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Dissertations / Theses on the topic 'Prediction of binding affinity'

Author: Grafiati

Published: 6 September 2023

Last updated: 31 July 2025

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1

Jovanovic, Srdan. "Rapid, precise and reproducible binding affinity prediction : applications in drug discovery." Thesis, University College London (University of London), 2018. http://discovery.ucl.ac.uk/10053853/.

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As we move towards an era of personalised medicine, the identification of lead compounds requires years of research and considerable financial backing, in the development of targeted therapies for cancer. We use molecular modelling and simulation to screen a library of active compounds, and understand the ligand-protein interaction at the molecular level in appropriate protein targets, in a bid to identify the most active lead drug candidates. In recent times, good progress has been made in accurately predicting binding affinities for drug candidates. Advances in high-performance computation (

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2

Uslan, Volkan. "Support vector machine-based fuzzy systems for quantitative prediction of peptide binding affinity." Thesis, De Montfort University, 2015. http://hdl.handle.net/2086/11170.

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Reliable prediction of binding affinity of peptides is one of the most challenging but important complex modelling problems in the post-genome era due to the diversity and functionality of the peptides discovered. Generally, peptide binding prediction models are commonly used to find out whether a binding exists between a certain peptide(s) and a major histocompatibility complex (MHC) molecule(s). Recent research efforts have been focused on quantifying the binding predictions. The objective of this thesis is to develop reliable real-value predictive models through the use of fuzzy systems. A

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3

Bodnarchuk, Michael. "Predicting the location and binding affinity of small molecules in protein binding sites." Thesis, University of Southampton, 2012. https://eprints.soton.ac.uk/348170/.

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In this thesis, various methods for locating and scoring the binding affinity of water molecules and molecular fragments in protein binding sites are described. The primary aim of this work is to understand how different methodologies compare to one another and how, by carefully choosing the correct method, they can be used to extract information on how small molecules interact with proteins. Three different methods are used to predict the location and affinity of water molecules; Just Add Water Molecules (JAWS), Grand Canonical Monte Carlo (GCMC) and double-decoupling. By applying the methods

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4

Erdas, Ozlem. "Modelling And Predicting Binding Affinity Of Pcp-like Compounds Using Machine Learning Methods." Master's thesis, METU, 2007. http://etd.lib.metu.edu.tr/upload/3/12608792/index.pdf.

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Machine learning methods have been promising tools in science and engineering fields. The use of these methods in chemistry and drug design has advanced after 1990s. In this study, molecular electrostatic potential (MEP) surfaces of PCP-like compounds are modelled and visualized in order to extract features which will be used in predicting binding affinity. In modelling, Cartesian coordinates of MEP surface points are mapped onto a spherical self-organizing map. Resulting maps are visualized by using values of electrostatic potential. These values also provide features for prediction system. S

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5

Guedes, Isabella Alvim. "Development of empirical scoring funcions forn predicting proteinligand binding affinity." Laboratório Nacional de Computação Científica, 2016. https://tede.lncc.br/handle/tede/247.

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Submitted by Maria Cristina (library@lncc.br) on 2017-04-12T19:05:59Z No. of bitstreams: 1 tese_isabella_vfinal.pdf: 6145955 bytes, checksum: e3ed369e970ad7eb06b79a77ef921a9b (MD5)<br>Approved for entry into archive by Maria Cristina (library@lncc.br) on 2017-04-12T19:06:11Z (GMT) No. of bitstreams: 1 tese_isabella_vfinal.pdf: 6145955 bytes, checksum: e3ed369e970ad7eb06b79a77ef921a9b (MD5)<br>Made available in DSpace on 2017-04-12T19:06:22Z (GMT). No. of bitstreams: 1 tese_isabella_vfinal.pdf: 6145955 bytes, checksum: e3ed369e970ad7eb06b79a77ef921a9b (MD5) Previous issue date: 2016-07-2

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6

Matereke, Lavious Tapiwa. "Analysis of predictive power of binding affinity of PBM-derived sequences." Thesis, Rhodes University, 2015. http://hdl.handle.net/10962/d1018666.

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A transcription factor (TF) is a protein that binds to specific DNA sequences as part of the initiation stage of transcription. Various methods of finding these transcription factor binding sites (TFBS) have been developed. In vivo technologies analyze DNA binding regions known to have bound to a TF in a living cell. Most widely used in vivo methods at the moment are chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) and DNase I hypersensitive sites sequencing. In vitro methods derive TFBS based on experiments with TFs and DNA usually in artificial settings or computationally

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7

Yoldas, Mine. "Predicting The Effect Of Hydrophobicity Surface On Binding Affinity Of Pcp-like Compounds Using Machine Learning Methods." Master's thesis, METU, 2011. http://etd.lib.metu.edu.tr/upload/12613215/index.pdf.

