In computational biology, de novo protein structure prediction refers to an algorithmic process by which protein tertiary structure is predicted from its amino acid primary sequence. The problem itself has occupied leading scientists for decades while still remaining unsolved. According to Science, the problem remains one of the top 125 outstanding issues in modern science.[1] At present, some of the most successful methods have a reasonable probability of predicting the folds of small, single-domain proteins within 1.5 angstroms over the entire structure.[2]
De novo methods tend to require vast computational resources, and have thus only been carried out for relatively small proteins. De novo protein structure modeling is distinguished from Template-based modeling (TBM) by the fact that no solved homologue to the protein of interest is used, making efforts to predict protein structure from amino acid sequence exceedingly difficult. Prediction of protein structure de novo for larger proteins will require better algorithms and larger computational resources such as those afforded by either powerful supercomputers (such as Blue Gene or MDGRAPE-3) or distributed computing projects (such as Folding@home, Rosetta@home, the Human Proteome Folding Project, or Nutritious Rice for the World). Although computational barriers are vast, the potential benefits of structural genomics (by predicted or experimental methods) to fields such as medicine and drug design make de novo structure prediction an active research field.
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and 26 Related for: De novo protein structure prediction information
Proteinstructureprediction is the inference of the three-dimensional structure of a protein from its amino acid sequence—that is, the prediction of its...
a protein sequence that is not based on existing, natural sequences Denovoproteinstructureprediction, the prediction of a protein's 3D structure, based...
Critical Assessment of StructurePrediction (CASP), sometimes called Critical Assessment of ProteinStructurePrediction, is a community-wide, worldwide...
related to the analysis and prediction of the three-dimensional structure of biological macromolecules such as proteins, RNA, and DNA. It deals with...
secondary structure states, namely helix, strand, and coil. Jpred Protein design Protein function predictionDenovoproteinstructureprediction Molecular...
biology, gene prediction or gene finding refers to the process of identifying the regions of genomic DNA that encode genes. This includes protein-coding genes...
Protein backbone fragment libraries have been used successfully in a variety of structural biology applications, including homology modeling, denovo...
understanding of protein function. Proteins can be designed from scratch (denovo design) or by making calculated variants of a known proteinstructure and its...
In mass spectrometry, denovo peptide sequencing is the method in which a peptide amino acid sequence is determined from tandem mass spectrometry. Knowing...
stood the test of time and is one of the key principles of denovoproteinstructureprediction. Kauzmann became an emeritus professor in 1982. His first...
biology, an intrinsically disordered protein (IDP) is a protein that lacks a fixed or ordered three-dimensional structure, typically in the absence of its...
condensation" where the structure begins to collapse onto the nucleus. Denovo or ab initio techniques for computational proteinstructureprediction can be used...
WW domains in ligand binding affinity and specificity. In denovoproteinstructureprediction, it has been shown that, when combined with a simple residue-residue...
This list of RNA structureprediction software is a compilation of software tools and web portals used for RNA structureprediction. The single sequence...
Denovo sequence assemblers List of gene prediction software List of disorder prediction software List of Protein subcellular localization prediction...
is an artificial protein, classified as a denovoprotein. This means that the protein itself was designed to have a specific structure and functional properties...
[page needed] Denovo generation of protein benefits from knowledge of existing proteinstructures. This knowledge of existing proteinstructure assists with...
Denovo gene birth is the process by which new genes evolve from non-coding DNA. Denovo genes represent a subset of novel genes, and may be protein-coding...
Strauss, Carol Rohl, David Baker. (2002) DeNovoPrediction of Three Dimensional Structures for Major Protein Families. JMB, 322(1):65-78. Bonneau R, Baliga...
mass spectrometry data viewers and format converters. List of proteinstructureprediction software Cox, Jürgen; Neuhauser, Nadin; Michalski, Annette; Scheltema...
from the prediction. Post-translational modifications or truncated termini may be identified by closer examination of the data (i.e. denovo sequencing)...
named Rosetta to predict the native structures of various proteins using special computer proteinstructureprediction algorithms. Rosetta was eventually...
phylogenetic tree visualization software List of proteinstructureprediction software List of RNA structureprediction software Durbin, Richard M.; Eddy, Sean...
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