scholarly journals Tools and strategies for physiological genomics: the Rat Genome Database

2005 ◽  
Vol 23 (2) ◽  
pp. 246-256 ◽  
Author(s):  
Simon N. Twigger ◽  
Dean Pasko ◽  
Jeff Nie ◽  
Mary Shimoyama ◽  
Susan Bromberg ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Computational Biology ◽  
Computational Techniques ◽  
Genome Database ◽  
Computational Tools ◽  
Functional Roles ◽  
Genomics Research ◽  
Human And Mouse ◽  
Rat Genome

The broad goal of physiological genomics research is to link genes to their functions using appropriate experimental and computational techniques. Modern genomics experiments enable the generation of vast quantities of data, and interpretation of this data requires the integration of information derived from many diverse sources. Computational biology and bioinformatics offer the ability to manage and channel this information torrent. The Rat Genome Database (RGD; http://rgd.mcw.edu ) has developed computational tools and strategies specifically supporting the goal of linking genes to their functional roles in rat and, using comparative genomics, to human and mouse. We present an overview of the database with a focus on these unique computational tools and describe strategies for the use of these resources in the area of physiological genomics.

Elucidating Protein-protein Interactions Through Computational Approaches and Designing Small Molecule Inhibitors Against them for Various Diseases

2018 ◽  
Vol 18 (20) ◽  
pp. 1719-1736 ◽  
Author(s):  
Sharanya Sarkar ◽  
Khushboo Gulati ◽  
Manikyaprabhu Kairamkonda ◽  
Amit Mishra ◽  
Krishna Mohan Poluri
Keyword(s):  
Small Molecule ◽  
Protein Interactions ◽  
Small Molecule Inhibitors ◽  
Computational Techniques ◽  
Protein Protein Interactions ◽  
Computational Tools ◽  
Computational Approaches ◽  
Protein Protein Interaction ◽  
Wide Range ◽  
Therapeutic Measures

Background: To carry out wide range of cellular functionalities, proteins often associate with one or more proteins in a phenomenon known as Protein-Protein Interaction (PPI). Experimental and computational approaches were applied on PPIs in order to determine the interacting partners, and also to understand how an abnormality in such interactions can become the principle cause of a disease. Objective: This review aims to elucidate the case studies where PPIs involved in various human diseases have been proven or validated with computational techniques, and also to elucidate how small molecule inhibitors of PPIs have been designed computationally to act as effective therapeutic measures against certain diseases. Results: Computational techniques to predict PPIs are emerging rapidly in the modern day. They not only help in predicting new PPIs, but also generate outputs that substantiate the experimentally determined results. Moreover, computation has aided in the designing of novel inhibitor molecules disrupting the PPIs. Some of them are already being tested in the clinical trials. Conclusion: This review delineated the classification of computational tools that are essential to investigate PPIs. Furthermore, the review shed light on how indispensable computational tools have become in the field of medicine to analyze the interaction networks and to design novel inhibitors efficiently against dreadful diseases in a shorter time span.

scholarly journals The Rat Genome Database 2013--data, tools and users

2013 ◽  
Vol 14 (4) ◽  
pp. 520-526 ◽  
Author(s):  
S. J. F. Laulederkind ◽  
G. T. Hayman ◽  
S.-J. Wang ◽  
J. R. Smith ◽  
T. F. Lowry ◽  
...  
Keyword(s):  
Genome Database ◽  
Rat Genome

scholarly journals Disease pathways at the Rat Genome Database Pathway Portal: genes in context-a network approach to understanding the molecular mechanisms of disease

2014 ◽  
Vol 8 (1) ◽  
Author(s):  
Victoria Petri ◽  
G Thomas Hayman ◽  
Marek Tutaj ◽  
Jennifer R Smith ◽  
Stanley JF Laulederkind ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Network Approach ◽  
Genome Database ◽  
Rat Genome ◽  
Disease Pathways

scholarly journals PhenoMiner: quantitative phenotype curation at the rat genome database

Database ◽  
2013 ◽  
Vol 2013 ◽  
Author(s):  
Stanley J F Laulederkind ◽  
Weisong Liu ◽  
Jennifer R Smith ◽  
G Thomas Hayman ◽  
Shur-Jen Wang ◽  
...  
Keyword(s):  
Biological Information ◽  
Ontology Development ◽  
Rat Strains ◽  
Genome Database ◽  
Quantitative Phenotype ◽  
Phenotype Data ◽  
Disease Associations ◽  
Data Objects ◽  
Cellular Components ◽  
Rat Genome

