Relevant bibliographies by topics / Proteins Bioinformatics. Computational biology / Dissertations / Theses
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Dissertations / Theses on the topic 'Proteins Bioinformatics. Computational biology'

Author: Grafiati
Published: 4 June 2021
Last updated: 8 February 2022

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1

Muhammad, Ashfaq. "Design and Development of a Database for the Classification of Corynebacterium glutamicum Genes, Proteins, Mutants and Experimental Protocols." Thesis, University of Skövde, School of Humanities and Informatics, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-23.

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<p>Coryneform bacteria are largely distributed in nature and are rod like, aerobic soil bacteria capable of growing on a variety of sugars and organic acids. Corynebacterium glutamicum is a nonpathogenic species of Coryneform bacteria used for industrial production of amino acids. There are three main publicly available genome annotations, Cg, Cgl and NCgl for C. glutamicum. All these three annotations have different numbers of protein coding genes and varying numbers of overlaps of similar genes. The original data is only available in text files. In this format of genome data, it was not easy
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2

Siu, Wing-yan. "Multiple structural alignment for proteins." Click to view the E-thesis via HKUTO, 2008. http://sunzi.lib.hku.hk/hkuto/record/B4068748X.

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3

Siu, Wing-yan, and 蕭穎欣. "Multiple structural alignment for proteins." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2008. http://hub.hku.hk/bib/B4068748X.

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4

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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5

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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6

Yao, Jianchao, and 姚劍超. "Predicting the 3D structure of human aquaporin-0 protein in eye lens using computational tools." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2003. http://hub.hku.hk/bib/B2948540X.

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7

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

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8

Bahena, Silvia. "Computational Methods for the structural and dynamical understanding of GPCR-RAMP interactions." Thesis, Uppsala universitet, Institutionen för biologisk grundutbildning, 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-416790.

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Protein-protein interaction dominates all major biology processes in living cells. Recent studies suggestthat the surface expression and activity of G protein-coupled receptors (GPCRs), which are the largestfamily of receptors in human cells, can be modulated by receptor activity–modifying proteins (RAMPs). Computational tools are essential to complement experimental approaches for the understanding ofmolecular activity of living cells and molecular dynamics simulations are well suited to providemolecular details of proteins function and structure. The classical atom-level molecular modeling o
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9

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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10

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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11

Wilman, Henry R. "Computational studies of protein helix kinks." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:21225f0e-efed-49c6-af27-5d3fe78fa731.

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Kinks are functionally important structural features found in the alpha-helices of many proteins, particularly membrane proteins. Structurally, they are points at which a helix abruptly changes direction. Previous kink definition and identification methods often disagree with one another. Here I describe three novel methods to characterise kinks, which improve on existing approaches. First, Kink Finder, a computational method that consistently locates kinks and estimates the error in the kink angle. Second the B statistic, a statistically robust method for identifying kinks. Third, Alpha Helic
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12

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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13

Adhikari, Sombudha. "IDENTIFICATION OF PROTEIN PARTNERS FOR NIBP, A NOVEL NIK-AND IKKB-BINDING PROTEIN THROUGH EXPERIMENTAL, COMPUTATIONAL AND BIOINFORMATICS TECHNIQUES." Master's thesis, Temple University Libraries, 2013. http://cdm16002.contentdm.oclc.org/cdm/ref/collection/p245801coll10/id/216569.

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Bioengineering<br>M.S.<br>NIBP is a prototype member of a novel protein family. It forms a novel subcomplex of NIK-NIBP-IKKB and enhances cytokine-induced IKKB-mediated NFKB activation. It is also named TRAPPC9 as a key member of trafficking particle protein (TRAPP) complex II, which is essential in trans-Golgi networking (TGN). The signaling pathways and molecular mechanisms for NIBP actions remain largely unknown. The aim of this research is to identify potential proteins interacting with NIBP, resulting in the regulation of NFKB signaling pathways and other unknown signaling pathways. At th
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14

Gomes, Mireille. "Role of mutual information for predicting contact residues in proteins." Thesis, University of Oxford, 2012. http://ora.ox.ac.uk/objects/uuid:5ec3c90c-73fb-494f-ad2e-efc718406aa4.

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Mutual Information (MI) based methods are used to predict contact residues within proteins and between interacting proteins. There have been many high impact papers citing the successful use of MI for determining contact residues in a particular protein of interest, or in certain types of proteins, such as homotrimers. In this dissertation we have carried out a systematic study to assess if this popularly employed contact prediction tool is useful on a global scale. After testing original MI and leading MI based methods on large, cross-species datasets we found that in general the performance
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15

Golumbeanu, Monica. "Statistical Analysis of PAR-CLIP data." Thesis, KTH, Beräkningsbiologi, CB, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-124347.

