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Relevant bibliographies by topics / Protein bioinformatics / Dissertations / Theses

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Dissertations / Theses on the topic 'Protein bioinformatics'

Author: Grafiati

Published: 4 June 2021

Last updated: 7 September 2023

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1

Simu, Tiberiu. "A method for extracting pathways from Scansite-predicted protein-protein interactions." Thesis, University of Skövde, School of Humanities and Informatics, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-34.

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<p>Protein interaction is an important mechanism for cellular functionality. Predicting protein interactions is available in many cases as computational methods in publicly available resources (for example Scansite). These predictions can be further combined with other information sources to generate hypothetical pathways. However, when using computational methods for building pathways, the process may become time consuming, as it requires multiple iterations and consolidating data from different sources. We have tested whether it is possible to generate graphs of protein-protein interaction b

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2

Snøve, Jr Ola. "Hardware-accelerated analysis of non-protein-coding RNAs." Doctoral thesis, Norwegian University of Science and Technology, Faculty of Information Technology, Mathematics and Electrical Engineering, 2005. http://urn.kb.se/resolve?urn=urn:nbn:no:ntnu:diva-713.

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<p>A tremendous amount of genomic sequence data of relatively high quality has become publicly available due to the human genome sequencing projects that were completed a few years ago. Despite considerable efforts, we do not yet know everything that is to know about the various parts of the genome, what all the regions code for, and how their gene products contribute in the myriad of biological processes that are performed within the cells. New high-performance methods are needed to extract knowledge from this vast amount of information.</p><p>Furthermore, the traditional view that DNA codes

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3

Hennerdal, Aron, and Arne Elofsson. "Rapid membrane protein topology prediction." Stockholms universitet, Institutionen för biokemi och biofysik, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-61921.

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State-of-the-art methods for topology of α-helical membrane proteins are based on the use of time-consuming multiple sequence alignments obtained from PSI-BLAST or other sources. Here, we examine if it is possible to use the consensus of topology prediction methods that are based on single sequences to obtain a similar accuracy as the more accurate multiple sequence-based methods. Here, we show that TOPCONS-single performs better than any of the other topology prediction methods tested here, but ~6% worse than the best method that is utilizing multiple sequence alignments. AVAILABILITY AND IMP

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4

Björkholm, Patrik. "Method for recognizing local descriptors of protein structures using Hidden Markov Models." Thesis, Linköping University, The Department of Physics, Chemistry and Biology, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-11408.

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<p>Being able to predict the sequence-structure relationship in proteins will extend the scope of many bioinformatics tools relying on structure information. Here we use Hidden Markov models (HMM) to recognize and pinpoint the location in target sequences of local structural motifs (local descriptors of protein structure, LDPS) These substructures are composed of three or more segments of amino acid backbone structures that are in proximity with each other in space but not necessarily along the amino acid sequence. We were able to align descriptors to their proper locations in 41.1% of the cas

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5

Rao, Aditya. "Tarfetpf: A Plasmodium faciparum protein localization predictor." Thesis, University of Skövde, School of Humanities and Informatics, 2004. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-24.

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6

Rao, Aditya. "TargetPf: A Plasmodium falciparum protein localization predictor." Thesis, University of Skövde, School of Humanities and Informatics, 2004. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-914.

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<p>Background: In P. falciparum a similarity between the transit peptides of apicoplast and mitochondrial proteins in the context of net positive charge has previously been observed in few proteins. Existing P. falciparum protein localization prediction tools were leveraged in this study to study this similarity in larger sets of these proteins.</p><p>Results: The online public-domain malarial repository PlasmoDB was utilized as the source of apicoplast and mitochondrial protein sequences for the similarity study of the two types of transit peptides. It was found that</p><p>many of the 551 api

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7

Campbell, M. P. "A bioinformatics approach to protein-protein interactions." Thesis, University of Essex, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.426014.

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8

Elfving, Eric. "Automated annotation of protein families." Thesis, Linköpings universitet, Bioinformatik, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-69393.