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This study aims to predict the binding affinity of the PCP-like compounds by means of molecular hydrophobicity. Molecular hydrophobicity is an important property which affects the binding affinity of molecules. The values of molecular hydrophobicity of molecules are obtained on three-dimensional coordinate system. Our aim is to reduce the number of points on the hydrophobicity surface of the molecules. This is modeled by using self organizing maps (SOM) and k-means clustering. The feature sets obtained from SOM and k-means clustering are used in order to predict binding affinity of molecules i

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8

Shoemake, Claire. "The use of static and dynamic models for the prediction of ligand binding affinity using oestrogen and androgen nuclear receptors as case studies." Thesis, University of Nottingham, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.478985.

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9

Atkovska, Kalina, Sergey A. Samsonov, Maciej Paszkowski-Rogacz, and M. Teresa Pisabarro. "Multipose Binding in Molecular Docking." Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2014. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-147177.

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Molecular docking has been extensively applied in virtual screening of small molecule libraries for lead identification and optimization. A necessary prerequisite for successful differentiation between active and non-active ligands is the accurate prediction of their binding affinities in the complex by use of docking scoring functions. However, many studies have shown rather poor correlations between docking scores and experimental binding affinities. Our work aimed to improve this correlation by implementing a multipose binding concept in the docking scoring scheme. Multipose binding, i.e.,

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10

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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11

Praig, Vera Gertraud. "Immobilised glutathione for affinity binding." Thesis, University of Cambridge, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.620379.

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12

Kuzmich, Oleksandra. "Metal Labeling for Low Affinity Binding Biomolecules." Doctoral thesis, Humboldt-Universität zu Berlin, 2018. http://dx.doi.org/10.18452/18862.

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Unter den Techniken der chemischen Proteomik hat Capture Compound – Massenspektrometrie (CCMS) den Vorteil, Interaktionen von Molekülen mit geringer Affinität zueinander effektiv untersuchen zu können. CCMS beruht auf kleinen molekularen Sonden (Capture Compounds, CCs), die aus drei funktionalen Bestandteilen bestehen: die Selektivitätsfunktion, ist ein kleines Molekül, das mit einem Zielprotein eine schwache Wechselwirkung eingeht. Die zweite Funktionalität erlaubt kovalente Anhaftung der molekularen Sonde an Proteine. Der dritte Anteil erlaubt Detektion mit sehr guten Sensitivität; allerding

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13

Mayes, Andrew Geoffrey. "Quantitative aspects of affinity adsorption." Thesis, University of Bath, 1992. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.303403.

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14

Lang, Birthe Agnetha. "Nanofibrous affinity membranes containing non-antibody binding proteins." Thesis, University of Leeds, 2016. http://etheses.whiterose.ac.uk/15326/.

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The specific removal of molecules from various media is an area receiving increasing attention. Affnity membranes, i.e. membranes containing ligands, which can specifically capture target molecules, can meet this demand. One important area, in which the use of affinity membranes will be beneficial, is blood filtration, specifically haemodialysis treatments. The specific removal of toxins can reduce treatment time and/or frequency and therefore increase patients' quality of life as well as reduce costs for the health care sector. The presented research investigates the feasibility of combining

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15

Reiersen, Herald. "Development of methods for modulating binding protein affinity." Thesis, University of Bath, 2000. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.323721.

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16

Eletr, Ziad Moustafa Kuhlman Brian A. "Determining and modulating E2-HECT binding affinity and specificity." Chapel Hill, N.C. : University of North Carolina at Chapel Hill, 2007. http://dc.lib.unc.edu/u?/etd,1365.

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Thesis (Ph. D.)--University of North Carolina at Chapel Hill, 2007.<br>Title from electronic title page (viewed Apr. 25, 2008). "... in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Biochemistry and Biophysics Program in Molecular and Cellular Biophysics." Discipline: Biochemistry and Biophysics; Department/School: Medicine.

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17

Donoghue, Gavin. "Structure and binding affinity in DNA minor groove binders." Thesis, University of Strathclyde, 2010. http://oleg.lib.strath.ac.uk:80/R/?func=dbin-jump-full&object_id=12768.

