(s):  
Photosynthetic Pigments ◽  
State Of The Art ◽  
Electronic Spectroscopy ◽  
Two Dimensional ◽  
Vibronic Structure ◽  
Tddft Calculations ◽  
Photoexcited Dynamics

Using polarized 2D spectroscopy and state-of-the-art TDDFT calculations to uncover the vibronic structure of primary photosynthetic pigments and its effect on ultrafast photoexcited dynamics.

Prototropic Reactivity in Salicylamide and Salicylanilide by Molecular Electronic Spectroscopy

1973 ◽  
Vol 62 (7) ◽  
pp. 1197-1199 ◽  
Author(s):  
Stephen G. Schulman ◽  
Peter J. Kovi ◽  
John F. Young
Keyword(s):  
Electronic Spectroscopy ◽  
Molecular Electronic
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