Predicting protein-DNA interactions by full search computational docking-Reference-Cited by-同舟云学术

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Predicting protein-DNA interactions by full search computational docking

Published:2013-10-18 Issue:12 Volume:81 Page:2106-2118
ISSN:0887-3585
Container-title:Proteins: Structure, Function, and Bioinformatics
language:en
Short-container-title:Proteins

Author:

Roberts Victoria A.¹,Pique Michael E.²,Ten Eyck Lynn F.¹³,Li Sheng⁴

Affiliation:

1. San Diego Supercomputer Center, University of California; San Diego, La Jolla California 92093

2. Department of Integrative Structural and Computational Biology; The Scripps Research Institute, La Jolla; California 92037

3. Department of Chemistry and Biochemistry; University of California; San Diego, La Jolla California 92093

4. Department of Medicine; University of California; San Diego, La Jolla California 92093

Funder

National Science Foundation

National Institutes of Health

University of California, San Diego, Center for AIDS Research

Publisher

Wiley

Subject

Molecular Biology,Biochemistry,Structural Biology

Link

http://onlinelibrary.wiley.com/wol1/doi/10.1002/prot.24395/fullpdf

Reference95 articles.

1. Crystallization of the yeast MATα2/MCM1/DNA ternary complex: general methods and principles for protein/DNA cocrystallization;Tan;J Mol Biol,2000

2. CAPRI: a Critical Assessment of Predicted Interactions;Janin;Proteins,2003

3. Assessment of blind predictions of protein-protein interactions: current status of docking methods;Méndez;Proteins,2003

4. Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures;Méndez;Proteins,2005

5. Simulations of nucleic acids and their complexes;Giudice;Acc Chem Res,2002

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1. Considering both small and large scale motions of vascular endothelial growth factor (VEGF) is crucial for reliably predicting its binding affinities to DNA aptamers;RSC Advances;2021

2. Computational structure modeling for diverse categories of macromolecular interactions;Current Opinion in Structural Biology;2020-10

3. Molecular Modeling Applied to Nucleic Acid-Based Molecule Development;Biomolecules;2018-08-27

4. Combining H/D Exchange Mass Spectrometry and Computational Docking To Derive the Structure of Protein–Protein Complexes;Biochemistry;2017-11-16

5. A fragment-based docking simulation for investigating peptide–protein bindings;Physical Chemistry Chemical Physics;2017

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