ArticlemAbs
Antibody CDR loops as ensembles in solution vs. canonical clusters from X-ray structures.
Article in mAbs. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
29 citing papers in PubMed.
- Tokenizing loops of antibodies.mAbs · 2026Article
- Article
- Paraplume: A fast and accurate antibody paratope prediction method provides insights into repertoire-scale binding dynamics.PLoS computational biology · 2026Article
- Article
- Structural trends in antibody-antigen binding interfaces: a computational analysis of 1833 experimentally determined 3D structures.Computational and structural biotechnology journal · 2024Article
- Structural basis for antibody recognition of the proximal MUC16 ectodomain.Journal of ovarian research · 2024Article
- Phage display assisted discovery of a pH-dependent anti-α-cobratoxin antibody from a natural variable domain library.Protein science : a publication of the Protein Society · 2023Article
- Structure and Dynamics Guiding Design of Antibody Therapeutics and Vaccines.Antibodies (Basel, Switzerland) · 2023Review
- Article
- Structural mechanism of Fab domain dissociation as a measure of interface stability.Journal of computer-aided molecular design · 2023Article
- Embedding Dynamics in Intrinsic Physicochemical Profiles of Market-Stage Antibody-Based Biotherapeutics.Molecular pharmaceutics · 2023Article
- Specific attributes of the VFrontiers in immunology · 2023Article
- Higher Affinity Antibodies Bind With Lower Hydration and Flexibility in Large Scale Simulations.Frontiers in immunology · 2022Article
- Comparison of hydrophobicity scales for predicting biophysical properties of antibodies.Frontiers in molecular biosciences · 2022Article
- The influence of antibody humanization on shark variable domain (VNAR) binding site ensembles.Frontiers in immunology · 2022Article
- Communication pathways bridge local and global conformations in an IgG4 antibody.Scientific reports · 2021Article
- Conformational Ensembles of Antibodies Determine Their Hydrophobicity.Biophysical journal · 2021Article
- Shark Antibody Variable Domains Rigidify Upon Affinity Maturation-Understanding the Potential of Shark Immunoglobulins as Therapeutics.Frontiers in molecular biosciences · 2021Article
- Production and characterization of antibody against Opisthorchis viverrini via phage display and molecular simulation.PloS one · 2021Article
- Germline-Dependent Antibody Paratope States and Pairing Specific VFrontiers in immunology · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In the past decade, the relevance of antibodies as therapeutics has increased substantially. Therefore, structural and functional characterization, in particular of the complementarity-determining regions (CDRs), is crucial to the design and engineering of antibodies with unique binding properties. Various studies have focused on classifying the CDR loops into a small set of main-chain conformations to facilitate antibody design by assuming that certain sequences can only adopt a limited number of conformations. Here, we present a kinetic classification of CDR loop structures as ensembles in solution. Using molecular dynamics simulations in combination with strong experimental structural information, we observe conformational transitions between canonical clusters and additional dominant solution structures in the micro-to-millisecond timescale for all CDR loops, independent of length and sequence composition. Besides identifying all relevant conformations in solution, our results revealed that various canonical cluster medians actually belong to the same kinetic minimum. Additionally, we reconstruct the kinetics and probabilities of the conformational transitions between canonical clusters, and thereby extend the model of static canonical structures to reveal a dynamic conformational ensemble in solution as a new paradigm in the field of antibody structure design.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.