Coupling Protein Side-Chain and Backbone Flexibility Improves the Re-design of Protein-Ligand Specificity
出版年份 2015 全文链接
标题
Coupling Protein Side-Chain and Backbone Flexibility Improves the Re-design of Protein-Ligand Specificity
作者
关键词
Protein interactions, Small molecules, Protein domains, Enzymes, Protein sequencing, Macromolecular design, Biochemical simulations, Amino acid sequence analysis
出版物
PLoS Computational Biology
Volume 11, Issue 9, Pages e1004335
出版商
Public Library of Science (PLoS)
发表日期
2015-09-24
DOI
10.1371/journal.pcbi.1004335
参考文献
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注意:仅列出部分参考文献,下载原文获取全部文献信息。- Quantification of the transferability of a designed protein specificity switch reveals extensive epistasis in molecular recognition
- (2014) C. Melero et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Motif-directed redesign of enzyme specificity
- (2014) Benjamin Borgo et al. PROTEIN SCIENCE
- Evolution of oligomeric state through allosteric pathways that mimic ligand binding
- (2014) Tina Perica et al. SCIENCE
- Computational design of protein-small molecule interfaces
- (2013) Brittany Allison et al. JOURNAL OF STRUCTURAL BIOLOGY
- Precision is essential for efficient catalysis in an evolved Kemp eliminase
- (2013) Rebecca Blomberg et al. NATURE
- PDBe: Protein Data Bank in Europe
- (2013) Aleksandras Gutmanas et al. NUCLEIC ACIDS RESEARCH
- Pfam: the protein families database
- (2013) Robert D. Finn et al. NUCLEIC ACIDS RESEARCH
- Computational Protein Design Quantifies Structural Constraints on Amino Acid Covariation
- (2013) Noah Ollikainen et al. PLoS Computational Biology
- Directed enzyme evolution: beyond the low-hanging fruit
- (2012) Moshe Goldsmith et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- Binding Pocket Optimization by Computational Protein Design
- (2012) Christoph Malisi et al. PLoS One
- Control of protein signaling using a computationally designed GTPase/GEF orthogonal pair
- (2012) G. T. Kapp et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- The Role of Local Backrub Motions in Evolved and Designed Mutations
- (2012) Daniel A. Keedy et al. PLoS Computational Biology
- Predicting the Tolerated Sequences for Proteins and Protein Interfaces Using RosettaBackrub Flexible Backbone Design
- (2011) Colin A. Smith et al. PLoS One
- Accessing protein conformational ensembles using room-temperature X-ray crystallography
- (2011) J. S. Fraser et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- A Smoothed Backbone-Dependent Rotamer Library for Proteins Derived from Adaptive Kernel Density Estimates and Regressions
- (2011) Maxim V. Shapovalov et al. STRUCTURE
- Determination of Ensemble-Average Pairwise Root Mean-Square Deviation from Experimental B-Factors
- (2010) Antonija Kuzmanic et al. BIOPHYSICAL JOURNAL
- Optimizing non-natural protein function with directed evolution
- (2010) Eric M Brustad et al. CURRENT OPINION IN CHEMICAL BIOLOGY
- Conformer Generation with OMEGA: Algorithm and Validation Using High Quality Structures from the Protein Databank and Cambridge Structural Database
- (2010) Paul C. D. Hawkins et al. Journal of Chemical Information and Modeling
- Structure-Based Prediction of the Peptide Sequence Space Recognized by Natural and Synthetic PDZ Domains
- (2010) Colin A. Smith et al. JOURNAL OF MOLECULAR BIOLOGY
- An exciting but challenging road ahead for computational enzyme design
- (2010) David Baker PROTEIN SCIENCE
- Manufacturing Molecules Through Metabolic Engineering
- (2010) J. D. Keasling SCIENCE
- Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling
- (2009) Daniel J Mandell et al. NATURE METHODS
- Computational structure-based redesign of enzyme activity
- (2009) C.-Y. Chen et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Alteration of enzyme specificity by computational loop remodeling and design
- (2009) P. M. Murphy et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Computational design of second-site suppressor mutations at protein-protein interfaces
- (2009) Deanne W. Sammond et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Backrub-Like Backbone Simulation Recapitulates Natural Protein Conformational Variability and Improves Mutant Side-Chain Prediction
- (2008) Colin A. Smith et al. JOURNAL OF MOLECULAR BIOLOGY
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