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From creation to its degradation, the RNA molecule is the action field of many binding proteins with different roles in regulation and RNA metabolism. Since these proteins are involved in a large number of processes, a variety of diseases are related to abnormalities occurring within the binding mechanisms. One of the experimental methods for detecting the binding sites of these proteins is PAR-CLIP built on the next generation sequencing technology. Due to its size and intrinsic noise, PAR-CLIP data analysis requires appropriate pre-processing and thorough statistical analysis. The present wo
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Oliveira, Saulo Henrique Pires de. "Desenvolvimento de um algoritmo para identificação e caracterização de cavidades em regiões específicas de estruturas tridimensionais de proteínas." Universidade de São Paulo, 2011. http://www.teses.usp.br/teses/disponiveis/95/95131/tde-14072011-052430/.

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A identificação e caracterização geométrica e físico-química de espaços vazios na estrutura tridimensional de proteínas é capaz de agregar informações importantes para guiar o desenho racional de drogas e a caracterização funcional de sítios de ligação e sítios catalíticos. Dessa forma, algumas ferramentas computacionais foram desenvolvidas nas últimas duas décadas, visando efetuar essas caracterizações. Contudo, as ferramentas existentes lidam com uma série de limitações, dais quais merecem destaque a falta de precisão, falta de capacidade de integração em protocolos de larga escala, falta d
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17

Sweeney, Deacon John. "A Computational Tool for Biomolecular Structure Analysis Based On Chemical and Enzymatic Modification of Native Proteins." Wright State University / OhioLINK, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=wright1316440232.

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18

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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19

Siu, Man-hung. "Finding motif pairs from protein interaction networks." Click to view the E-thesis via HKUTO, 2008. http://sunzi.lib.hku.hk/hkuto/record/B40987760.

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20

Lang, Tiange. "Evolution of transmembrane and gel-forming mucins studied with bioinformatic methods /." Göteborg : The Sahlgrenska Academy at Göteborg University, Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, 2007. http://hdl.handle.net/2077/7502.

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21

Dunbar, James. "Variable domain orientations in antigen receptors." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:30c18b4d-18a2-4f0d-895f-35cc24880955.

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Specific recognition of pathogenic molecules by the immune system is mediated by proteins known as antigen receptors. One such component is the antibody. Binding properties of natural and engineered antibodies can be understood by studying the structure of their variable domains, VH and VL. In this thesis we investigate how the two variable domains orientate with respect to one another and therefore influence the geometry of the antigen binding site which is formed between them. We describe a method which fully characterises the VH-VL orientation in a consistent and absolute sense using five a
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22

Olsson, Elin. "Deriving Genetic Networks Using Text Mining." Thesis, University of Skövde, Department of Computer Science, 2002. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-708.

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<p>On the Internet an enormous amount of information is available that is represented in an unstructured form. The purpose with a text mining tool is to collect this information and present it in a more structured form. In this report text mining is used to create an algorithm that searches abstracts available from PubMed and finds specific relationships between genes that can be used to create a network. The algorithm can also be used to find information about a specific gene. The network created by Mendoza et al. (1999) was verified in all the connections but one using the algorithm. This co
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23

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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Borrman, Tyler M. "Measuring Stability of 3D Chromatin Conformations and Identifying Neuron Specific Chromatin Loops Associated with Schizophrenia Risk." eScholarship@UMMS, 2020. https://escholarship.umassmed.edu/gsbs_diss/1111.

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The 23 pairs of chromosomes comprising the human genome are intricately folded within the nucleus of each cell in a manner that promotes efficient gene regulation and cell function. Consequently, active gene rich regions are compartmentally segregated from inactive gene poor regions of the genome. To better understand the mechanisms driving compartmentalization we investigated what would occur if this system was disrupted. By digesting the genome to varying sizes and analyzing the fragmented 3D structure over time, our work revealed essential laws governing nuclear compartmentalization. At a f
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Siu, Man-hung, and 蕭文鴻. "Finding motif pairs from protein interaction networks." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2008. http://hub.hku.hk/bib/B40987760.

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26

Brown, Andrew S. "Identification of a phospho-hnRNP E1 Nucleic Acid Consensus Sequence Mediating Epithelial to Mesenchymal Transition." Kent State University / OhioLINK, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=kent1437943957.