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Introduction: The great challenge in bioinformatics is data integration. The amount of available data is always increasing and there are no common unified standards of where, or how, the data should be stored. The aim of this workis to build an automated tool to annotate the different member families within the protein superfamily of medium-chain dehydrogenases/reductases (MDR), by finding common properties among the member proteins. The goal is to increase the understanding of the MDR superfamily as well as the different member families.This will add to the amount of knowledge gained for free

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9

Bottoms, Christopher A. "Bioinformatics of protein bound water." Diss., Columbia, Mo. : University of Missouri-Columbia, 2005. http://hdl.handle.net/10355/4188.

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Thesis (Ph. D.)--University of Missouri-Columbia, 2005.<br>The entire dissertation/thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file (which also appears in the research.pdf); a non-technical general description, or public abstract, appears in the public.pdf file. Title from title screen of research.pdf file viewed on (July 17, 2006) Vita. Includes bibliographical references.

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10

Wakadkar, Sachin. "Analysis of transmembrane and globular protein depending on their solvent energy." Thesis, University of Skövde, School of Life Sciences, 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-2971.

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<p>The number of experimentally determined protein structures in the protein data bank (PDB) is continuously increasing. The common features like; cellular location, function, topology, primary structure, secondary structure, tertiary structure, domains or fold are used to classify them. Therefore, there are various methods available for classification of proteins. In this work we are attempting an additional method for making appropriate classification, i.e. solvent energy. Solvation is one of the most important properties of macromolecules and biological membranes by which they remain stabil

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11

Truvé, Katarina. "Using combined methods to reveal the dynamic organization of protein networks." Thesis, University of Skövde, School of Humanities and Informatics, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-962.

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<p>Proteins combine in various ways to execute different essential functions. Cellular processes are enormously complex and it is a great challenge to explain the underlying organization. Various methods have been applied in attempt to reveal the organization of the cell. Gene expression analysis uses the mRNA levels in the cell to predict which proteins are present in the cell simultaneously. This method is useful but also known to sometimes fail. Proteins that are known to be functionally related do not always show a significant correlation in gene expression. This fact might be explained by

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12

Chen, Huiling Zhou Huan Xiang Ferrone Frank A. "Prediction of protein structures and protein-protein interactions : a bioinformatics approach /." Philadelphia, Pa. : Drexel University, 2005. http://dspace.library.drexel.edu/handle/1860/481.

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13

Dean, M. K. "Bioinformatics approach to predicting protein interactions." Thesis, University of Essex, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.275862.

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14

Bresell, Anders. "Characterization of protein families, sequence patterns, and functional annotations in large data sets." Doctoral thesis, Linköping : Department of Physics, Chemistry and Biology, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-10565.

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15

Hon, Jiří. "Vyhledávání příbuzných proteinů s modifikovanou funkcí." Master's thesis, Vysoké učení technické v Brně. Fakulta informačních technologií, 2015. http://www.nusl.cz/ntk/nusl-234914.

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Protein engineering is a young dynamic discipline with great amount of potential practical applications. However, its success is primarily based on perfect knowledge and usage of all existing information about protein function and structure. To achieve that, protein engineering is supported by plenty of bioinformatic tools and analysis. The goal of this project is to create a new tool for protein engineering that would enable researchers to identificate related proteins with modified function in still growing biological databases. The tool is designed as an automated workflow of existing bioin

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16

Reddy, Joseph. "Identification and Analysis of Important Proteins in Protein Interaction Networks Using Functional and Topological Information." Thesis, University of Skövde, School of Life Sciences, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-2395.

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<p>Studying protein interaction networks using functional and topological information is important for understanding cellular organization and functionality. This study deals with identifying important proteins in protein interaction networks using SWEMODE (Lubovac, et al, 2006) and analyzing topological and functional properties of these proteins with the help of information derived from modular organization in protein interaction networks as well as information available in public resources, in this case, annotation sources describing the functionality of proteins. Multi-modular proteins are

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17

Gunnarsson, Ida. "Deriving Protein Networks by Combining Gene Expression and Protein Chip Analysis." Thesis, University of Skövde, Department of Computer Science, 2002. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-706.

