Consensus protein design

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Protein folding and misfolding

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The Universal Protein Resource (UniProt)

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Engineering the third wave of biocatalysis

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Twilight zone of protein sequence alignments

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SMART: recent updates, new developments and status in 2015

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New and continuing developments at PROSITE

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Evolutionarily Conserved Pathways of Energetic Connectivity in Protein Families

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Serpin Structure, Mechanism, and Function

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Protein stability promotes evolvability

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De Novo Computational Design of Retro-Aldol Enzymes

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Structure of a serpin–protease complex shows inhibition by deformation

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An Introduction to Sequence Similarity (“Homology”) Searching

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Protein Dynamism and Evolvability

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PROSITE: a documented database using patterns and profiles as motif descriptors

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Correlated mutations and residue contacts in proteins

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Stability effects of mutations and protein evolvability

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The Universal Protein Resource (UniProt)

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Pfam: multiple sequence alignments and HMM-profiles of protein domains

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An overview of the serpin superfamily.

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A relationship between protein stability and protein function.

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A new method of inference of ancestral nucleotide and amino acid sequences.

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Resurrecting the Ancestral Steroid Receptor: Ancient Origin of Estrogen Signaling

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Analysis of Catalytic Residues in Enzyme Active Sites

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How Protein Stability and New Functions Trade Off

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Immunogenicity of protein therapeutics

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Beyond directed evolution—semi-rational protein engineering and design

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Understanding protein folding via free-energy surfaces from theory and experiment

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SUPERFAMILY—sophisticated comparative genomics, data mining, visualization and phylogeny

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STRUCTURAL AND GENETIC ANALYSIS OF PROTEIN STABILITY

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Evolutionary information for specifying a protein fold

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Prediction of protein secondary structure and active sites using the alignment of homologous sequences

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The Stability Effects of Protein Mutations Appear to be Universally Distributed

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Directed evolution of biocatalysts

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Resurrecting ancient genes: experimental analysis of extinct molecules

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Database resources of the National Center for Biotechnology Information

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Protein kinetic stability

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Localizing frustration in native proteins and protein assemblies

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Consensus-derived structural determinants of the ankyrin repeat motif

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Thermodynamic prediction of protein neutrality

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Sequence Statistics Reliably Predict Stabilizing Mutations in a Protein Domain

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Chemical Paleogenetics. Molecular "Restoration Studies" of Extinct Forms of Life.

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De novo design of a transmembrane Zn 2+ -transporting four-helix bundle

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Engineering proteins for thermostability: the use of sequence alignments versus rational design and directed evolution

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Design of Stable α-Helical Arrays from an Idealized TPR Motif

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T-cell dependent immunogenicity of protein therapeutics: Preclinical assessment and mitigation

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Computationally designed libraries for rapid enzyme stabilization

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The consensus concept for thermostability engineering of proteins: further proof of concept

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Correlations Among Amino Acid Sites in bHLH Protein Domains: An Information Theoretic Analysis

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A Designed Ankyrin Repeat Protein Evolved to Picomolar Affinity to Her2

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Optimizing non-natural protein function with directed evolution

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Intense Neutral Drifts Yield Robust and Evolvable Consensus Proteins

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Semirational design of active tumor suppressor p53 DNA binding domain with enhanced stability

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Upcoming challenges for multiple sequence alignment methods in the high-throughput era

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Structural analysis of WW domains and design of a WW prototype.

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Serpinopathies and the conformational dementias

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Bridging the gaps in design methodologies by evolutionary optimization of the stability and proficiency of designed Kemp eliminase KE59

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Large increases in general stability for subtilisin BPN' through incremental changes in the free energy of unfolding

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Structure- and sequence-analysis inspired engineering of proteins for enhanced thermostability

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From DNA sequence to improved functionality: using protein sequence comparisons to rapidly design a thermostable consensus phytase

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The Biologic Activity and Molecular Characterization of a Novel Synthetic Interferon-Alpha Species, Consensus Interferon

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Minimizing the immunogenicity of protein therapeutics

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Design of a Split Intein with Exceptional Protein Splicing Activity

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Mechanism of rescue of common p53 cancer mutations by second‐site suppressor mutations

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Stability and function: two constraints in the evolution of barstar and other proteins

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The accuracy of several multiple sequence alignment programs for proteins

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The Linkage Between Protein Folding and Functional Cooperativity: Two Sides of the Same Coin?

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De novo protein design: how do we expand into the universe of possible protein structures?

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Protein stability: computation, sequence statistics, and new experimental methods

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Structure determination of human and murine beta-defensins reveals structural conservation in the absence of significant sequence similarity

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Co-operative interactions during protein folding

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Construction of stabilized proteins by combinatorial consensus mutagenesis

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Designed Armadillo Repeat Proteins as General Peptide-Binding Scaffolds: Consensus Design and Computational Optimization of the Hydrophobic Core

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Strategies and computational tools for improving randomized protein libraries

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Long-Range, Small Magnitude Nonadditivity of Mutational Effects in Proteins

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Folding landscapes of ankyrin repeat proteins: experiments meet theory

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Structure determination of human and murine beta-defensins reveals structural conservation in the absence of significant sequence similarity

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Energy landscapes of functional proteins are inherently risky

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Stabilizing Proteins from Sequence Statistics: The Interplay of Conservation and Correlation in Triosephosphate Isomerase Stability

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Design of novel FN3 domains with high stability by a consensus sequence approach

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Consensus Protein Design without Phylogenetic Bias

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Multiple Global Suppressors of Protein Stability Defects Facilitate the Evolution of Extended-Spectrum TEM β-Lactamases

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Beyond Consensus: Statistical Free Energies Reveal Hidden Interactions in the Design of a TPR Motif

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Structure‐guided consensus approach to create a more thermostable penicillin G acylase

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Thermostable variants constructed via the structure-guided consensus method also show increased stability in salts solutions and homogeneous aqueous-organic media

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Intrabody construction and expression III: Engineering hyperstable V H domains

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Design of highly stable functional GroEL minichaperones

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Triosephosphate Isomerase by Consensus Design: Dramatic Differences in Physical Properties and Activity of Related Variants

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Stabilizing IκBα by “Consensus” Design

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Inferring Stabilizing Mutations from Protein Phylogenies: Application to Influenza Hemagglutinin

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Dynamic local unfolding in the serpin α-1 antitrypsin provides a mechanism for loop insertion and polymerization

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Phenotypic comparisons of consensus variants versus laboratory resurrections of Precambrian proteins

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The creation of a novel fluorescent protein by guided consensus engineering

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Covariation Is a Poor Measure of Molecular Coevolution

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Understanding the frustration arising from the competition between function, misfolding, and aggregation in a globular protein

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Protein stability by number: high-throughput and statistical approaches to one of protein science's most difficult problems

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Evolutionary Approaches to Protein Engineering

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Increasing protein stability using a rational approach combining sequence homology and structural alignment: Stabilizing the WW domain

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Higher-Order Packing Interactions in Triple and Quadruple Mutants of Staphylococcal Nuclease

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Structural and dynamic properties that govern the stability of an engineered fibronectin type III domain

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Protein Engineering and Stabilization from Sequence Statistics

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Is Sequence Alignment an Art or a Science?

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