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18

Lawden, Kim Hilary. "The design and synthesis of endotoxin-binding affinity ligands." Thesis, University of Cambridge, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.627354.

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19

Lee, Hui-Chih 1963. "Theoretical and experimental studies of the plasma protein binding of high affinity binding drugs." Thesis, The University of Arizona, 1991. http://hdl.handle.net/10150/277955.

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A disadvantage of traditional equilibrium dialysis for highly protein bound drugs is the analytically low drug concentration found on the buffer side. We propose to replace a certain percentage of buffer with plasma containing drug in order to increase the total drug concentration on the buffer side. Computer simulations were performed to examine the effects of the percentage of plasma replacement of the buffer upon the increase of the total drug concentration on the buffer side after equilibrium dialysis. Further simulation results indicated that the development of a concise equation estimati

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20

Pokhrel, Pujan. "Prediction of DNA-Binding Proteins and their Binding Sites." ScholarWorks@UNO, 2018. https://scholarworks.uno.edu/honors_theses/114.

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DNA-binding proteins play an important role in various essential biological processes such as DNA replication, recombination, repair, gene transcription, and expression. The identification of DNA-binding proteins and the residues involved in the contacts is important for understanding the DNA-binding mechanism in proteins. Moreover, it has been reported in the literature that the mutations of some DNA-binding residues on proteins are associated with some diseases. The identification of these proteins and their binding mechanism generally require experimental techniques, which makes large scale

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21

Sundaramoorthy, Meena. "MODULATION OF HIGH AFFINITY HORMONE BINDING TO LH/CG RECEPTOR." UKnowledge, 2002. http://uknowledge.uky.edu/gradschool_theses/209.

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Precise control of physiological phenomena is performed by various kinds of receptormediated signaling. The vast majority of receptors belong to the superfamily of G proteincoupled receptors (GPCRs), which form one of the largest protein families. In theclassical model of GPCR signaling, stimulation of seven transmembrane spanning GPCRleads to the activation of heterotrimeric G proteins, which dissociate into a and bgsubunits. The subunits activate effector molecules, which include second messengergenerating systems, giving rise to various kinds of cellular responses. The LH/CGreceptor is a me

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22

Ades, Sarah Ellen. "The engrailed homeodomain : determinants of DNA-binding affinity and specificity." Thesis, Massachusetts Institute of Technology, 1995. http://hdl.handle.net/1721.1/32174.

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23

Ek, Moira. "Bacterial Display of a Tau-Binding Affibody Construct:Towards Affinity Maturation." Thesis, KTH, Skolan för kemi, bioteknologi och hälsa (CBH), 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-278580.

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Aggregation of microtubule-associated protein tau is involved in the pathology of several neurodegenerative diseases, including Alzheimer’s disease. The affibody TP4 has been shown to inhibit this aggregation process, and its target-binding positions were previously grafted onto a dimeric affibody scaffold, creating the sequestrin seqTP4. This project constitutes a part of the affinity maturation process of seqTP4, using two different bacterial display methods. An error-prone PCR library was first expressed on Staphylococcus carnosus cells for selection of variants with improved tau-binding pr

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24

Jiang, Tian. "Drug affinity and binding site signatures in extrasynaptic GABAA receptors." Thesis, The University of Sydney, 2021. https://hdl.handle.net/2123/27104.

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GABAA receptors are ligand-gated ion channels that play vital roles in the central nervous system due to their widespread distribution and involvement in vital biochemical process. GABAA receptors that express extrasynaptically are suggested as important targets for treating disorders such as epilepsy, sleep disturbances, stress, and mood disorders. Various pharmaceutical campaigns have succeeded in developing pharmacologically and clinically important drugs for the active sites of GABAA receptors. However, as the drugs do not exclusively bind to the targeted subtypes, they are usually associa

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25

Newell, John Glen. "Identification of a determinant of high affinity agonist binding of ã-aminobutyric acid type A receptors and the role of high affinity agonist binding in desensitization." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 2000. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape4/PQDD_0010/NQ59643.pdf.

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26

Nilvebrant, Johan. "An albumin-binding domain as a scaffold for bispecific affinity proteins." Doctoral thesis, KTH, Proteomik, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-105425.