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27

Lind, Christoffer. "Computational Studies of Protein Synthesis on the Ribosome and Ligand Binding to Riboswitches." Doctoral thesis, Uppsala universitet, Beräkningsbiologi och bioinformatik, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-328583.

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The ribosome is a macromolecular machine that produces proteins in all kingdoms of life. The proteins, in turn, control the biochemical processes within the cell. It is thus of extreme importance that the machine that makes the proteins works with high precision. By using three dimensional structures of the ribosome and homology modelling, we have applied molecular dynamics simulations and free-energy calculations to study the codon specificity of protein synthesis in initiation and termination on an atomistic level. In addition, we have examined the binding of small molecules to riboswitches,
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Ramraj, Varun. "Exploiting whole-PDB analysis in novel bioinformatics applications." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:6c59c813-2a4c-440c-940b-d334c02dd075.

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The Protein Data Bank (PDB) is the definitive electronic repository for experimentally-derived protein structures, composed mainly of those determined by X-ray crystallography. Approximately 200 new structures are added weekly to the PDB, and at the time of writing, it contains approximately 97,000 structures. This represents an expanding wealth of high-quality information but there seem to be few bioinformatics tools that consider and analyse these data as an ensemble. This thesis explores the development of three efficient, fast algorithms and software implementations to study protein struct
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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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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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Dahl, Anna Caroline E. "Membrane protein mechanotransduction : computational studies and analytics development." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:67798647-8ed5-46e0-bde9-c71235fe70ba.

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Membrane protein mechanotransduction is the altered function of an integral membrane protein in response to mechanical force. Such mechanosensors are found in all kingdoms of life, and increasing numbers of membrane proteins have been found to exhibit mechanosensitivity. How they mechanotransduce is an active research area and the topic of this thesis. The methodology employed is classical molecular dynamics (MD) simulations. MD systems are complex, and two programs were developed to reduce this apparent complexity in terms of both visual abstraction and statistical analysis. Bendix detects an
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32

Nordesjö, Olle. "Searching for novel protein-protein specificities using a combined approach of sequence co-evolution and local structural equilibration." Thesis, Uppsala universitet, Institutionen för biologisk grundutbildning, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-275040.

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Greater understanding of how we can use protein simulations and statistical characteristics of biomolecular interfaces as proxies for biological function will make manifest major advances in protein engineering. Here we show how to use calculated change in binding affinity and coevolutionary scores to predict the functional effect of mutations in the interface between a Histidine Kinase and a Response Regulator. These proteins participate in the Two-Component Regulatory system, a system for intracellular signalling found in bacteria. We find that both scores work as proxies for functional muta
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Abeln, Sanne. "Protein fold evolution on completed genomes : distinguishing between young and old folds." Thesis, University of Oxford, 2007. http://ora.ox.ac.uk/objects/uuid:b520fd65-e829-4ae0-bed6-47d642909889.

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We review fold usage on completed genomes in order to explore protein structure evolution and assess the evolutionary relevance of current structural classification systems (SCOP and CATH). We assign folds on a set of 150 completed genomes using fold recognition methods (PSI-BLAST, SUPERFAMILY and Gene3D). The patterns of presence or absence of folds on genomes gives us insights into the relationships between folds and how we have arrived at the set of folds we see today. In particular, we develop a technique to estimate the relative ages of a protein fold based on genomic occurrence patterns
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Herman, Stephanie. "Automatic detection of protein degradation markers in mass spectrometry imaging." Thesis, Uppsala universitet, Institutionen för biologisk grundutbildning, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-275072.

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Today we are collecting a large amount of tissue samples to store for future studies of different health conditions, in hopes that the focus in health care will shift from treatments to early detection and prevention, by the use of biomarkers. To make sure that the storing of tissue is done in a reliable way, where the molecular profile of the samples are preserved, we first need to characterise how these changes occur. In this thesis, data from mice brains were collected using MALDI imaging mass spectrometry (IMS) and an analysis pipeline for robust MALDI IMS data handling and evaluation was
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Kumar, Vivek. "Computational Prediction of Protein-Protein Interactions on the Proteomic Scale Using Bayesian Ensemble of Multiple Feature Databases." University of Akron / OhioLINK, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=akron1322489637.

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Bampalikis, Dimitrios. "Recognizing biological and technical differences in scRNAseq : A comparison of two protocols." Thesis, Uppsala universitet, Institutionen för biologisk grundutbildning, 2018. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-366169.

