Protein structure prediction based on fragment assembly and parameter optimization.
TLDR
A novel method for ab-initio prediction of protein tertiary structures based on the fragment assembly and global optimization is proposed, which optimize the linear parameters of the energy function, so that the native-like conformations become energetically more favorable than the non-native ones for proteins with known structures.About:
This article is published in Biophysical Chemistry.The article was published on 2005-04-01 and is currently open access. It has received 45 citations till now. The article focuses on the topics: Protein fragment library & Protein structure prediction.read more
Citations
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Protein loop modeling by using fragment assembly and analytical loop closure.
TL;DR: This article develops a novel method for protein loop modeling, where the loop conformations are generated by fragment assembly and analytical loop closure, and derives an analytic formula for the gradient of any analytical function of dihedral angles in the space of closed loops.
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A comparative study of the reported performance of ab initio protein structure prediction algorithms.
TL;DR: Two of the algorithmic settings—protein representation and fragment assembly—were found to have definite positive influence on the running time and the predicted structures, respectively, and there appears to be a clear benefit from incorporating this knowledge in the design of new prediction algorithms.
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Reconstruction of protein backbones from the BriX collection of canonical protein fragments.
Lies Baeten,Joke Reumers,Vicente Tur,Francois Stricher,Tom Lenaerts,Luis Serrano,Frederic Rousseau,Joost Schymkowitz +7 more
TL;DR: A discretisation of the conformational states accessible to the protein backbone similar to the successful rotamer approach in side chains is developed, and many loop regions that appear irregular at first glance are also found to form a recurrent structural motif, albeit with lower frequency of occurrence than regular secondary structures.
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AIMOES: Archive information assisted multi-objective evolutionary strategy for ab initio protein structure prediction
TL;DR: A three-objective evolution algorithm called AIMOES, an evolution scheme which flexibly reuse past search experiences is incorporated to enhance the efficiency of conformation search, is proposed and demonstrated by the performance comparison with other five state-of-the-art PSP methods.
References
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MOLMOL: a program for display and analysis of macromolecular structures.
TL;DR: Special efforts were made to allow for appropriate display and analysis of the sets of typically 20-40 conformers that are conventionally used to represent the result of an NMR structure determination, using functions for superimposing sets of conformers, calculation of root mean square distance (RMSD) values, identification of hydrogen bonds, and identification and listing of short distances between pairs of hydrogen atoms.
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Principles that Govern the Folding of Protein Chains
TL;DR: Anfinsen as discussed by the authors provided a sketch of the rich history of research that provided the foundation for his work on protein folding and the Thermodynamic Hypothesis, and outlined potential avenues of current and future scientific exploration.
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Modeling of loops in protein structures.
TL;DR: A new automated modeling technique that significantly improves the accuracy of loop predictions in protein structures by predicting loops of known structure in only approximately correct environments with errors typical of comparative modeling without misalignment is described.
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Protein Structure Prediction and Structural Genomics
David Baker,Andrej Sali +1 more
TL;DR: This Viewpoint begins by describing the essential features of the methods, the accuracy of the models, and their application to the prediction and understanding of protein function, both for single proteins and on the scale of whole genomes.
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Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation
TL;DR: In this paper, the number of residue-residue contacts formed in a large number of protein crystal structures is estimated by means of the quasi-chemical approximation with an approximate treatment of the effects of chain connectivity.