Functional Constraint Profiling of a Viral Protein Reveals Discordance of Evolutionary Conservation and Functionality

Predicting Evolutionary Site Variability from Structure in Viral Proteins: Buriedness, Packing, Flexibility, and Design

(2014) Amir Shahmoradi et al.   JOURNAL OF MOLECULAR EVOLUTION

The N Terminus of the Influenza B Virus Nucleoprotein Is Essential for Virus Viability, Nuclear Localization, and Optimal Transcription and Replication of the Viral Genome

(2014) L. Sherry et al.   JOURNAL OF VIROLOGY

High-Throughput Identification of Loss-of-Function Mutations for Anti-Interferon Activity in the Influenza A Virus NS Segment

(2014) N. C. Wu et al.   JOURNAL OF VIROLOGY

An Experimentally Determined Evolutionary Model Dramatically Improves Phylogenetic Fit

(2014) Jesse D. Bloom   MOLECULAR BIOLOGY AND EVOLUTION

Deep mutational scanning: a new style of protein science

(2014) Douglas M Fowler et al.   NATURE METHODS

High-throughput profiling of point mutations across the HIV-1 genome

(2014) Laith Q Al-Mawsawi et al.   Retrovirology

A Quantitative High-Resolution Genetic Profile Rapidly Identifies Sequence Determinants of Hepatitis C Viral Fitness and Drug Sensitivity

(2014) Hangfei Qi et al.   PLoS Pathogens

The inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin

(2014) Bargavi Thyagarajan et al.   eLife

Crystallographic Fragment Screening and Structure-Based Optimization Yields a New Class of Influenza Endonuclease Inhibitors

(2013) Joseph D. Bauman et al.   ACS Chemical Biology

High-throughput docking for the identification of new influenza A virus polymerase inhibitors targeting the PA–PB1 protein–protein interaction

(2013) Cristina Tintori et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

High-throughput Analysis ofin vivoProtein Stability

(2013) Ikjin Kim et al.   MOLECULAR & CELLULAR PROTEOMICS

FUBAR: A Fast, Unconstrained Bayesian AppRoximation for Inferring Selection

(2013) B. Murrell et al.   MOLECULAR BIOLOGY AND EVOLUTION

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mutational and fitness landscapes of an RNA virus revealed through population sequencing

(2013) Ashley Acevedo et al.   NATURE

Cross-species comparison of site-specific evolutionary-rate variation in influenza haemagglutinin

(2013) A. G. Meyer et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Maximum Allowed Solvent Accessibilites of Residues in Proteins

(2013) Matthew Z. Tien et al.   PLoS One

Coupling mutagenesis and parallel deep sequencing to probe essential residues in a genome or gene

(2013) William P. Robins et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Influenza Research Database: an integrated bioinformatics resource for influenza research and surveillance

(2012) R. Burke Squires et al.   Influenza and Other Respiratory Viruses

A Small-RNA Enhancer of Viral Polymerase Activity

(2012) J. T. Perez et al.   JOURNAL OF VIROLOGY

Systematic Identification of H274Y Compensatory Mutations in Influenza A Virus Neuraminidase by High-Throughput Screening

(2012) N. C. Wu et al.   JOURNAL OF VIROLOGY

Integrating Sequence Variation and Protein Structure to Identify Sites under Selection

(2012) Austin G. Meyer et al.   MOLECULAR BIOLOGY AND EVOLUTION

The structural biology of HIV-1: mechanistic and therapeutic insights

(2012) Alan Engelman et al.   NATURE REVIEWS MICROBIOLOGY

Mutational Analyses of the Influenza A Virus Polymerase Subunit PA Reveal Distinct Functions Related and Unrelated to RNA Polymerase Activity

(2012) Yuhong Liang et al.   PLoS One

Functional Analysis of Conserved Motifs in Influenza Virus PB1 Protein

(2012) Caroline Chu et al.   PLoS One

Screen Anti-influenza Lead Compounds That Target the PAC Subunit of H5N1 Viral RNA Polymerase

(2012) Lin Li et al.   PLoS One

Small molecule inhibitors of influenza A and B viruses that act by disrupting subunit interactions of the viral polymerase