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<p>In order to derive reliable protein networks it has recently been suggested that the combination of information from both gene and protein level is required. In this thesis a combination of gene expression and protein chip analysis was performed when constructing protein networks. Proteins with high affinity to the same substrates and encoded by genes with high correlation is here thought to constitute reliable protein networks. The protein networks derived are unfortunately not as reliable as were hoped for. According to the tests performed, the method derived in this thesis does not perfo

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18

Nyirongo, Vysaul Bwanamare. "Statistical approaches to protein matching in bioinformatics." Thesis, University of Leeds, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.431995.

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19

Adeyemi, Samson Adebowale. "Structural bioinformatics analysis of the Hsp40 and Hsp70 molecular chaperones from humans." Thesis, Rhodes University, 2014. http://hdl.handle.net/10962/d1020962.

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HSP70 is one of the most important families of molecular chaperone that regulate the folding and transport of client proteins in an ATP dependent manner. The ATPase activity of HSP70 is stimulated through an interaction with its family of HSP40 co-chaperones. There is evidence to suggest that specific partnerships occur between the different HSP40 and HSP70 isoforms. While some of the residues involved in the interaction are known, many of the residues governing the specificity of HSP40-HSP70 partnerships are not precisely defined. It is not currently possible to predict which HSP40 and HSP70

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20

Leonardi, Emanuela. "Bioinformatic Analysis of Protein Mutations." Doctoral thesis, Università degli studi di Padova, 2012. http://hdl.handle.net/11577/3426280.

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Many gene defects have been associated to genetic disorders, but the details of molecular mechanisms by which they contribute to the disease are often unclear. The study of mutation effects at the protein level can help elucidate the biological processes involved in the disease and the role of the protein in it. Bioinformatics can help to address this problem, being the connection between different disciplines including clinical, genetics, structural biology, and biochemistry. By using a computational approach I tackled the analysis of some examples of biomedical interesting proteins integrati

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21

Wallner, Björn. "Protein Structure Prediction : Model Building and Quality Assessment." Doctoral thesis, Stockholm University, Department of Biochemistry and Biophysics, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-649.

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<p>Proteins play a crucial roll in all biological processes. The wide range of protein functions is made possible through the many different conformations that the protein chain can adopt. The structure of a protein is extremely important for its function, but to determine the structure of protein experimentally is both difficult and time consuming. In fact with the current methods it is not possible to study all the billions of proteins in the world by experiments. Hence, for the vast majority of proteins the only way to get structural information is through the use of a method that predicts

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22

Callahan, Nicholas. "Bioinformatics-Driven Enzyme Engineering: Work On Adenylate Kinase." The Ohio State University, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=osu1420802270.

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23

Jüttemann, Thomas. "Adding 3D-structural context to protein-protein interaction data from high-throughput experiments." Thesis, University of Edinburgh, 2011. http://hdl.handle.net/1842/5666.

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In the past decade, automatisation has led to an immense increase of data in biology. Next generation sequencing techniques will produce a vast amount of sequences across all species in the coming years. In many cases, identifying the function and biological role of a protein from its sequence can be a complicated and time-intensive task. The identification of a protein's interaction partners is a tremendous help for understanding the biological context in which it is involved. In order to fully characterise a protein-protein interaction (PPIs), it is necessary to know the three-dimensional st

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24

Podowski, Raf M. "Applied bioinformatics for gene characterization /." Stockholm, 2006. http://diss.kib.ki.se/2006/91-7140-818-5/.

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25

Helgadóttir, Hanna Sigrún. "Using semantic similarity measures across Gene Ontology to predict protein-protein interactions." Thesis, University of Skövde, School of Humanities and Informatics, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-971.

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<p>Living cells are controlled by proteins and genes that interact through complex molecular pathways to achieve a specific function. Therefore, determination of protein-protein interaction is fundamental for the understanding of the cell’s lifecycle and functions. The function of a protein is also largely determined by its interactions with other proteins. The amount of protein-protein interaction data available has multiplied by the emergence of large-scale technologies for detecting them, but the drawback of such measures is the relatively high amount of noise present in the data. It is tim

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26

Viklund, Håkan. "Formalizing life : Towards an improved understanding of the sequence-structure relationship in alpha-helical transmembrane proteins." Doctoral thesis, Stockholm University, Department of Biochemistry and Biophysics, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-7144.

