Protein Function Prediction Methods and Protocols

• Author : Jingyu Hou
• Publisher : Academic Press
• Release : 13 January 2017

New Approaches of Protein Function Prediction from Protein Interaction Networks contains the critical aspects of PPI network based protein function prediction, including semantically assessing the reliability of PPI data, measuring the functional similarity between proteins, dynamically selecting prediction domains, predicting functions, and establishing corresponding prediction frameworks. Functional annotation of proteins is vital to biological and clinical research and other applications due to the important roles proteins play in various biological processes. Although the functions of some proteins have been annotated

• Author : Daisuke Kihara
• Publisher : Methods in Molecular Biology
• Release : 12 May 2019

• Author : Daniel John Rigden
• Publisher : Springer Science & Business Media
• Release : 11 December 2008

Proteins lie at the heart of almost all biological processes and have an incredibly wide range of activities. Central to the function of all proteins is their ability to adopt, stably or sometimes transiently, structures that allow for interaction with other molecules. An understanding of the structure of a protein can therefore lead us to a much improved picture of its molecular function. This realisation has been a prime motivation of recent Structural Genomics projects, involving large-scale experimental determination of

• Author : Daisuke Kihara
• Publisher : Springer Science & Business Media
• Release : 19 April 2011

Gene function annotation has been a central question in molecular biology. The importance of computational function prediction is increasing because more and more large scale biological data, including genome sequences, protein structures, protein-protein interaction data, microarray expression data, and mass spectrometry data, are awaiting biological interpretation. Traditionally when a genome is sequenced, function annotation of genes is done by homology search methods, such as BLAST or FASTA. However, since these methods are developed before the genomics era, conventional use of

• Author : Janusz M. Bujnicki
• Publisher : John Wiley & Sons
• Release : 23 December 2008

The growing flood of new experimental data generated by genome sequencing has provided an impetus for the development of automated methods for predicting the functions of proteins that have been deduced by sequence analysis and lack experimental characterization. Prediction of Protein Structures, Functions and Interactions presents a comprehensive overview of methods for prediction of protein structure or function, with the emphasis on their availability and possibilities for their combined use. Methods of modeling of individual proteins, prediction of their interactions,

• Author : Brett Poulin
• Publisher : Unknown
• Release : 07 June 2023

• Author : Sovan Saha,Piyali Chatterjee
• Publisher : LAP Lambert Academic Publishing
• Release : 07 June 2023

Proteins perform every function in a cell. With the advent of genome sequencing projects for different organisms, large amounts of DNA and protein sequence data is available, whereas their biological function is still unknown in the most of the cases. Predicting protein function is the most challenging problem in post-genomic era. Using sequence homology, phylogenetic profiles, gene expression data, and function of unknown protein can be predicted. Recently, the large interaction networks constructed from high throughput techniques like Yeast2Hybrid

• Author : Harley Coleman
• Publisher : Createspace Independent Publishing Platform
• Release : 30 January 2017

Most commonly, protein function is inferred from the known functions of homologous proteins. For homologous proteins with easily recognizable sequence similarity, this type of prediction is based on the 'similar sequence-similar structure-similar function' paradigm. - Domains can be seen as 'units of evolution', and, therefore, both structural and functional similarity between proteins needs to be analyzed at the domain level. - Sequence comparison is most sensitive at the protein level and the detection of distantly related sequences is easier in

• Author : Jing Hu
• Publisher : Unknown
• Release : 07 June 2023

High-throughput genomics projects have resulted in a rapid accumulation of protein sequences. Therefore, computational methods that can predict protein functions and functional sites efficiently and accurately are in high demand. In addition, prediction methods utilizing only sequence information are of particular interest because for most proteins, 3-dimensional structures are not available. However, there are several key challenges in developing methods for predicting protein function and functional sites. These challenges include the following: the construction of representative datasets to train and

• Author : Lukasz Kurgan
• Publisher : World Scientific
• Release : 06 December 2022

Machine Learning in Bioinformatics of Protein Sequences guides readers around the rapidly advancing world of cutting-edge machine learning applications in the protein bioinformatics field. Edited by bioinformatics expert, Dr Lukasz Kurgan, and with contributions by a dozen of accomplished researchers, this book provides a holistic view of the structural bioinformatics by covering a broad spectrum of algorithms, databases and software resources for the efficient and accurate prediction and characterization of functional and structural aspects of proteins. It spotlights key advances

• Author : Eric W. Stawiski
• Publisher : Unknown
• Release : 07 June 2023

• Author : Huiying Zhao
• Publisher : Unknown
• Release : 07 June 2023

Proteins are nano-machines that work inside every living organism. Functional disruption of one or several proteins is the cause for many diseases. However, the functions for most proteins are yet to be annotated because inexpensive sequencing techniques dramatically speed up discovery of new protein sequences (265 million and counting) and experimental examinations of every protein in all its possible functional categories are simply impractical. Thus, it is necessary to develop computational function-prediction tools that complement and guide experimental studies. In this

• Author : Huzefa Rangwala,George Karypis
• Publisher : John Wiley & Sons
• Release : 16 March 2011

A look at the methods and algorithms used to predict proteinstructure A thorough knowledge of the function and structure of proteinsis critical for the advancement of biology and the life sciences aswell as the development of better drugs, higher-yield crops, andeven synthetic bio-fuels. To that end, this reference sheds lighton the methods used for protein structure prediction and revealsthe key applications of modeled structures. This indispensable bookcovers the applications of modeled protein structures and unravelsthe relationship between pure sequence information

• Author : Venkata Rama Kumar Swamy Yedida
• Publisher : Unknown
• Release : 07 June 2023

The human genome project and numerous other genome projects have produced a large and ever increasing amount of sequence data. One of the main research challenges in the post-genomic era is to understand the relationship between the nucleotide sequences of genes and the functions of the proteins they encode. The objective of this thesis is to develop an automated protein function prediction system that is based on a set of homologous proteins and gene ontology categories. A novel measure based

• Author : G.D. Fasman
• Publisher : Springer Science & Business Media
• Release : 06 December 2012

The prediction of the conformation of proteins has developed from an intellectual exercise into a serious practical endeavor that has great promise to yield new stable enzymes, products of pharmacological significance, and catalysts of great potential. With the application of predic tion gaining momentum in various fields, such as enzymology and immunology, it was deemed time that a volume be published to make available a thorough evaluation of present methods, for researchers in this field to expound fully the virtues