Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin

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Antibody Recognition of a Highly Conserved Influenza Virus Epitope

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Protein–Protein Docking with Simultaneous Optimization of Rigid-body Displacement and Side-chain Conformations

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Structural and functional bases for broad-spectrum neutralization of avian and human influenza A viruses

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Clinical Aspects of Pandemic 2009 Influenza A (H1N1) Virus Infection

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Macromolecular Modeling with Rosetta

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Isolating and engineering human antibodies using yeast surface display

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Practically useful protein-design methods combining phylogenetic and atomistic calculations

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Computational Design of Novel Protein Binders and Experimental Affinity Maturation

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Protein Engineering by Combined Computational and In Vitro Evolution Approaches

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Sampling and energy evaluation challenges in ligand binding protein design

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Epitope mapping of diverse influenza Hemagglutinin drug candidates using HDX-MS

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Influenza Virus with Increased pH of Hemagglutinin Activation Has Improved Replication in Cell Culture but at the Cost of Infectivity in Human Airway Epithelium

Singanayagam, A., Zambon, M. C. F. A., & Barclay, W. (2019) · Journal of Virology · doi:10.1128/jvi.00058-19 · Cited by 41

Protein folding, structure prediction and design

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Rosetta and the Design of Ligand Binding Sites

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Disposable Autonomous Device for Swab-to-Result Diagnosis of Influenza

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Computational design of an epitope-specific Keap1 binding antibody using hotspot residues grafting and CDR loop swapping

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Machine learning methods for protein-protein binding affinity prediction in protein design

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Delaying pyroptosis with an AI-screened gasdermin D pore blocker mitigates inflammatory response

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Beyond antibodies: using biological principles to guide the development of next-generation protein therapeutics

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A Balance between Inhibitor Binding and Substrate Processing Confers Influenza Drug Resistance

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Designed Two- and Three-Dimensional Protein Nanocage Networks Driven by Hydrophobic Interactions Contributed by Amyloidogenic Motifs

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Computational design and experimental verification of a symmetric protein homodimer

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Second career of a biosynthetic enzyme: Lumazine synthase as a virus-like nanoparticle in vaccine development

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Max Bergmann lecture Protein epitope mimetics in the age of structural vaccinology

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Comparison of Rosetta flexible‐backbone computational protein design methods on binding interactions

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Building synthetic gene circuits from combinatorial libraries: screening and selection strategies

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The genetic code constrains yet facilitates Darwinian evolution

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Learning from structure-based drug design and new antivirals targeting the ribonucleoprotein complex for the treatment of influenza

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The Role of Local Backrub Motions in Evolved and Designed Mutations

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Why reinvent the wheel? Building new proteins based on ready‐made parts

Khersonsky, O., & Fleishman, S. J. (2016) · Protein Science · doi:10.1002/pro.2892 · Cited by 35

Designing protein structures and complexes with the molecular modeling program Rosetta

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Protein- and Peptide-Based Virus Inactivators: Inactivating Viruses Before Their Entry Into Cells

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Computational de novo design of antibodies binding to a peptide with high affinity

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De novo design of antibody complementarity determining regions binding a FLAG tetra-peptide

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Assessment of protein side-chain conformation prediction methods in different residue environments

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Tertiary Structural Motif Sequence Statistics Enable Facile Prediction and Design of Peptides that Bind Anti-apoptotic Bfl-1 and Mcl-1

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Leveraging Artificial Intelligence to Expedite Antibody Design and Enhance Antibody–Antigen Interactions

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Accurate de novo design of heterochiral protein–protein interactions

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Computational design of protein-small molecule interfaces

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A Markov‐chain model description of binding funnels to enhance the ranking of docked solutions

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De novo design of protein minibinder agonists of TLR3

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Redesigned HIV antibodies exhibit enhanced neutralizing potency and breadth

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Hierarchical design of artificial proteins and complexes toward synthetic structural biology

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Towards structure-based protein drug design

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Introducing a Clustering Step in a Consensus Approach for the Scoring of Protein-Protein Docking Models

