Affinity enhancement of an in vivo matured therapeutic antibody using structure‐based computational design

No abstract is available for this paper.

• Publication year

  2006

• Venue

  Protein Science

• Publication date

  2006-05-01

• Fields of study

  Medicine, Chemistry

• Identifiers
  DOI 10.1110/ps.052030506PMID 16597831PMCID PMC2242497
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Artificial Intelligence in Medicine: 23rd International Conference, AIME 2025, Pavia, Italy, June 23–26, 2025, Proceedings, Part I

  2025cited by this paper
• One‐ and two‐body decomposable Poisson‐Boltzmann methods for protein design calculations

  2005cited by this paper
• A monoclonal antibody to alpha1beta1 blocks antigen-induced airway responses in sheep.

  2004cited by this paper
• A Monoclonal Antibody to α1β1 Blocks Antigen-induced Airway Responses in Sheep

  2004cited by this paper
• Computational Design of a Biologically Active Enzyme

  2004cited by this paper
• Preprocessing of rotamers for protein design calculations

  2004cited by this paper
• Substantial energetic improvement with minimal structural perturbation in a high affinity mutant antibody.

  2004cited by this paper
• The role of very late antigen-1 in immune-mediated inflammation.

  2004cited by this paper
• Biomolecular ligand design : enhancing binding affinity and specificity utilizing electrostatic charge optimization and packing techniques

  2004influential reference
• The Many Roles of Computation in Drug Discovery

  2004cited by this paper
• Computational redesign of protein-protein interaction specificity

  2004cited by this paper
• Redesigning an antibody fragment for faster association with its antigen.

  2003cited by this paper
• Therapeutic antibodies for human diseases at the dawn of the twenty-first century

  2003cited by this paper
• Faculty Opinions recommendation of Design of a novel globular protein fold with atomic-level accuracy.

  2003cited by this paper
• A large scale test of computational protein design: folding and stability of nine completely redesigned globular proteins.

  2003cited by this paper
• An empirical model for electrostatic interactions in proteins incorporating multiple geometry‐dependent dielectric constants

  2003cited by this paper
• Repacking the Core of T4 lysozyme by automated design.

  2003cited by this paper
• X-ray snapshots of the maturation of an antibody response to a protein antigen

  2003cited by this paper
• Crystal structure of the alpha1beta1 integrin I domain in complex with an antibody Fab fragment.

  2003cited by this paper
• Crystal Structure of the α1β1 Integrin I Domain in Complex with an Antibody Fab Fragment

  2003cited by this paper
• Design of a Novel Globular Protein Fold with Atomic-Level Accuracy

  2003cited by this paper
• Affinity maturation of Fab antibody fragments by fluorescent‐activated cell sorting of yeast‐displayed libraries

  2003cited by this paper
• Design, activity, and structure of a highly specific artificial endonuclease.

  2002cited by this paper
• Electrostatics and packing in biomolecules : accounting for conformational change in protein folding and binding

  2002cited by this paper
• Antibody discovery: phage display.

  2002cited by this paper
• CHARMM: The Energy Function and Its Parameterization

  2002influential reference
• Molecular recognition in antibody-antigen complexes.

  2002cited by this paper
• Protein design with hierarchical treatment of solvation and electrostatics

  2002influential reference
• Generalized dead-end elimination algorithms make large-scale protein side-chain structure prediction tractable: implications for protein design and structural genomics.

  2001influential reference
• Rational design of faster associating and tighter binding protein complexes

  2000cited by this paper
• Rational design of nascent metalloenzymes.

  2000cited by this paper
• Native protein sequences are close to optimal for their structures.

  2000cited by this paper
• Quantitative analysis of the effect of the mutation frequency on the affinity maturation of single chain Fv antibodies.

  2000cited by this paper
• Conformational splitting: A more powerful criterion for dead‐end elimination

  2000cited by this paper
• The atomic structure of protein-protein recognition sites.

  1999cited by this paper
• Improved modeling of side‐chains in proteins with rotamer‐based methods: A flexible rotamer model

  1999cited by this paper
• Improving biosensor analysis

  1999cited by this paper
• Contribution of intra- and intermolecular hydrogen bonds to the conformational stability of human lysozyme(,).

  1999cited by this paper
• Divalent cations stabilize the alpha 1 beta 1 integrin I domain.

  1999cited by this paper
• Affinity dependence of the B cell response to antigen: a threshold, a ceiling, and the importance of off-rate.