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Protein engineering and in vitro selection systems are powerful methods to generate binding proteins. In nature, antibodies are the primary affinity proteins and their usefulness has led to a widespread use both in basic and applied research. By means of combinatorial protein engineering and protein library technology, smaller antibody fragments or alternative non-immunoglobulin protein scaffolds can be engineered for various functions based on molecular recognition. In this thesis, a 46 amino acid small albumin-binding domain derived from streptococcal protein G was evaluated as a scaffold fo

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27

Tang, Wen. "Bioactive Surface-Targeting Modular Peptide-Dendrons: Synthesis, Binding Affinity and Applicaiton." University of Akron / OhioLINK, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=akron1406049913.

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28

Puckett, Nathan. "Effects of Binding Affinity between Bovine Serum Albumin and Platinum Drugs." TopSCHOLAR®, 2017. http://digitalcommons.wku.edu/theses/1977.

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Platinum complex drugs such as cisplatin have been used as highly successful chemotherapy drugs since the 1970s. We are interested in how the ligands attached to cisplatin analogs influences their reactivity with biologically relevant targets along with time and amount. For this study, reactions were conducted to determine the reactivity between different platinum compounds and the protein bovine serum albumin. Various platinum compounds with different ligands were reacted in varying amounts with albumin in ammonium acetate buffer for either 1 hour, 4 hours, or 24 hours. Each reaction was quen

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29

Chmura, A. J. "Rational engineering of antibodies with irreversible binding : antibodies with infinite affinity /." Connect to Digital dissertations. Restricted to UC campuses. Access is free to UC campus dissertations, 2001. http://uclibs.org/PID/11984.

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Thesis (Ph. D.)--University of California, Davis, 2002.<br>Degree granted in Chemistry. Dissertation completed in 2001; degree granted in 2002. Also available via the World Wide Web. (Restricted to UC campuses).

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30

Lindgren, Joel. "Chemical Engineering of Small Affinity Proteins." Doctoral thesis, KTH, Proteinteknologi, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-141014.

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Small robust affinity proteins have shown great potential for use in therapy, in vivo diagnostics, and various biotechnological applications. However, the affinity proteins often need to be modified or functionalized to be successful in many of these applications. The use of chemical synthesis for the production of the proteins can allow for site-directed functionalization not achievable by recombinant routes, including incorporation of unnatural building blocks. This thesis focuses on chemical engineering of Affibody molecules and an albumin binding domain (ABD), which both are three-helix bu

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31

Brooks, Anthony J. "Computational prediction of HLA-DR binding peptides." Thesis, University of Aberdeen, 1999. http://digitool.abdn.ac.uk/R?func=search-advanced-go&find_code1=WSN&request1=AAIU118106.

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The experimental determination of peptide binding affinity to Major Histocompatibility Complex (MHC) molecules yields information which is often important to our understanding of the mechanics of autoimmunity, a widely occurring phenomenon giving rise to extensive pathological changes in many disease conditions. However, the most common biochemical technique by which this information is obtained (Competitive binding assaying) is a time consuming and costly procedure. Consequently, many groups have been using computational methods to try and predict which peptides are likely to bind to MHC mole

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32

Huang, Bingding. "Improving protein docking with binding site prediction." Doctoral thesis, [S.l. : s.n.], 2008. http://nbn-resolving.de/urn:nbn:de:bsz:14-ds-1216305428189-09951.

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33

Myers, Terence Anthony. "Assessment of chitosans as support matrices for dye-ligand affinity chromatography." Thesis, Queen's University Belfast, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.295399.

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34

陳磊碩 and Lui-sek Chan. "Chemical modification of immunoglobulins and the effects on antigen binding site affinity." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 1993. http://hub.hku.hk/bib/B29913378.

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35

Hoang, Vi K. B. "Binding Affinity and Antifungal Activity of Immune-Fusion Proteins against Candida albicans." Thesis, California State University, Long Beach, 2018. http://pqdtopen.proquest.com/#viewpdf?dispub=10825595.

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<p> <i>Candida albicans</i> is a yeast-like fungal pathogen that can cause infections ranging from superficial to life-threatening systemic candidiasis. Current treatments for systemic candidiasis are available but often ineffective and toxic. Consequently, it is necessary to develop new therapeutic approaches. The purpose of this study was to construct antibody-based fusion proteins that can bind to <i>C. albicans</i> cells and eliminate them. Two such fusion proteins were constructed. Each one is composed of M1 Fab as the antibody component that binds to <i> C. albicans</i> mannan and the an

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36

Chan, Lui-sek. "Chemical modification of immunoglobulins and the effects on antigen binding site affinity /." [Hong Kong] : University of Hong Kong, 1993. http://sunzi.lib.hku.hk/hkuto/record.jsp?B13731506.

