ArticleProtein engineering, design & selection : PEDS2016
Revisiting antibody modeling assessment for CDR-H3 loop.
Article in Protein engineering, design & selection : PEDS, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- AI-Driven Design Platforms of Next-Generation Antibody Therapeutics.Topics in current chemistry (Cham) · 2026Review
- Feasibility of Combining Biomolecular Conformational Sampling Techniques for Molecular Dynamics Simulation.Journal of computational chemistry · 2025Article
- Binding Mechanism of Riboswitch to Natural Ligand Elucidated by McMD-Based Dynamic Docking Simulations.ACS omega · 2024Article
- Structure and Dynamics Guiding Design of Antibody Therapeutics and Vaccines.Antibodies (Basel, Switzerland) · 2023Review
- Elucidation of binding mechanism, affinity, and complex structure between mWT1 tumor-associated antigen peptide and HLA-A*24:02.Protein science : a publication of the Protein Society · 2023Article
- Mutual induced-fit mechanism drives binding between intrinsically disordered Bim and cryptic binding site of Bcl-xL.Communications biology · 2023Article
- Embedding Dynamics in Intrinsic Physicochemical Profiles of Market-Stage Antibody-Based Biotherapeutics.Molecular pharmaceutics · 2023Article
- Structural Considerations in Affinity Maturation of Antibody-Based Biotherapeutic Candidates.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Thermal Stability Estimation of Single Domain Antibodies Using Molecular Dynamics Simulations.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Non-Ewald methods for evaluating the electrostatic interactions of charge systems: similarity and difference.Biophysical reviews · 2022Review
- Quantum chemical studies on hydrogen bonds in helical secondary structures.Biophysical reviews · 2022Review
- Depolarizing Effects in Hydrogen Bond Energy in 3International journal of molecular sciences · 2022Article
- Cyclosporin A: Conformational Complexity and Chameleonicity.Journal of chemical information and modeling · 2021Article
- Cryptic-site binding mechanism of medium-sized Bcl-xL inhibiting compounds elucidated by McMD-based dynamic docking simulations.Scientific reports · 2021Article
- Elucidating Solution Structures of Cyclic Peptides Using Molecular Dynamics Simulations.Chemical reviews · 2021Review
- Methods for sequence and structural analysis of B and T cell receptor repertoires.Computational and structural biotechnology journal · 2020Review
- Hydrogen bond donors and acceptors are generally depolarized in α-helices as revealed by a molecular tailoring approach.Journal of computational chemistry · 2019Article
- Conformation and Permeability: Cyclic Hexapeptide Diastereomers.Journal of chemical information and modeling · 2019Article
- Thermal stability of single-domain antibodies estimated by molecular dynamics simulations.Protein science : a publication of the Protein Society · 2019Article
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3 authors.
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Abstract
The antigen-binding site of antibodies, also known as complementarity-determining region (CDR), has hypervariable sequence properties. In particular, the third CDR loop of the heavy chain, CDR-H3, has such variability in its sequence, length, and conformation that ordinary modeling techniques cannot build a high-quality structure. At Stage 2 of the Second Antibody Modeling Assessment (AMA-II) held in 2013, the model structures of the CDR-H3 loops were submitted by the seven modelers and were critically assessed. After our participation in AMA-II, we rebuilt one of the long CDR-H3 loops with 13 residues (A52 antibody) by a more precise method, using enhanced conformational sampling with the explicit water model, as compared to our previous method employed at AMA-II. The current stable models obtained from the free energy landscape at 300 K include structures similar to the X-ray crystal structures. Those models were not built in our previous work at AMA-II. The current free energy landscape suggested that the CDR-H3 loop structures in the crystal are not stable in solution, but they are stabilized by the crystal packing effect.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.