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Artificial Affinity Proteins as Ligands of Immunoglobulins

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Mechanism of Drug Resistance of Hemagglutinin of Influenza Virus and Potent Scaffolds Inhibiting Its Function

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Cold Spots in Protein Binding

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Protein-Based Degraders: From Chemical Biology Tools to Neo-Therapeutics

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All Repeats Are Not Equal: A Module-Based Approach to Guide Repeat Protein Design

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Enhancing Structure Prediction and Design of Soluble and Membrane Proteins with Explicit Solvent-Protein Interactions

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Multistate design of influenza antibodies improves affinity and breadth against seasonal viruses

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Inhibition of Influenza H7 Hemagglutinin-Mediated Entry

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New designed protein assemblies

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Performance of ZDOCK in CAPRI rounds 20–26

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De Novo Proteins with Life-Sustaining Functions Are Structurally Dynamic

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Emerging and state of the art hemagglutinin-targeted influenza virus inhibitors.

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Antibody Determinants of Influenza Immunity

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A global map of the protein shape universe

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A “Fuzzy”-Logic Language for Encoding Multiple Physical Traits in Biomolecules

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Engineered Biosensors from Dimeric Ligand-Binding Domains

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Rational Design of a Modality‐Specific Inhibitor of TRPM8 Channel against Oxaliplatin‐Induced Cold Allodynia

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Antiviral Peptides as Anti-Influenza Agents

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Inhibition of Influenza A Virus Infection In Vitro by Peptides Designed In Silico

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Protein Calligraphy: A New Concept Begins To Take Shape

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Crosstalk between endogenous and synthetic components – synthetic signaling meets endogenous components

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Antibody affinity maturation by computational design

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Low-stringency selection of TEM1 for BLIP shows interface plasticity and selection for faster binders

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Engineering a genetically encoded competitive inhibitor of the KEAP1–NRF2 interaction via structure-based design and phage display

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Protein engineering: navigating between chance and reason

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Predicting the side-chain dihedral angle distributions of nonpolar, aromatic, and polar amino acids using hard sphere models

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Rapid Diagnostic Assay for Intact Influenza Virus Using a High Affinity Hemagglutinin Binding Protein

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Crowdsourced Protein Design: Lessons From the Adaptyv EGFR Binder CompetitionPreprint

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Exploring the early stages of the pH-induced conformational change of influenza hemagglutinin

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An improved Protein G with higher affinity for human/rabbit IgG Fc domains exploiting a computationally designed polar network

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Multistate Protein Design Using CLEVER and CLASSY

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Novel Structural Parameters of Ig–Ag Complexes Yield a Quantitative Description of Interaction Specificity and Binding Affinity

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An integrated technology for quantitative wide mutational scanning of human antibody Fab libraries

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Assessing and enhancing foldability in designed proteins

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Computational Protein Design for COVID-19 Research and Emerging Therapeutics

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Protein arrays made to order

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Computational de novo design of a four‐helix bundle protein— DND _4 HB

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Computational design of dynamic receptor—peptide signaling complexes applied to chemotaxis

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Development of single-chain variable fragments (scFv) against influenza virus targeting hemagglutinin subunit 2 (HA2)

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Structure‐based redesign of proteins for minimal T‐cell epitope content

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Advances in distributed computing with modern drug discovery

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Break CDK2/Cyclin E1 Interface Allosterically with Small Peptides

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De novo design of mini-protein binders broadly neutralizing Clostridioides difficile toxin B variants

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Recent developments in molecular simulation approaches to study spherical virus capsids

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De novo selection of oncogenes

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Computational design of protein antigens that interact with the CDR H3 loop of HIV broadly neutralizing antibody 2F5

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Predicting the Binding Patterns of Hub Proteins: A Study Using Yeast Protein Interaction Networks

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What Have We Learned from Design of Function in Large Proteins?

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Expanding the frontiers of protein–protein modeling: From docking and scoring to binding affinity predictions and other challenges

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Inclusion of the orientational entropic effect and low‐resolution experimental information for protein–protein docking in Critical Assessment of PRedicted Interactions (CAPRI)

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