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Progress in super long loop prediction

Published:2011-08-23 Issue:10 Volume:79 Page:2920-2935
ISSN:0887-3585
Container-title:Proteins: Structure, Function, and Bioinformatics
language:en
Short-container-title:Proteins

Author:

Zhao Suwen,Zhu Kai,Li Jianing,Friesner Richard A.

Funder

NIH

RAF is a stockholder in Schrodinger, Inc

Board of Directors and Scientific Advisory Board of Schrodinger, Inc.

Publisher

Wiley

Subject

Molecular Biology,Biochemistry,Structural Biology

Link

http://onlinelibrary.wiley.com/wol1/doi/10.1002/prot.23129/fullpdf

Reference31 articles.

1. Electrostatics of nanosystems: application to microtubules and the ribosome;Baker;Proc Natl Acad Sci USA,2001

2. Ab initio construction of polypeptide fragments: accuracy of loop decoy discrimination by an all-atom statistical potential and the AMBER force field with the Generalized Born solvation model;de Bakker;Proteins,2003

3. Ab initio construction of polypeptide fragments: efficient generation of accurate, representative ensembles;DePristo;Protein Struct Funct Bioinformat,2003

4. Modeling of loops in protein structures;Fiser;Protein Sci,2000

5. SuperLooper-a prediction server for the modeling of loops in globular and membrane proteins;Hildebrand;Nucl Acids Res,2009

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1. Highly Accurate and Efficient Deep Learning Paradigm for Full-Atom Protein Loop Modeling with KarmaLoop;Research;2024-01

2. Ab Initio Prediction of 3-D Conformations for Protein Long Loops with High Accuracy and Applications to Antibody CDRH3 Modeling;Journal of Chemical Information and Modeling;2023-11-29

3. Comprehensive assessment of protein loop modeling programs on large-scale datasets: prediction accuracy and efficiency;Briefings in Bioinformatics;2023-11-22

4. Enhanced conformational exploration of protein loops using a global parameterization of the backbone geometry;Journal of Computational Chemistry;2023-02-02

5. Enhanced conformational exploration of protein loops using a global parameterization of the backbone geometry;2022-06-25

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