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Recent advances in sequencing technology have given access to information extracted on a single cell level. Single cell RNA sequencing enables for transcriptomes to be sequenced, allowing for studies within and between cell types. A recently developed protocol, based on Smart-seq2, and the Proximity ligation essay, allows for the detection of protein data from single cells, in parallel with RNA. The combination of the transcriptomic and proteomic data will enhance researchers’ ability to explore cell states. In this study, we are comparing a new pulldown protocol with the widely-used Smart-seq
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Engström, Mathias, and Erik Olby. "Evaluating Response Images From Protein Quantification." Thesis, Uppsala universitet, Institutionen för biologisk grundutbildning, 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-416108.

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Gyros Protein Technologies develops instruments for automated immunoassays. Fluorescent antibodies are added to samples and excited with a laser. This results in a 16-bit image where the intensity is correlated to concentration of bound antibody. Artefacts may appear on the images due to dust, fibers or other problems, which affect the quantification. This project seeks to automatically detect such artifacts by classifying the images as good or bad using Deep Convolutional Neural Networks (DCNNs). To augment the dataset a simulation approach is used and a simulation program is developed that g
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Galiez, Clovis. "Fragments structuraux : comparaison, prédictibilité à partir de la séquence et application à l'identification de protéines de virus." Thesis, Rennes 1, 2015. http://www.theses.fr/2015REN1S124/document.

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Cette thèse propose de nouveaux outils pour la caractérisation locale de familles de protéines au niveau de la séquence et de la structure. Nous introduisons les fragments en contact (CF) comme des portions de structure conciliant localité spatiale et voisinage séquentiel. Nous montrons qu'ils bénéficient d'une meilleure prédictibilité de structure depuis la séquence que des fragments contigus ou encore que des paires de fragments qui ne seraient pas en contact en structure. Pour comparer structuralement ces CF, nous introduisons l'ASD, une nouvelle mesure de similarité ne nécessitant pas d'al
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Wang, Wei. "Unveiling Molecular Mechanisms of piRNA Pathway from Small Signals in Big Data: A Dissertation." eScholarship@UMMS, 2010. http://escholarship.umassmed.edu/gsbs_diss/805.

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PIWI-interacting RNAs (piRNA) are a group of 23–35 nucleotide (nt) short RNAs that protect animal gonads from transposon activities. In Drosophila germ line, piRNAs can be categorized into two different categories— primary and secondary piRNAs— based on their origins. Primary piRNAs, generated from transcripts of specific genomic regions called piRNA clusters, which are enriched in transposon fragments that are unlikely to retain transposition activity. The transcription and maturation of primary piRNAs from those cluster transcripts are poorly understood. After being produced, a group of prim
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Wang, Wei. "Unveiling Molecular Mechanisms of piRNA Pathway from Small Signals in Big Data: A Dissertation." eScholarship@UMMS, 2015. https://escholarship.umassmed.edu/gsbs_diss/805.

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PIWI-interacting RNAs (piRNA) are a group of 23–35 nucleotide (nt) short RNAs that protect animal gonads from transposon activities. In Drosophila germ line, piRNAs can be categorized into two different categories— primary and secondary piRNAs— based on their origins. Primary piRNAs, generated from transcripts of specific genomic regions called piRNA clusters, which are enriched in transposon fragments that are unlikely to retain transposition activity. The transcription and maturation of primary piRNAs from those cluster transcripts are poorly understood. After being produced, a group of prim
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Mishra, Avdesh. "Three-Dimensional Ideal Gas Reference State based Energy Function." ScholarWorks@UNO, 2015. http://scholarworks.uno.edu/td/1986.

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Energy functions are found to be a key of protein structure prediction. In this work, we propose a novel 3-dimensional energy function based on hydrophobic-hydrophilic properties of amino acid where we consider at least three different possible interaction of amino acid in a 3-dimensional sphere categorized as hydrophilic versus hydrophilic, hydrophobic versus hydrophobic and hydrophobic versus hydrophilic. Each of these interactions are governed by a 3-dimensional parameter alpha used to model the interaction and 3-dimensional parameter beta used to model weight of contribution. We use Geneti
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Mishra, Avdesh. "Effective Statistical Energy Function Based Protein Un/Structure Prediction." ScholarWorks@UNO, 2019. https://scholarworks.uno.edu/td/2674.

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Proteins are an important component of living organisms, composed of one or more polypeptide chains, each containing hundreds or even thousands of amino acids of 20 standard types. The structure of a protein from the sequence determines crucial functions of proteins such as initiating metabolic reactions, DNA replication, cell signaling, and transporting molecules. In the past, proteins were considered to always have a well-defined stable shape (structured proteins), however, it has recently been shown that there exist intrinsically disordered proteins (IDPs), which lack a fixed or ordered 3D
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43

Kallberg, Yvonne. "Bioinformatic methods in protein characterization /." Stockholm, 2002. http://diss.kib.ki.se/2002/91-7349-370-8/.