  1998influential reference
• Encyclopedia of computational chemistry

  1998cited by this paper
• CLAMP: a biosensor kinetic data analysis program.

  1998cited by this paper
• Crystallography & NMR system: A new software suite for macromolecular structure determination.

  1998cited by this paper
• Exploring the conformational space of protein side chains using dead‐end elimination and the A* algorithm

  1998cited by this paper
• Ribosome display efficiently selects and evolves high-affinity antibodies in vitro from immune libraries.

  1998cited by this paper
• Optimizing electrostatic affinity in ligand-receptor binding: Theory, computation, and ligand properties

  1998cited by this paper
• De novo protein design: fully automated sequence selection.

  1997cited by this paper
• MOLREP: an Automated Program for Molecular Replacement

  1997cited by this paper
• Processing of X-ray diffraction data collected in oscillation mode.

  1997cited by this paper
• Construction and evolution of antibody–phage libraries by DMA shuffling

  1996cited by this paper
• Kinetic and affinity limits on antibodies produced during immune responses.

  1995influential reference
• Efficient rotamer elimination applied to protein side-chains and related spin glasses.

  1994cited by this paper
• Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models

  1994cited by this paper
• Backbone-dependent rotamer library for proteins. Application to side-chain prediction.

  1993cited by this paper
• The fuzzy-end elimination theorem: correctly implementing the side chain placement algorithm based on the dead-end elimination theorem.

  1993cited by this paper
• The dead-end elimination theorem and its use in protein side-chain positioning

  1992influential reference
• Improved methods for building protein models in electron density maps and the location of errors in these models.

  1991cited by this paper
• Electrostatic interactions in macromolecules: theory and applications.

  1990cited by this paper
• WHAT IF: a molecular modeling and drug design program.

  1990influential reference
• Calculating the electrostatic potential of molecules in solution: Method and error assessment

  1988cited by this paper
• CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

  1983influential reference
• Continuous cultures of fused cells secreting antibody of predefined specificity

  1975cited by this paper

• Engineering affinity-matured variants of an anti-polysialic acid monoclonal antibody with superior cytotoxicity-mediating potency.

  2025cites this paper
• Revolutionizing oncology: the role of Artificial Intelligence (AI) as an antibody design, and optimization tools

  2025cites this paper
• AbBiBench: A Benchmark for Antibody Binding Affinity Maturation and Design

  2025cites this paper
• Engineering affinity-matured variants of an anti-polysialic acid monoclonal antibody with superior cytotoxicity-mediating potency

  2025cites this paper
• Design and Preclinical Validation of an Anti-B7-H3-Specific Radiotracer: A Non-Invasive Imaging Tool to Guide B7-H3-Targeted Therapies

  2025cites this paper
• Biophysics of SARS-CoV-2 spike protein’s receptor-binding domain interaction with ACE2 and neutralizing antibodies: from computation to functional insights

  2025cites this paper
• Benchmarking inverse folding models for antibody CDR sequence design

  2025cites this paper
• Novel Strategy of Antibody Affinity Maturation and Enhancement of Nucleolin‐Mediated Antibody‐Dependent Cellular Cytotoxicity Against Triple‐Negative Breast Cancer

  2025cites this paper
• Enhancing the Affinity of a Novel Selective scFv for Soluble ST2 through Computational Design

  2025cites this paper
• intDesc-AbMut: Describing and understanding how antibody mutations impact their environmental interactions1

  2025cites this paper
• Accurate prediction of CDR-H3 loop structures of antibodies with deep learning

  2024cites this paper
• A new era of antibody discovery: an in-depth review of AI-driven approaches.

  2024cites this paper
• Enhancing affinity of neutralizing SARS-CoV-2 nanobody through facile structure-guided mutations in CDRs

  2024cites this paper
• Structure-guided mutations in CDRs for enhancing the affinity of neutralizing SARS-CoV-2 nanobody.

  2024cites this paper
• Optimizing Antibody-Antigen Binding Affinities with the ADAPT Platform.

  2023cites this paper
• Structure-Based Affinity Maturation of Antibody Based on Double-Point Mutations.

  2023cites this paper
• Identifying and overcoming the sampling challenges in relative binding free energy calculations of a model protein:protein complex

  2023cites this paper
• High-throughput analysis system of interaction kinetics for data-driven antibody design

  2023cites this paper
• Structure and Dynamics Guiding Design of Antibody Therapeutics and Vaccines

  2023cites this paper
• Identifying and overcoming the sampling challenges in relative binding free energy calculations of a model protein:protein complex

  2023cites this paper
• Toward real-world automated antibody design with combinatorial Bayesian optimization

  2023cites this paper
• Analytical Method for Experimental Validation of Computer-Designed Antibody.

