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Showing 1 to 20 of 409 for “"protein structure"”.
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Evolution of Protein Structure
… aminoacyl-tRNA synthetases are one of the major protein components in the translation machinery. These essential proteins are found in all forms of life, and are responsible for charging their cognate tRNAs with the correct amino acid. The evolution of the tRNA synthetases is of fundamental …
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Protein Structure Analysis and Prediction
The protein structure prediction problem consists of three separate subproblems: modeling the protein structure, modeling the protein energetics, and the problem of searching for low-energy structures in high-dimensional space in the presence of many local minima. This study presents a new approach …
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Evolution of protein structure function
Proteins are generated as a result of millions of evolutionary experiments over a billion years. These experiments are constrained by proteins structure and function. Investigating genomics data is a natural way for mining these constraints to address long-standing biological challenges. In this …
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Protein structure determination using evolutionary information
… to optimize its sequence to perform a task. For protein-coding genes, the task includes folding, stability, and function. The record of the evolutionary process, which in itself is probabilistic, is contained within a multiple sequence alignment. A statistical model that accurately describes …
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Protein structure prediction and conformational transitions
<p>There is a critical need for protein structure and function prediction. Accurate protein secondary structure prediction is essential for many bioinformatics applications, including protein tertiary structure prediction. We developed an algorithm (Fragment Data Mining, FDM) for protein secondary …
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Heme protein structure and ligand binding
Binding of carbon monoxide to a variety of heme proteins is a multistep process and can be described by a sequence of activation barriers. In the separated alpha and beta chains of hemoglobin three barriers are found which are sensitive to the structural differences between the two chains. The …
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Multiple Protein Structure Alignment and its Applications
… development of algorithms for aligning multiple protein structures. Although these algorithms can potentially be applied to a number of problems, they have primarily been used for protein core identification. A method that is capable of solving a variety of problems using structure comparison is …
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Interactive Analysis of Protein Structure and Dynamics
Understanding the structure-function relationship of proteins such as G protein-coupled receptors (GPCRs) requires detailed information on their three-dimensional (3D) structure and dynamics. Recent progress in the structural elucidation of receptor-G protein or -arrestin complexes yields valuable …
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New Methods to Improve Protein Structure Modeling
<p>Proteins are considered the central compound necessary for life, as they play a crucial role in governing several life processes by performing the most essential biological and chemical functions in every living cell. Understanding protein structures and functions will lead to a significant …
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Computational and NMR Investigations of Protein Structure
… represents an effort to better understand the structure of proteins, and to suggest new spectroscopic information which might be used to improve the resolution of such structures. Variations in spectroscopic observables are correlated with variations in the local geometry and electrostatic …
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Inference Time Search for Protein Structure Prediction
… not yet been made in the field of biomolecular structure prediction. We introduce a new paradigm for inference-time search by adding architectural components and a finetuning procedure to state-of-the-art structure prediction models that give rise to a discrete latent space. We implement …
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Improving Structural Features Prediction in Protein Structure Modeling
<p>Proteins play a vital role in the biological activities of all living species. In nature, a protein folds into a specific and energetically favorable three-dimensional structure which is critical to its biological function. Hence, there has been a great effort by researchers in both …
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An analysis of representations for protein structure prediction
Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1994.
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Protein Structure and Ion Binding in Potassium Selective Channels
… structural motif, the selectivity filter. This structure, made of backbone carbonyls and threonine side chains, directly coordinates the ions as they diffuse through the channel and appears central to this sub-angstrom discrimination between cations. Utilizing the non-selective Sodium and …
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Explorations into protein structure with the knob-socket model
<p>Protein sequences contain the information in order for a protein to fold to a unique compact, three-dimensional native structure. The forces that drive protein structures to form compact folds are largely dominated by burial of hydrophobic amino acids, which results in non-specific packing of …
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De Novo Protein Structure Modeling and Energy Function Design
<p>The two major challenges in protein structure prediction problems are (1) the lack of an accurate energy function and (2) the lack of an efficient search algorithm. A protein energy function accurately describing the interaction between residues is able to supervise the optimization of a protein …
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Protein structure prediction and structure-based protein function annotation
… tends to modify rather than invent function of protein molecules, and the log of the modifications is encrypted in the gene sequence. Analysis of these modification events in evolutionarily related genes is important for assigning function to hypothetical genes and their products surging in …
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A dynamic model for the evolution of protein structure
Protein domains are three-dimensional arrangements of atomic structure that are recurrent in the proteomes of organisms. Since the three-dimensional structure of a protein determines its function, it is the fold, much more than the underlying protein sequence and underlying chemistry, that is …
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