Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 20 of 65 for “"Homology Modeling"”.
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The structure of the nitrilase from Rhodococcus Rhodochrous J1: homology modeling and three-dimensional reconstruction
… ~5 dimers per turn in a pitch of 77.23 Å. Homology modeling and subsequent fitting into the EM map has revealed the helix is built primarily from dimers, which interact via the C and D surfaces. The residues, which potentially interact across the D surface, have been identified and these …
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Plausible Inference: A Knowledge-Intensive Approach to Induction (An Application of PI to the Problem of Hidden Homology Modeling)
… tool that assists in complex domain modeling. Using this perspective we develop Plausible Inference (PI)--a framework based on the tradeoffs suggested by this learning-as-a-tool perspective. Four aspects of the approach distinguish it from other learning approaches, and are …
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Computational approaches for the design and prediction of protein-protein interactions
… biological phenomena, yet explicit atomic-level modeling is computationally prohibitive. Computational protein design, homology modeling, protein interaction prediction, docking and structure recognition are among these applications. Models that are commonly applied to these problems combine …
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A thermodynamic definition of protein folds
Modern techniques in structural biology, like homology modeling, protein threading, protein fold classification, and homology detection have proven extremely useful. For example, they have provided us with evolutionary information about protein homology which has in some many cases lead directly to …
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A Web Service for Protein Refinement and Refinement of Membrane Proteins
<p>The structures obtained from homology modeling methods are of intermediate resolution 1-3Ã… from true structure. Energy minimization methods allow us to refine the proteins and obtain native like structures. Previous work shows that some of these methods performed well on soluble proteins. So we …
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Structure and dynamics of soluble guanylyl cyclase
… of sGC, was determined. Using AC as template and homology modeling, the 3D structure of sGC is predicted. Prior experimental work has suggested two binding modes of YC- 1. In the current investigation, molecular dynamics simulations (MD) were conducted to seek more detail of molecular mechanism of …
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Specificity and structural characterization of the PDZ domain from DegS, an extracytoplasmic E. coli protease
… response. The C-terminal domain has limited homology to PDZ domains and was thought to be involved in regulation or substrate recognition. A model of this PDZ domain was generated from NMR solution studies and homology modeling. Peptide selection studies identified the sequence Tyr-Tyr-Phe …
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Using structure to explore the sequence alignment space of remote homologs
The success of protein structure modeling by homology requires an accurate sequence alignment between the query sequence and its structural template. However, sequence alignment methods based on dynamic programming (DP) are typically unable to generate accurate alignments for remote sequence …
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Calculating the structure-based phylogenetic relationship of distantly related homologous proteins utilizing maximum likelihood structural alignment combinatorics and a novel structural molecular clock hypothesis
… establish the evolutionary relationships and homology of species, proteins, or genes. Homology modeling, ligand binding, and pharmaceutical testing all depend upon the homology ascertained by dendrograms. Regardless of the specific algorithm, all dendrograms that ascertain protein evolutionary …
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Dynamic Molecular Mechanisms and Drug Design of Important Therapeutic Targets
… GaMD, LiGaMD, Pep-GaMD, molecular docking and homology modeling) and collaborative experiments.
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Improving Profile Similarity Search and Alignment of Protein Sequences
… similar functional sites. Current sequence-based homology search methods are still unable to detect many similarities evident from protein spatial structures. We present a new method, COMPADRE, to assess the relationship between the query sequence and a hit in the database by considering the …
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Chemogenomic approaches to drug design : docking-based virtual screening of nematode GPCRs for potential anthelmintic agents
… GPCR receptor (FLP18R1) was determined using homology modeling using the beta-2-adrenergic receptor as a template. The homology model developed had 24.87 % sequence identity with the template. Explicit membrane molecular dynamic simulations were used to optimize and refine the helices of the …
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Discovery of Function in the Enolase Superfamily
… MLE subgroup, based on sequence information and homology modeling, has been successful. A novel D-Ala-D/L-Ala and a unique L-Ala-D/L-Glu epimerase (AEE) were identified and kinetically characterized from Cytophaga hutchinsonii (k cat/KM of 5.5 x 104 M -1s-1) and Bacteroides thetaiotaomicron …
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Protein kinases: Structure modeling, inhibition, and protein-protein interactions
… targets. For these reasons, we developed a new homology modeling approach to facilitate modeling non-crystallized protein kinases and protein kinase states. Our homology modeling approach was able to model proteins having long amino acid sequences and multiple protein domains with reliable model …
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Accelerated simulations and computer-aided drug design of membrane proteins
… techniques including molecular docking, homology modeling and free energy calculations for accelerated simulations and computer-aided drug design of different membrane proteins. In Chapters 1 and 2, I focus on applying GaMD and Pep-GaMD to determine the mechanisms of γ-secretase …
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Identification, Validation, and Mapping of Phytophthora sojae and Soybean Mosaic Virus Resistance Genes in Soybean
… a combination of transient expression and homology modeling; we provide evidence that Glyma14g38533 encodes Rsv3.
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STRUCTURAL AND CATALYTIC FEATURES AFFECTING INACTIVATION OF TYPICAL 2-CYS HUMAN PEROXIREDOXINS 2 AND 3
Reactive oxygen species are key mediators of intracellular signaling and significantly influence the progression of several pathophysiologies. Oxidative stress damages macromolecules (lipids, nucleic acids and proteins). Antioxidant enzymes play a critical homeostatic role in modulating the …
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Molecular mechanisms and complete antigen formation in allergic contact dermatitis
… loss of T cell recognition. We finally used homology modeling to construct a model of the H2-Aq/antigen/TCR complex, a part of the ”immunological synapse”. Our new model could explain the experimental T cell responses in terms of a defined structure of the MHC/antigen, and how this structure …
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Estudo de modelagem molecular de derivados de desoxiuridina como inibidores da dUTPase de Plasmodium falciparum.
… structural model of Pf dUTPase (PDB ID: 1VYQ) by homology modeling, since the crystal structure stored in the Protein Data Bank s hows regions of undetermined conformation. In this work we used, in addition to conventional molecular dynamics, the Steered Molecular Dynamics technique to simulat e …
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