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<p>Genes coding for alpha-helical transmembrane proteins constitute roughly 25% of the total number of genes in a typical organism. As these proteins are vital parts of many biological processes, an improved understanding of them is important for achieving a better understanding of the mechanisms that constitute life.</p><p>All proteins consist of an amino acid sequence that fold into a three-dimensional structure in order to perform its biological function. The work presented in this thesis is directed towards improving the understanding of the relationship between sequence and structure for

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27

Kirac, Mustafa. "Pattern Oriented Methods for Inferring Protein Annotations within Protein Interaction Networks." Case Western Reserve University School of Graduate Studies / OhioLINK, 2009. http://rave.ohiolink.edu/etdc/view?acc_num=case1222368001.

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28

Lee, Semin. "Molecular characterization of protein-nucleic acid interfaces : applications in bioinformatics." Thesis, University of Cambridge, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.609284.

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29

Garma, L. D. (Leonardo D. ). "Structural bioinformatics tools for the comparison and classification of protein interactions." Doctoral thesis, Oulun yliopisto, 2017. http://urn.fi/urn:isbn:9789526216065.

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Abstract Most proteins carry out their functions through interactions with other molecules. Thus, proteins taking part in similar interactions are likely to carry out related functions. One way to determine whether two proteins do take part in similar interactions is by quantifying the likeness of their structures. This work focuses on the development of methods for the comparison of protein-protein and protein-ligand interactions, as well as their application to structure-based classification schemes. A method based on the MultiMer-align (or MM-align) program was developed and used to compare

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30

Nordström, Karl J. V. "Characterization and Evolution of Transmembrane Proteins with Focus on G-protein coupled receptors in Pre-vertebrate Species." Doctoral thesis, Uppsala universitet, Funktionell farmakologi, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-121696.

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G protein-coupled receptors (GPCRs) are one of the largest protein families in mammals. GPCRs are instrumental for hormonal and neurotransmitter signalling and are important in all major physiological systems of the body. Paper I describes the repertoire of GPCRs in Branchiostoma floridae, which is one of the species most closely related species to vertebrates. Mining and phylogenetic analysis of the amphioxus genome showed the presence of at least 664 distinct GPCRs distributed among all the main families of GPCRs; Glutamate (18), Rhodopsin (570), Adhesion (37), Frizzled (6) and Secretin (16)

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31

Gardini, Simone. "STRUCTURAL BIOINFORMATICS: A WINDOW TO OBSERVE THE PROTEIN UNIVERSE." Doctoral thesis, Università di Siena, 2018. http://hdl.handle.net/11365/1043622.

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Analyzing huge amounts of data that are stored in biologically relevant databases to find information to be translated into new general knowledge, is the essence of Bioinformatics. During my PhD training, have implemented Structural Bioinformatics procedures to derive information from the wealth of structural data that is publically available from the Protein Data Bank. From the thousands of experimentally derived structures where proteins are bound to other proteins, nucleic acids or small organic molecules, We found signals for interpreting the rationale underneath Nature’s assignment of cod

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32

Michel, Mirco. "From Sequence to Structure : Using predicted residue contacts to facilitate template-free protein structure prediction." Doctoral thesis, Stockholms universitet, Institutionen för biokemi och biofysik, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-141946.

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Despite the fundamental role of experimental protein structure determination, computational methods are of essential importance to bridge the ever growing gap between available protein sequence and structure data. Common structure prediction methods rely on experimental data, which is not available for about half of the known protein families. Recent advancements in amino acid contact prediction have revolutionized the field of protein structure prediction. Contacts can be used to guide template-free structure predictions that do not rely on experimentally solved structures of homologous prote

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33

Lin, Guang. "Protein fold recognition using neural networks." Thesis, Open University, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.273307.

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34

Söderquist, Fredrik. "Proteus : A new predictor for protean segments." Thesis, Linköpings universitet, Teknisk biologi, 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-121260.