  2023cites this paper
• In Silico Maturation of a Nanomolar Antibody against the Human CXCR2

  2022cites this paper
• Hallucinating structure-conditioned antibody libraries for target-specific binders

  2022cites this paper
• Structured Q-learning For Antibody Design

  2022cites this paper
• Engineered fast-dissociating antibody fragments for multiplexed super-resolution microscopy

  2022cites this paper
• AntBO: Towards Real-World Automated Antibody Design with Combinatorial Bayesian Optimisation

  2022cites this paper
• Structural and Functional Properties of Proteins

  2021cites this paper
• Development of an integrated structural biology platform specialized for sub-100 kDa protein complexes to support biologics discovery and rational engineering

  2021cites this paper
• Pierce into Structural Changes of Interactions Between Mutated Spike Glycoproteins and ACE2 to Evaluate Its Potential Biological and Therapeutic Consequences

  2021cites this paper
• An integrated computational pipeline for designing high-affinity nanobodies with expanded genetic codes

  2021cites this paper
• An Antibody Engineering Platform Using Amino Acid Networks: A Case Study in Development of Antiviral Therapeutics.

  2021cites this paper
• Structure‐based engineering of an antiangiogenic scFv antibody for soluble production in E. coli without loss of activity

  2021cites this paper
• Redesigning an antibody H3 loop by virtual screening of a small library of human germline-derived sequences

  2021cites this paper
• Computational and Rational Design of Single-Chain Antibody against Tick-Borne Encephalitis Virus for Modifying Its Specificity

  2021cites this paper
• Structure-based design and discovery of novel anti-tissue factor antibodies with cooperative double-point mutations, using interaction analysis

  2020cites this paper
• In silico Techniques for Prospecting and Characterizing Monoclonal Antibodies

  2020cites this paper
• Design of an engineered ACE2 as a novel therapeutics against COVID-19

  2020cites this paper
• Optimisation of human VH domain antibodies specific to Mycobacterium tuberculosis heat shock protein (HSP16.3)

  2019cites this paper
• Ursolic Acid in Cancer Treatment and Metastatic Chemoprevention: From Synthesized Derivatives to Nanoformulations in Preclinical Studies.

  2019cites this paper
• Cell‐Based Cancer Immunotherapy

  2019cites this paper
• Computer-guided library generation applied to the optimization of single-domain antibodies.

  2019cites this paper
• Antibody Structure and Function: The Basis for Engineering Therapeutics

  2019cites this paper
• Directed evolution methods for overcoming trade-offs between protein activity and stability.

  2019cites this paper
• Efficient Screening and Design of Variable Domain of Heavy Chain Antibody Ligands Through High Throughput Sequencing for Affinity Chromatography to Purify Fab Fragments

  2019cites this paper
• Trends in therapeutic antibody affinity maturation: From in-vitro towards next-generation sequencing approaches.

  2019cites this paper
• De novo discovery of antibody drugs – great promise demands scrutiny

  2019cites this paper
• Experimentally guided computational antibody affinity maturation with de novo docking, modelling and rational design

  2019cites this paper
• Computational Analysis for the Rational Design of Anti-Amyloid Beta (Aβ) Antibodies.

  2018cites this paper
• SKEMPI 2.0: an updated benchmark of changes in protein–protein binding energy, kinetics and thermodynamics upon mutation

  2018cites this paper
• Computational design of antibodies.

  2018cites this paper
• ScienceDirect Computational design of antibod ies

  2018cites this paper
• Application of Assisted Design of Antibody and Protein Therapeutics (ADAPT) improves efficacy of a Clostridium difficile toxin A single-domain antibody

  2018cites this paper
• Antibody Modeling, Engineering, and Design

  2018cites this paper
• Computational affinity maturation of camelid single-domain intrabodies against the nonamyloid component of alpha-synuclein

  2018cites this paper
• Antibody Affinity Maturation by Computational Design.

  2018cites this paper
• Production of Antigen-Binding Fragment against O,O-Diethyl Organophosphorus Pesticides and Molecular Dynamics Simulations of Antibody Recognition

  2018cites this paper
• Facile Affinity Maturation of Antibody Variable Domains Using Natural Diversity Mutagenesis

  2017cites this paper
• Sphinx: merging knowledge‐based and ab initio approaches to improve protein loop prediction

  2017cites this paper
• Sphinx: merging knowledge-based and ab initio approaches to improve protein loop prediction

  2017cites this paper
• Evidence for the formation of ScbR/ScbR2 heterodimers and identification of one of the regulatory targets in Streptomyces coelicolor

  2017cites this paper
• Computer-Aided Antibody Design: An Overview.