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37

Guba, Nina Marie. "THE ANALYSIS OF EMDOGAIN BINDING AFFINITY FOR DIFFERENT PARTICULATE BONE GRAFT MATERIALS." Master's thesis, Temple University Libraries, 2018. http://cdm16002.contentdm.oclc.org/cdm/ref/collection/p245801coll10/id/506081.

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Oral Biology<br>M.S.<br>Objectives: Traditional guided tissue regeneration procedures use particulate bone graft materials and occlusive membranes with the primary aim of reconstitution of the supporting periodontal tissues. Currently, the Food and Drug Administration has cleared only four treatment modalities for true periodontal regeneration. These materials are autogenous bone, demineralized freeze dried bone allograft, LANAP (Millennium Dental Technologies INC, Cerritos, CA) and Emdogain (Institut Straumann AG, Basel, Switzerland). The biologically inactive nature of many commercially avai

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Poosapati, Anusha. "Disorder Levels of c-Myb Transactivation Domain Regulate its Binding Affinity to the KIX Domain of CREB Binding Protein." Scholar Commons, 2017. https://scholarcommons.usf.edu/etd/7436.

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Intrinsically disordered proteins (IDPs) do not form stable tertiary structures like their ordered partners. They exist as heterogeneous ensembles that fluctuate over a time scale. Intrinsically disordered regions and proteins are found across different phyla and exert crucial biological functions. They exhibit transient secondary structures in their free state and become folded upon binding to their protein partners via a mechanism called coupled folding and binding. Some IDPs form alpha helices when bound to their protein partners. We observed a set of cancer associated I

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39

Karlsson, Mikael. "Determination of antibody affinity and kinetic binding constants in Gyrolab Bioaffy microfluidic CD." Thesis, Linköping University, The Department of Physics, Chemistry and Biology, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-11616.

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<p>Studies of binding reactions are of highest importance in a vast number of areas of biomedicine and biotechnology. A demand for fast and accurate small-volume measurements grows stronger, partly due to the development of therapeutic antibodies. In this report, a novel method for studies of binding reactions of antibodies is described. The use of a microfluidic platform shows promising results in determination of affinity binding constants.</p><p>Affinities between 1E-09 and 1E-11 M have been determined for four TSH antibodies. Reproducibility tests give a CV below 10%, using different Gyrol

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Naples, Mark. "Determinants of high affinity ligand binding to the group III metabotropic glutamate receptors." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 2001. http://www.collectionscanada.ca/obj/s4/f2/dsk3/ftp05/MQ63174.pdf.

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Chattopadhyay, Madhuri. "Copper binding in the prion protein : coordination, affinity and effects on amyloid formation /." Diss., Digital Dissertations Database. Restricted to UC campuses, 2006. http://uclibs.org/PID/11984.

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Cook, Ian Haston. "Affinity isolation and characterisation of PtdIns(3,4,5)P3 binding proteins from brain tissue." Thesis, University of Cambridge, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.597915.

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The aim of this project was to identify proteins capable of specifically binding PtdIns(3,4,5)P<sub>3</sub> in the brain and then to establish the cellular significance of their ability to respond to P13K signalling. Potential phosphoinositide binding proteins from mouse brain cytosolic fractions, were captured using matrices carrying the tethered homologs of PtdIns(3,4,5)P<sub>3</sub>. Individual PtdIns(3,4,5)P<sub>3</sub> bead binding assays enabled mass spectrometric identification of over 100 proteins. They included several proteins with established phosphoinositide binding domains and man

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Chunsrivirot, Surasak. "Binding affinity of a small molecule to an amorphous polymer in a solvent." Thesis, Massachusetts Institute of Technology, 2011. http://hdl.handle.net/1721.1/65771.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Computational and Systems Biology Program, 2011.<br>Page 169 blank. Cataloged from PDF version of thesis.<br>Includes bibliographical references (p. 165-168).<br>Crystallization is a commonly used purification process in industrial practice. It usually begins with heterogeneous nucleation on a foreign surface. The complicated mechanism of heterogeneous nucleation is not well understood, but we hypothesize a possible correlation between binding affinity to a surface and nucleation enhancement. Amorphous polymers have been used in controlli

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Hoffman, Crystal Joyce. "Glucocorticoid Receptor Density and Binding Affinity in Horses with Systemic Inflammatory Response Syndrome." Thesis, Virginia Tech, 2014. http://hdl.handle.net/10919/48423.