Abstract The Rat Genome Database (RGD) is the premier repository of rat genomic and genetic data and currently houses >40 000 rat gene records as well as human and mouse orthologs, >2000 rat and 1900 human quantitative trait loci (QTLs) records and >2900 rat strain records. Biological information curated for these data objects includes disease associations, phenotypes, pathways, molecular functions, biological processes and cellular components. Recently, a project was initiated at RGD to incorporate quantitative phenotype data for rat strains, in addition to the currently existing qualitative phenotype data for rat strains, QTLs and genes. A specialized curation tool was designed to generate manual annotations with up to six different ontologies/vocabularies used simultaneously to describe a single experimental value from the literature. Concurrently, three of those ontologies needed extensive addition of new terms to move the curation forward. The curation interface development, as well as ontology development, was an ongoing process during the early stages of the PhenoMiner curation project. Database URL: http://rgd.mcw.edu

scholarly journals Computational biology for enzymatic removal of mycotoxins

2021 ◽  
Author(s):  
Natalie Sandlin ◽  
Darius Russell Kish ◽  
John Kim ◽  
Marco Zaccaria ◽  
Babak Momeni
Keyword(s):  
Computational Biology ◽  
Empirical Data ◽  
Computational Tools ◽  
Cellular Processes ◽  
Food And Feed ◽  
Biological Organisms

Biological organisms carry a rich potential for removing toxins from our environment, but the search to identify suitable candidates remains challenging. We survey and explore the use of computational tools to discover and optimize the detoxification of harmful compounds. In particular, we will focus on mycotoxins—fungi-produced toxins that contaminate food and feed—and biological enzymes that are capable of rendering them less harmful. We discuss the use of computational tools to complement existing empirical data in three main directions: discovering the prospect of detoxification among underexplored organisms, finding important cellular processes that contribute to detoxification, and optimizing the performance of enzymes with detoxification capability.

scholarly journals PlantRep: a resource of plant repeats

2021 ◽  
Author(s):  
Yu Zhang ◽  
Xizhi Luo ◽  
Shiyu Chen
Keyword(s):  
Comparative Genomics ◽  
Taxonomic Group ◽  
Repeat Elements ◽  
Plant Genomes ◽  
Repeat Sequences ◽  
Free Resource ◽  
Genomics Research

Abstract We re-annotated repeats sequence of 459 plant genomes and release a new resource of plant repeats: PlantRep (http://www.plantrep.cn/). We compared the structural and evolutionary characteristics of repeat sequences in different plant taxonomic group. The contribution of repeat sequences to the genes was examined systematically. PlantRep sheds lights of evolution of plant repeats and provides a free-resource for deep annotation of genome and comparative genomics research of repeat elements in plants.

scholarly journals Challenges and Limitations in the Studies of Glycoproteins: A Computational Chemist’s Perspective

2021 ◽  
Author(s):  
Oyku Balli ◽  
Vladimir Uversky ◽  
Serdar Durdagi ◽  
Orkid Coskuner-Weber
Keyword(s):  
Computational Biology ◽  
Structural Properties ◽  
Structural Property ◽  
Computational Studies ◽  
Computational Tools ◽  
Future Developments ◽  
High Flexibility

Experimenters face challenges and limitations while analyzing glycoproteins due to their high flexibility, stereochemistry, anisotropic effects, and hydration phenomena. Computational studies complement experiments and have been used in characterization of the structural properties of glycoproteins. However, recent investigations revealed that computational studies face significant challenges as well. Here, we introduce and discuss some of these challenges and weaknesses in the investigations of glycoproteins. We also present requirements of future developments in computational biochemistry and computational biology areas that could be necessary for providing more accurate structural property analyses of glycopro-teins using computational tools. Further theoretical strategies that need to be and can be developed are discussed herein.

Biophysical Techniques in Structural Biology

2019 ◽  
Vol 88 (1) ◽  
pp. 25-33 ◽  
Author(s):  
Christopher M. Dobson
Keyword(s):  
Structural Biology ◽  
Weak Interactions ◽  
Biological Systems ◽  
Computational Techniques ◽  
X Rays ◽  
Physical Sciences ◽  
Time Resolved ◽  
New Era ◽  
Functional Roles ◽  
New Information

Over the past six decades, steadily increasing progress in the application of the principles and techniques of the physical sciences to the study of biological systems has led to remarkable insights into the molecular basis of life. Of particular significance has been the way in which the determination of the structures and dynamical properties of proteins and nucleic acids has so often led directly to a profound understanding of the nature and mechanism of their functional roles. The increasing number and power of experimental and theoretical techniques that can be applied successfully to living systems is now ushering in a new era of structural biology that is leading to fundamentally new information about the maintenance of health, the origins of disease, and the development of effective strategies for therapeutic intervention. This article provides a brief overview of some of the most powerful biophysical methods in use today, along with references that provide more detailed information about recent applications of each of them. In addition, this article acts as an introduction to four authoritative reviews in this volume. The first shows the ways that a multiplicity of biophysical methods can be combined with computational techniques to define the architectures of complex biological systems, such as those involving weak interactions within ensembles of molecular components. The second illustrates one aspect of this general approach by describing how recent advances in mass spectrometry, particularly in combination with other techniques, can generate fundamentally new insights into the properties of membrane proteins and their functional interactions with lipid molecules. The third reviewdemonstrates the increasing power of rapidly evolving diffraction techniques, employing the very short bursts of X-rays of extremely high intensity that are now accessible as a result of the construction of free-electron lasers, in particular to carry out time-resolved studies of biochemical reactions. The fourth describes in detail the application of such approaches to probe the mechanism of the light-induced changes associated with bacteriorhodopsin's ability to convert light energy into chemical energy.

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