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The discovery of intrinsically disordered proteins has led to a paradigm shift in protein science. Many disordered proteins have regions that can transform from a disordered state to an ordered. Those regions are called protean segments. Many intrinsically disordered proteins are involved in diseases, including Alzheimer's disease, Parkinson's disease and Down's syndrome, which makes them prime targets for medical research. As protean segments often are the functional part of the proteins, it is of great importance to identify those regions. This report presents Proteus, a new predictor for pr

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Habtemariam, Mesay. "Bioinformatics Approach to Probe Protein-Protein Interactions: Understanding the Role of Interfacial Solvent in the Binding Sites of Protein-Protein Complexes;Network Based Predictions and Analysis of Human Proteins that Play Critical Roles in HIV Pathogenesis." VCU Scholars Compass, 2013. http://scholarscompass.vcu.edu/etd/2997.

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The thesis work contains two projects under the same umbrella. The first project is to provide a detailed analysis on the behavior of interfacial water molecules at protein-protein complexes, in this case focusing on homodimeric complexes, and to investigate their effect with respect to different residue types. For that reason the homodimeric data-set, which includes high-resolution (≤ 2.30 Å) X-ray crystal structures of 252 (140 Biological & 112 Non-biological) protein complexes was chosen to explore fundamental differences between interfaces that Nature has “engineered” vs. compared to inter

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Vajdi, Hoojghan Amir. "Application of Graphical Models in Protein-Protein Interactions and Dynamics." Thesis, University of Massachusetts Boston, 2019. http://pqdtopen.proquest.com/#viewpdf?dispub=10982841.

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<p> Every organism contains a few hundred to thousands of proteins. A protein is made of a sequence of molecular building blocks named amino acids. Amino acids will be referred to as residues. Every protein performs one or more functions in the cell. In order for a protein to do its job, it requires to bind properly to other partner proteins. Many genetic diseases such as cancer are caused by mutations (changes) of specific residues which cause disturbances in the functions of those proteins. The problem of prediction of protein binding site is a crucial topic in computational biology. A prot

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Abreu, Marco A. "Prediction of Protein-Protein Interactions in Escherichia coli from Experimental Data in Treponema pallidum." VCU Scholars Compass, 2015. http://scholarscompass.vcu.edu/etd/3821.

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Protein – Protein interactions (PPIs) are thought to be conserved between species, although this has not been systematically investigated. This problem was explored in Escherichia coli from experimental data in Treponema pallidum by predicting PPIs, focusing on protein domains of little or unknown function. The comparison of T. pallidum to a model organism such as E. coli can not only reveal additional data about T. pallidum but also reveals how E. coli is similar to this distantly related, obligate parasite. A set of novel T. pallidum interactions, enriched for proteins of unknown function, w

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38

McDowall, Mark. "Human protein-protein interaction prediction." Thesis, University of Dundee, 2011. https://discovery.dundee.ac.uk/en/studentTheses/697e465a-edbd-41d2-acda-5910a49e4157.

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Protein-protein interactions are essential for the survival of all living cells, allowing for processes such as cell signalling, metabolism and cell division to occur. Yet in humans there are only >38k annotated interactions of an interactome estimated to range between 150k to 600k interactions and out of a potential 300M protein pairs.Experimental methods to define the human interactome generate high quality results, but are expensive and slow. Computational methods play an important role to fill the gap.To further this goal, the prediction of human protein-protein interactions was investi

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Repo, Susanna. "Structural bioinformatics in the study of protein function and evolution /." Turku, Finland : Dept. of Biochemistry and Pharmacy, Abo Akademi University, 2008. http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&doc_number=017048818&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA.

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Johansson, Joakim. "Modifying a Protein-Protein Interaction Identifier with a Topology and Sequence-Order Independent Structural Comparison Method." Thesis, Linköpings universitet, Bioinformatik, 2018. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-147777.

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Using computational methods to identify protein-protein interactions (PPIs) supports experimental techniques by using less time and less resources. Identifying PPIs can be made through a template-based approach that describes how unstudied proteins interact by aligning a common structural template that exists in both interacting proteins. A pipeline that uses this is InterPred, that combines homology modelling and massive template comparison to construct coarse interaction models. These models are reviewed by a machine learning classifier that classifies models that shows traits of being true,

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Song, Zhao Xu Dong. "Bioinformatics methods for protein identification using peptide mass fingerprinting data." Diss., Columbia, Mo. : University of Missouri--Columbia, 2009. http://hdl.handle.net/10355/6125.