  2017cites this paper
• Protein Engineering: Methods and Applications

  2017cites this paper
• Full Protein Sequence Redesign with an MMGBSA Energy Function.

  2017cites this paper
• Arginine mutations in antibody complementarity-determining regions display context-dependent affinity/specificity trade-offs

  2017cites this paper
• Elucidation of potential sites for antibody engineering by fluctuation editing

  2017cites this paper
• Robotics-inspired methods to enhance protein design

  2017cites this paper
• Antibody H3 Structure Prediction

  2017cites this paper
• RosettaAntibodyDesign (RAbD): A general framework for computational antibody design

  2017cites this paper
• Assisted Design of Antibody and Protein Therapeutics (ADAPT)

  2017cites this paper
• How B-Cell Receptor Repertoire Sequencing Can Be Enriched with Structural Antibody Data

  2017cites this paper
• Biophysical Evidence Relevant to the Patentability of Engineered Antibodies: Using Computational Simulations to Assist the Objective Analysis Required by Section § 112(a)

  2016cites this paper
• The Parasol Protocol for computational mutagenesis.

  2016cites this paper
• Protein side chain conformation predictions with an MMGBSA energy function

  2016cites this paper
• AB‐Bind: Antibody binding mutational database for computational affinity predictions

  2016cites this paper
• Computational Molecular Design of Cellulose-based Delivery Vehicles for Vaginal Microbicide Gels

  2016cites this paper
• AbDesign: An algorithm for combinatorial backbone design guided by natural conformations and sequences

  2015cites this paper
• Thermodynamics of antibody-antigen interaction revealed by mutation analysis of antibody variable regions.

  2015cites this paper
• Fast gap‐free enumeration of conformations and sequences for protein design

  2015cites this paper
• Development of an NOE driven method for obtaining robust and reliable models of large protein complexes

  2015cites this paper
• Design and construction of small perturbation mutagenesis libraries for antibody affinity maturation using massive microchip-synthesized oligonucleotides.

  2015cites this paper
• Man-made antibodies and immunoconjugates with desired properties: function optimization using structural engineering

  2015cites this paper
• A Combination of Structural and Empirical Analyses Delineates the Key Contacts Mediating Stability and Affinity Increases in an Optimized Biotherapeutic Single-chain Fv (scFv)*

  2015cites this paper
• Computational protein design: assessment and applications

  2015cites this paper
• Advances in Antibody Design.

  2015cites this paper
• Protein engineering to capture and kill cancer cells

  2015cites this paper
• Computational tools for epitope vaccine design and evaluation.

  2015cites this paper
• Rigidity Emerges during Antibody Evolution in Three Distinct Antibody Systems: Evidence from QSFR Analysis of Fab Fragments

  2015cites this paper
• Computational Protein Design with Ensembles, Flexibility and Mathematical Guarantees, and its Application to Drug Resistance Prediction, and Antibody Design

  2015cites this paper
• Antibody engineering for increased potency, breadth and half-life

  2015cites this paper
• Amino acid interaction networks provide a new lens for therapeutic antibody discovery and anti-viral drug optimization.

  2015cites this paper
• Random mutagenesis of BoNT/E Hc nanobody to construct a secondary phage‐display library

  2014cites this paper
• Direct prediction of profiles of sequences compatible with a protein structure by neural networks with fragment‐based local and energy‐based nonlocal profiles

  2014cites this paper
• Affinity improvement of a therapeutic antibody to methamphetamine and amphetamine through structure-based antibody engineering

  2014cites this paper
• Structure-based non-canonical amino acid design to covalently crosslink an antibody-antigen complex.

  2014cites this paper
• Affinity Improvement of a Therapeutic Antibody by Structure-Based Computational Design: Generation of Electrostatic Interactions in the Transition State Stabilizes the Antibody-Antigen Complex

  2014cites this paper
• OptMAVEn – A New Framework for the de novo Design of Antibody Variable Region Models Targeting Specific Antigen Epitopes

  2014cites this paper
• PURE ribosome display and its application in antibody technology.

  2014cites this paper
• Pairwise decomposition of an MMGBSA energy function for computational protein design

  2014cites this paper
• Antibodies: Computer-Aided Prediction of Structure and Design of Function

  2014cites this paper