Coevolutionary Landscape Inference and the Context-Dependence of Mutations in Beta-Lactamase TEM-1
出版年份 2015 全文链接
标题
Coevolutionary Landscape Inference and the Context-Dependence of Mutations in Beta-Lactamase TEM-1
作者
关键词
-
出版物
MOLECULAR BIOLOGY AND EVOLUTION
Volume 33, Issue 1, Pages 268-280
出版商
Oxford University Press (OUP)
发表日期
2015-10-08
DOI
10.1093/molbev/msv211
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- (2015) Zhengting Zou et al. MOLECULAR BIOLOGY AND EVOLUTION
- How Structural and Physicochemical Determinants Shape Sequence Constraints in a Functional Enzyme
- (2015) Luciano A. Abriata et al. PLoS One
- Dissecting enzyme function with microfluidic-based deep mutational scanning
- (2015) Philip A. Romero et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Pervasive degeneracy and epistasis in a protein-protein interface
- (2015) A. I. Podgornaia et al. SCIENCE
- Merging molecular mechanism and evolution: theory and computation at the interface of biophysics and evolutionary population genetics
- (2014) Adrian WR Serohijos et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- A Comprehensive, High-Resolution Map of a Gene’s Fitness Landscape
- (2014) Elad Firnberg et al. MOLECULAR BIOLOGY AND EVOLUTION
- Empirical fitness landscapes and the predictability of evolution
- (2014) J. Arjan G.M. de Visser et al. NATURE REVIEWS GENETICS
- Large pseudocounts andL2-norm penalties are necessary for the mean-field inference of Ising and Potts models
- (2014) J. P. Barton et al. PHYSICAL REVIEW E
- Fast and Accurate Multivariate Gaussian Modeling of Protein Families: Predicting Residue Contacts and Protein-Interaction Partners
- (2014) Carlo Baldassi et al. PLoS One
- Inferring fitness landscapes by regression produces biased estimates of epistasis
- (2014) J. Otwinowski et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Toward rationally redesigning bacterial two-component signaling systems using coevolutionary information
- (2014) Ryan R. Cheng et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Coevolutionary information, protein folding landscapes, and the thermodynamics of natural selection
- (2014) F. Morcos et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- The Fitness Landscape of HIV-1 Gag: Advanced Modeling Approaches and Validation of Model Predictions by In Vitro Testing
- (2014) Jaclyn K. Mann et al. PLoS Computational Biology
- Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information
- (2014) Sergey Ovchinnikov et al. eLife
- Sequence co-evolution gives 3D contacts and structures of protein complexes
- (2014) Thomas A Hopf et al. eLife
- Translating HIV Sequences into Quantitative Fitness Landscapes Predicts Viral Vulnerabilities for Rational Immunogen Design
- (2013) Andrew L. Ferguson et al. IMMUNITY
- The network of stabilizing contacts in proteins studied by coevolutionary data
- (2013) Sara Lui et al. JOURNAL OF CHEMICAL PHYSICS
- Analyses of the Effects of All Ubiquitin Point Mutants on Yeast Growth Rate
- (2013) Benjamin P. Roscoe et al. JOURNAL OF MOLECULAR BIOLOGY
- Patterns of Epistasis between Beneficial Mutations in an Antibiotic Resistance Gene
- (2013) Martijn F. Schenk et al. MOLECULAR BIOLOGY AND EVOLUTION
- Emerging methods in protein co-evolution
- (2013) David de Juan et al. NATURE REVIEWS GENETICS
- Evolutionary biochemistry: revealing the historical and physical causes of protein properties
- (2013) Michael J. Harms et al. NATURE REVIEWS GENETICS
- Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions
- (2013) Jaina Mistry et al. NUCLEIC ACIDS RESEARCH
- Pfam: the protein families database
- (2013) Robert D. Finn et al. NUCLEIC ACIDS RESEARCH
- Spin models inferred from patient-derived viral sequence data faithfully describe HIV fitness landscapes
- (2013) Karthik Shekhar et al. PHYSICAL REVIEW E
- Improved contact prediction in proteins: Using pseudolikelihoods to infer Potts models
- (2013) Magnus Ekeberg et al. PHYSICAL REVIEW E
- Maximum Allowed Solvent Accessibilites of Residues in Proteins
- (2013) Matthew Z. Tien et al. PLoS One
- Mutational effects on stability are largely conserved during protein evolution
- (2013) O. Ashenberg et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Capturing the mutational landscape of the beta-lactamase TEM-1