(2012) G. Muratore et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Repeatability and Contingency in the Evolution of a Key Innovation in Phage Lambda

(2012) J. R. Meyer et al.   SCIENCE

Mapping the Phosphoproteome of Influenza A and B Viruses by Mass Spectrometry

(2012) Edward C. Hutchinson et al.   PLoS Pathogens

Structural and Biochemical Basis for Development of Influenza Virus Inhibitors Targeting the PA Endonuclease

(2012) Rebecca M. DuBois et al.   PLoS Pathogens

Structural Analysis of Specific Metal Chelating Inhibitor Binding to the Endonuclease Domain of Influenza pH1N1 (2009) Polymerase

(2012) Eva Kowalinski et al.   PLoS Pathogens

LigPlot+: Multiple Ligand–Protein Interaction Diagrams for Drug Discovery

(2011) Roman A. Laskowski et al.   Journal of Chemical Information and Modeling

Mutations in the Membrane-Proximal Region of the Influenza A Virus M2 Protein Cytoplasmic Tail Have Modest Effects on Virus Replication

(2011) S. M. Stewart et al.   JOURNAL OF VIROLOGY

Reassortment and Mutation of the Avian Influenza Virus Polymerase PA Subunit Overcome Species Barriers

(2011) A. Mehle et al.   JOURNAL OF VIROLOGY

Nonconserved Lysine Residues Attenuate the Biological Function of the Low-Risk Human Papillomavirus E7 Protein

(2011) N. J. Genovese et al.   JOURNAL OF VIROLOGY

firestar —advances in the prediction of functionally important residues

(2011) Gonzalo Lopez et al.   NUCLEIC ACIDS RESEARCH

Regulation of Protein Kinase C function by phosphorylation on conserved and non-conserved sites

(2010) Michael Freeley et al.   CELLULAR SIGNALLING

Mutational effects and the evolution of new protein functions

(2010) Misha Soskine et al.   NATURE REVIEWS GENETICS

Structures of influenza A proteins and insights into antiviral drug targets

(2010) Kalyan Das et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Role of conformational sampling in computing mutation-induced changes in protein structure and stability

(2010) Elizabeth H. Kellogg et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Comparing the Functional Roles of Nonconserved Sequence Positions in Homologous Transcription Repressors: Implications for Sequence/Function Analyses

(2009) Sudheer Tungtur et al.   JOURNAL OF MOLECULAR BIOLOGY

Mutational Analysis of Conserved Amino Acids in the Influenza A Virus Nucleoprotein

(2009) Z. Li et al.   JOURNAL OF VIROLOGY

Crystal structure of an avian influenza polymerase PAN reveals an endonuclease active site

(2009) Puwei Yuan et al.   NATURE

The cap-snatching endonuclease of influenza virus polymerase resides in the PA subunit

(2009) Alexandre Dias et al.   NATURE

Assessing computational methods for predicting protein stability upon mutation: good on average but not in the details

(2009) V. Potapov et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Structure-function studies of the influenza virus RNA polymerase PA subunit

(2009) YingFang Liu et al.   Science in China. Series C, Life sciences / Chinese Academy of Sciences

Macromolecular Modeling with Rosetta

(2008) Rhiju Das et al.   Annual Review of Biochemistry

Prediction of protein functional residues from sequence by probability density estimation

(2008) J. D. Fischer et al.   BIOINFORMATICS

Crystal structure of the polymerase PAC–PB1N complex from an avian influenza H5N1 virus

(2008) Xiaojing He et al.   NATURE

The structural basis for an essential subunit interaction in influenza virus RNA polymerase

(2008) Eiji Obayashi et al.   NATURE

The structural basis for cap binding by influenza virus polymerase subunit PB2

(2008) Delphine Guilligay et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli

(2008) Z. D. Blount et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mapping the domain structure of the influenza A virus polymerase acidic protein (PA) and its interaction with the basic protein 1 (PB1) subunit

(2008) Tom S.Y. Guu et al.   VIROLOGY

The Population Genetics of dN/dS

(2008) Sergey Kryazhimskiy et al.   PLoS Genetics

Differential role of the influenza A virus polymerase PA subunit for vRNA and cRNA promoter binding

(2007) Helena J. Maier et al.   VIROLOGY