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44

Chegancas, Rito Tiago Miguel. "Modelling and comparing protein interaction networks using subgraph counts." Thesis, University of Oxford, 2012. http://ora.ox.ac.uk/objects/uuid:dcc0eb0d-1dd8-428d-b2ec-447a806d6aa8.

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The astonishing progress of molecular biology, engineering and computer science has resulted in mature technologies capable of examining multiple cellular components at a genome-wide scale. Protein-protein interactions are one example of such growing data. These data are often organised as networks with proteins as nodes and interactions as edges. Albeit still incomplete, there is now a substantial amount of data available and there is a need for biologically meaningful methods to analyse and interpret these interactions. In this thesis we focus on how to compare protein interaction networks (
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Iqbal, Sumaiya. "Machine Learning based Protein Sequence to (un)Structure Mapping and Interaction Prediction." ScholarWorks@UNO, 2017. http://scholarworks.uno.edu/td/2379.

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Proteins are the fundamental macromolecules within a cell that carry out most of the biological functions. The computational study of protein structure and its functions, using machine learning and data analytics, is elemental in advancing the life-science research due to the fast-growing biological data and the extensive complexities involved in their analyses towards discovering meaningful insights. Mapping of protein’s primary sequence is not only limited to its structure, we extend that to its disordered component known as Intrinsically Disordered Proteins or Regions in proteins (IDPs/IDRs
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46

Schmidtke, Peter. "Protein-ligand binding sites. Identification, characterization and interrelations." Doctoral thesis, Universitat de Barcelona, 2011. http://hdl.handle.net/10803/51340.

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El trabajo presentado en esta tesis cubre varios campos de investigación relacionados con el desarrollo de moléculas bioactivas. Se compone de cinco partes distintas que se resumen aquí. Predicción de la utilidad farmacológica de dianas terapéuticas. El desarrollo de fármacos está generalmente dirigido a inhibir la función de una proteína específica. Pero para validar esta proteína como diana terapéutica, al principio de un proyecto de descubrimiento de fármacos se tiene que saber si una molécula de tipo fármaco puede unirse con suficiente afinidad a la proteína como para alterar su func
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Dong, Shuyun. "Transcript-Specific Cytoplasmic Degradation of YRA1 Pre-mRNA Mediated by the Yeast EDC3 Protein: A Dissertation." eScholarship@UMMS, 2007. https://escholarship.umassmed.edu/gsbs_diss/352.

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mRNA degradation is a fundamental process that controls both the level and the fidelity of gene expression. Using a combination of bioinformatic, genomic, genetic, and molecular biology approaches, we have shown that Edc3p, a yeast mRNA decay factor, controls the stability of the intron-containing YRA1 pre-mRNA. We found that Edc3p-mediated degradation of YRA1 pre-mRNA: 1) is a component of a negative feedback loop involved in the autoregulation of YRA1, 2) takes place in the cytoplasm, 3) is independent of translation, 4) occurs through a deadenylation-independent decapping and 5΄ to 3΄ exonu
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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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Verma, Rajni [Verfasser]. "Development and Application of Novel Bioinformatics and Computational Modeling Tools for Protein Engineering Advanced Computational Tools for Protein Engineering / Rajni Verma." Bremen : IRC-Library, Information Resource Center der Jacobs University Bremen, 2013. http://d-nb.info/103526966X/34.

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Oikonomopoulos, Spyridon. "Inferring structural properties of protein-DNA binding using high-throughput sequencing : the paradigm of GATA1, KLF1 and their complexes GATA1/FOG1 and GATA1/KLF1 : insights into the transcriptional regulation of the erythroid cell lineage." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:72b92906-4ef6-4c1d-9155-484521027e2e.

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GATA1 and KLF1 are transcription factors that regulate genes which are important for the development of erythroid cells. The GATA1 transcriptional co-factor FOG1 has been shown to be essential in a wide range of GATA1 dependent cellular functions. Here we tried to understand the diverse mechanisms by which GATA1 and KLF1 recognize their binding sites, how the GATA1 recognition mechanisms are affected by complexation with either FOG1 or KLF1 and how the GATA1 recognition mechanisms affect the transcriptional regulation of the erythroid differentiation. We profiled the DNA binding specificities/
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