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Title from PDF of title page (University of Missouri--Columbia, viewed on Feb 16, 2010). The entire thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file; a non-technical public abstract appears in the public.pdf file. Dissertation advisor: Dr. Dong Xu. Vita. Includes bibliographical references.

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Peterson, Mark Erik. "Evolutionary constraints on the structural similarity of proteins and applications to comparative protein structure modeling." Diss., Search in ProQuest Dissertations & Theses. UC Only, 2008. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3339202.

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Chapman, Samuel D. "Applying Evolutionary Computation and Ensemble Approaches to Protein Contact Map and Protein Function Determination." Thesis, North Carolina Agricultural and Technical State University, 2017. http://pqdtopen.proquest.com/#viewpdf?dispub=10191042.

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<p> Proteins are important biological molecules that perform many different functions in an organism. They are composed of sequences of amino acids that play a large part in determining both their structure and function. In turn, the structures of proteins are related to their functions. Using computational methods for protein study is a popular approach, offering the possibility of being faster and cheaper than experimental methods. These software-based methods are able to take information such as the protein sequence and other empirical data and output predictions such as protein structure o

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Hetti, Arachchilage Madara Dilhani. "Coevolution of epitopes in HIV-1 pre-integration complex proteins: protein-protein interaction insights." Kent State University / OhioLINK, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=kent1530646538935895.

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Johansson-Åkhe, Isak. "PePIP : a Pipeline for Peptide-Protein Interaction-site Prediction." Thesis, Linköpings universitet, Institutionen för fysik, kemi och biologi, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-138411.

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Protein-peptide interactions play a major role in several biological processes, such as cellproliferation and cancer cell life-cycles. Accurate computational methods for predictingprotein-protein interactions exist, but few of these method can be extended to predictinginteractions between a protein and a particularly small or intrinsically disordered peptide. In this thesis, PePIP is presented. PePIP is a pipeline for predicting where on a given proteina given peptide will most probably bind. The pipeline utilizes structural aligning to perusethe Protein Data Bank for possible templates for th

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Hedin, Linnea E., Kristoffer Illergård, and Arne Elofsson. "An Introduction to Membrane Proteins." Stockholms universitet, Institutionen för biokemi och biofysik, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-69241.

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alpha-Helical membrane proteins are important for many biological functions. Due to physicochemical constraints, the structures of membrane proteins differ from the structure of soluble proteins. Historically, membrane protein structures were assumed to be more or less two-dimensional, consisting of long, straight, membrane-spanning parallel helices packed against each other. However, during the past decade, a number of the new membrane protein structures cast doubt on this notion. Today, it is evident that the structures of many membrane proteins are equally complex as for many soluble protei

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Genheden, Samuel. "A fast protein-ligand docking method." Thesis, University of Skövde, School of Humanities and Informatics, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-69.

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<p>In this dissertation a novel approach to protein-ligand docking is presented. First an existing method to predict putative active sites is employed. These predictions are then used to cut down the search space of an algorithm that uses the fast Fourier transform to calculate the geometrical and electrostatic complementarity between a protein and a small organic ligand. A simplified hydrophobicity score is also calculated for each active site. The docking method could be applied either to dock ligands in a known active site or to rank several putative active sites according to their biologic

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48

Liu, Yichuan Tozeren Aydin. "Functional signatures in protein-protein interactions and their impact on signaling pathways /." Philadelphia, Pa. : Drexel University, 2010. http://hdl.handle.net/1860/3257.

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49

Choi, Yoonjoo. "Protein loop structure prediction." Thesis, University of Oxford, 2011. http://ora.ox.ac.uk/objects/uuid:bd5c1b9b-89ba-4225-bc17-85d3f5067e58.

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This dissertation concerns the study and prediction of loops in protein structures. Proteins perform crucial functions in living organisms. Despite their importance, we are currently unable to predict their three dimensional structure accurately. Loops are segments that connect regular secondary structures of proteins. They tend to be located on the surface of proteins and often interact with other biological agents. As loops are generally subject to more frequent mutations than the rest of the protein, their sequences and structural conformations can vary significantly even within the same pr

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50

Kemmer, Danielle. "Genomics and bioinformatics approaches to functional gene annotation /." Stockholm, 2006. http://diss.kib.ki.se/2006/91-7140-636-0/.

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