- (2013) H. Jacquier et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Deep mutational scanning of an RRM domain of the Saccharomyces cerevisiae poly(A)-binding protein
- (2013) D. Melamed et al. RNA
- Three-Dimensional Structures of Membrane Proteins from Genomic Sequencing
- (2012) Thomas A. Hopf et al. CELL
- SIMONA 1.0: An efficient and versatile framework for stochastic simulations of molecular and nanoscale systems
- (2012) T. Strunk et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Deep Sequencing of Systematic Combinatorial Libraries Reveals β-Lactamase Sequence Constraints at High Resolution
- (2012) Zhifeng Deng et al. JOURNAL OF MOLECULAR BIOLOGY
- The spatial architecture of protein function and adaptation
- (2012) Richard N. McLaughlin Jr et al. NATURE
- Epistasis as the primary factor in molecular evolution
- (2012) Michael S. Breen et al. NATURE
- Protein structure prediction from sequence variation
- (2012) Debora S Marks et al. NATURE BIOTECHNOLOGY
- Accurate de novo structure prediction of large transmembrane protein domains using fragment-assembly and correlated mutation analysis
- (2012) T. Nugent et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Amino acid coevolution induces an evolutionary Stokes shift
- (2012) D. D. Pollock et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Structural basis of histidine kinase autophosphorylation deduced by integrating genomics, molecular dynamics, and mutagenesis
- (2012) A. E. Dago et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Genomics-aided structure prediction
- (2012) J. I. Sulkowska et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- PoPMuSiC 2.1: a web server for the estimation of protein stability changes upon mutation and sequence optimality
- (2011) Yves Dehouck et al. BMC BIOINFORMATICS
- Predicting the functional impact of protein mutations: application to cancer genomics
- (2011) Boris Reva et al. NUCLEIC ACIDS RESEARCH
- Dissecting the Specificity of Protein-Protein Interaction in Bacterial Two-Component Signaling: Orphans and Crosstalks
- (2011) Andrea Procaccini et al. PLoS One
- Direct-coupling analysis of residue coevolution captures native contacts across many protein families
- (2011) F. Morcos et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- A biophysical protein folding model accounts for most mutational fitness effects in viruses
- (2011) C. S. Wylie et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Negative Epistasis Between Beneficial Mutations in an Evolving Bacterial Population
- (2011) A. I. Khan et al. SCIENCE
- Diminishing Returns Epistasis Among Beneficial Mutations Decelerates Adaptation
- (2011) H.-H. Chou et al. SCIENCE
- A method and server for predicting damaging missense mutations
- (2010) Ivan A Adzhubei et al. NATURE METHODS
- Uncovering the roles of rare variants in common disease through whole-genome sequencing
- (2010) Elizabeth T. Cirulli et al. NATURE REVIEWS GENETICS
- The Role of a Second-Shell Residue in Modifying Substrate and Inhibitor Interactions in the SHV β-Lactamase: A Study of Ambler Position Asn276
- (2009) Sarah M. Drawz et al. BIOCHEMISTRY
- Protein Sectors: Evolutionary Units of Three-Dimensional Structure
- (2009) Najeeb Halabi et al. CELL
- Structural Determinants of Protein Evolution Are Context-Sensitive at the Residue Level
- (2009) E. A. Franzosa et al. MOLECULAR BIOLOGY AND EVOLUTION
- High-resolution protein complexes from integrating genomic information with molecular simulation
- (2009) Alexander Schug et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Inferring Stabilizing Mutations from Protein Phylogenies: Application to Influenza Hemagglutinin
- (2009) Jesse D. Bloom et al. PLoS Computational Biology
- Increased Folding Stability of TEM-1 β-Lactamase by In Vitro Selection
- (2008) Insa Kather et al. JOURNAL OF MOLECULAR BIOLOGY
- SPROUTS: a database for the evaluation of protein stability upon point mutation
- (2008) Mathieu Lonquety et al. NUCLEIC ACIDS RESEARCH
- Identification of direct residue contacts in protein-protein interaction by message passing
- (2008) M. Weigt et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
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