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Protein tertiary structure

About: Protein tertiary structure is a research topic. Over the lifetime, 5690 publications have been published within this topic receiving 308076 citations. The topic is also known as: tertiary structure.


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Journal ArticleDOI
TL;DR: An updated protocol for Phyre2, which uses advanced remote homology detection methods to build 3D models, predict ligand binding sites and analyze the effect of amino acid variants for a user's protein sequence.
Abstract: Phyre2 is a web-based tool for predicting and analyzing protein structure and function. Phyre2 uses advanced remote homology detection methods to build 3D models, predict ligand binding sites, and analyze amino acid variants in a protein sequence. Phyre2 is a suite of tools available on the web to predict and analyze protein structure, function and mutations. The focus of Phyre2 is to provide biologists with a simple and intuitive interface to state-of-the-art protein bioinformatics tools. Phyre2 replaces Phyre, the original version of the server for which we previously published a paper in Nature Protocols. In this updated protocol, we describe Phyre2, which uses advanced remote homology detection methods to build 3D models, predict ligand binding sites and analyze the effect of amino acid variants (e.g., nonsynonymous SNPs (nsSNPs)) for a user's protein sequence. Users are guided through results by a simple interface at a level of detail they determine. This protocol will guide users from submitting a protein sequence to interpreting the secondary and tertiary structure of their models, their domain composition and model quality. A range of additional available tools is described to find a protein structure in a genome, to submit large number of sequences at once and to automatically run weekly searches for proteins that are difficult to model. The server is available at http://www.sbg.bio.ic.ac.uk/phyre2 . A typical structure prediction will be returned between 30 min and 2 h after submission.

7,941 citations

Journal ArticleDOI
TL;DR: The iterative threading assembly refinement (I-TASSER) server is an integrated platform for automated protein structure and function prediction based on the sequence- to-structure-to-function paradigm.
Abstract: The iterative threading assembly refinement (I-TASSER) server is an integrated platform for automated protein structure and function prediction based on the sequence-to-structure-to-function paradigm. Starting from an amino acid sequence, I-TASSER first generates three-dimensional (3D) atomic models from multiple threading alignments and iterative structural assembly simulations. The function of the protein is then inferred by structurally matching the 3D models with other known proteins. The output from a typical server run contains full-length secondary and tertiary structure predictions, and functional annotations on ligand-binding sites, Enzyme Commission numbers and Gene Ontology terms. An estimate of accuracy of the predictions is provided based on the confidence score of the modeling. This protocol provides new insights and guidelines for designing of online server systems for the state-of-the-art protein structure and function predictions. The server is available at http://zhanglab.ccmb.med.umich.edu/I-TASSER.

5,792 citations

Book ChapterDOI
TL;DR: The chapter reviews that the denaturation is a process in which the spatial arrangement of the polypeptide chains within the molecule is changed from that typical of the native protein to a more disordered arrangement.
Abstract: Publisher Summary This chapter explores that the changes that take place in the protein molecules during denaturation constitute one of the most interesting and complex classes of reactions that can be found either in nature or in the laboratory These reactions are important because of the information they can provide about the more intimate details of protein structure and function They are also significant because they challenge the chemist with a difficult area for the application of chemical principles The chapter reviews that the denaturation is a process in which the spatial arrangement of the polypeptide chains within the molecule is changed from that typical of the native protein to a more disordered arrangement The chapter also discusses the classification of protein structures: primary, secondary, and tertiary structures The primary structure is that expressed by the structural chemical formula and depends entirely on the chemical valence bonds that the classical organic chemist would write down for the protein molecule The secondary structure is the configuration of the polypeptide chain that results from the satisfaction of the hydrogen bonding potential between the peptide N-H and C=O groups The tertiary structure is the pattern according to which the secondary structures are packed together within the native protein molecule The term “denaturation” as used in this chapter is indented to include changes in both the secondary and tertiary structures

4,528 citations

Book
01 Oct 1986
TL;DR: This paper discusses the physical properties of polypeptides, the structure of which has been determined Crystallographically to High Resolution and its role in the biosynthesis of Proteins.
Abstract: Chemical Properties of Polypeptides Biosynthesis of Proteins Evolutionary and Genetic Origins of Protein Sequences Physical Interactions that Determine the Properties of Proteins Conformational Properties of Polypeptide Chains The Folded Conformations of Globular Proteins Proteins in Solution and in Membranes Interactions with Other Molecules Enzyme Catalysis Degradation Appendix: References to Protein Structures Determined Crystallographically to High Resolution

4,285 citations

Book
01 Jan 1991
TL;DR: Part 1 BASIC STRUCTURAL PRINCIPLES: The Building Blocks and Motifs of Protein Structure and Part 2 STRUCTURE, FUNCTION and ENGINEERING: Structure, Function and Engineering.
Abstract: PART 1 BASIC STRUCTURAL PRINCIPLES 1. The Building Blocks 2. Motifs of Protein Structure 3. alpha-Domain Structures 4. alpha/ss Structures 5. ss Structures 6. Folding and Flexibility 7. DNA Structures PART 2 STRUCTURE, FUNCTION AND ENGINEERING 8. DNA Recognition in Procaryotes by Helix-Turn-Helix Motifs 9. DNA Recognition by Eukaryotic Transcription Factors 10. Specific Transcription Factors Belong to a Few Families 11. An Example of Enzyme Catalysis: Serine Proteinases 12. Membrane Proteins 13. Signal Transduction 14. Fibrous Proteins 15. Recognition of Foreign Molecules by the Immune System 16. The Structure of Spherical Viruses 17. Prediction, Engineering, and Design of Protein Structures 18. Determination of Protein Structures

3,714 citations


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Performance
Metrics
No. of papers in the topic in previous years
YearPapers
202332
202259
2021136
2020111
2019101
2018105