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There were three objectives of this study. The first was to determine if commercially available fluorochromes could be used to determine the glucocorticoid receptor (GR) density and binding affinity (BA) in equine peripheral blood mononuclear cells. The second was to determine if there was a correlation between elevated plasma cortisol and GR density or binding affinity in healthy adult horses. The third objective was to evaluate the HPA axis in adult horses presenting with systemic inflammatory response syndrome (SIRS), and to determine where any alterations in HPA axis function occur in t

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Linhult, Martin. "Protein engineering to explore and improve affinity ligands." Doctoral thesis, KTH, Biotechnology, 2003. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-3632.

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<p>In order to produce predictable and robust systems forprotein purification and detection, well characterized, small,folded domains descending from bacterial receptors have beenused. These bacterial receptors, staphylococcal protein A (SPA)and streptococcal protein G (SPG), possess high affinity to IgGand / or HSA. They are composed of repetitive units in whicheach one binds the ligand independently. The domains foldindependently and are very stable. Since the domains also havewellknown three-dimensional structures and do not containcysteine residues, they are very suitable as frameworks for

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Zhao, Huiying. "Protein function prediction by integrating sequence, structure and binding affinity information." Thesis, 2014. http://hdl.handle.net/1805/3913.

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Indiana University-Purdue University Indianapolis (IUPUI)<br>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 complemen

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Hou, Tien-Yi, and 侯天儀. "Prediction of Estrogen Receptor Alpha Binding Affinity by Pharmacophore Ensemble/Support Vector Machine." Thesis, 2015. http://ndltd.ncl.edu.tw/handle/20144702474560764707.

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碩士<br>國立東華大學<br>化學系<br>103<br>The estrogen receptor alpha (ERα) is one of estrogen receptor subtype which can be activated by the hormone estrogen to affect a variety of physiological functions such as growth of mammary glands, pubertal development, and reproductive behavior. Moreover, ERα is the main therapeutic target for treating ER positive breast cancer. The endocrine disrupting chemicals (EDCs) can disturb the endocrine system via receptors especially ERα. An in silico model was developed to predict the binding affinity of ERα using the pharmacophore ensemble/support vector machine (P

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Chang, Tien-Chu, and 張添嵀. "Improving Scoring Function Model for Predicting Protein-Ligand Binding Affinity." Thesis, 2011. http://ndltd.ncl.edu.tw/handle/39955217161511685223.

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碩士<br>國立臺灣大學<br>工程科學及海洋工程學研究所<br>99<br>Our study proposes a novel MIXScore, a scoring function which improves the prediction of protein-ligand binding affinities. The prediction is an important issue in structure-based drug discovery and design. Typically, scoring functions can be classified into three groups: force-field, knowledge-based, and empirical. Traditional validation methods such as 5-fold cross validation and Leave-One-Out cross validation (LOO) do not encounter over-fitting problem, but the assessments may be too optimistic because the complexes in the same protein families may be

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Chiang, Ming-Keng, and 江銘耿. "Predicting ABCG2 Inhibitor Binding Affinity Using Pharmacophore Ensemble/Support Vector Machine." Thesis, 2011. http://ndltd.ncl.edu.tw/handle/23232490754898853810.

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碩士<br>國立東華大學<br>化學系<br>99<br>ABCG2 (BCRP) is an ATP-dependent membrane transporter that plays a pivotal role in eliminating xenobiotics by active extrusion of xenobiotics from the cell. Because of this phenomenon which results in ABCG2 repels a variety of drugs and hence the resulting in increased efflux of chemotherapeutical agents and reduction of intracellular drug accumulation. Finally, the effect of cure is hard to attain. Accordingly, using inhibitor revers function and expression of ABCG2 on a cancer cell is the method of solving ABCG2 extrusion drugs An in silico model was derived

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Chao, Chien-Ho, and 趙健合. "Predicting Binding Affinity of Protein-DNA Interactions Using Machine Learning-based Scoring Functions." Thesis, 2011. http://ndltd.ncl.edu.tw/handle/82595131989538619851.

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碩士<br>國立臺灣大學<br>生物產業機電工程學研究所<br>99<br>Proteins and DNA play important roles to maintaining life in living cells. The binding of protein to specific DNA sequences is the beginning of lots of bio-activities. For instance, the binding of regulatory sites of DNA by transcription factors, which are a kind of proteins that trigger transcription of a particular gene, initiates the transcription process. Research on this issue could facilitate the studies of gene regulation and regulatory networks. For these reasons, the study of interactions between protein and DNA has attracted much attention for a

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