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A representation of the CDR definition based on different numbering schemes...
Published: 01 April 2025
Figure 5
A representation of the CDR definition based on different numbering schemes. The 2D map of the residues in the CDR loops are defined based on the Kabat, Chothia, and AbM numbering scheme respectively. The number in the box represents the residue number based on the Kabat numbering schemes. Several
Journal Article
Antibody numbering schemes: advances, comparisons and tools for antibody engineering
Protein Engineering, Design and Selection, Volume 38, 2025, gzaf005, https://doi.org/10.1093/protein/gzaf005
Published: 01 April 2025
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The structural alignments of the CDRs based on different numbering schemes....
Published: 01 April 2025
Figure 2
The structural alignments of the CDRs based on different numbering schemes. (Upper) The structure of the HCDR1 loop of a Fab structure (PDB: 4NYL) defined based on the Kabat, IMGT and AbM numbering schemes respectively. (Lower) The structure of the HCDR2 loop of a Fab structure (PDB: 4NYL) define
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The structural alignments of the LCDR2 defined by different numbering schem...
Published: 01 April 2025
Figure 3
The structural alignments of the LCDR2 defined by different numbering schemes. The structure of the LCDR2 loop of a Fab structure (PDB: 4NYL) defined based on the IMGT, Kabat, Chothia and AbM numbering scheme respectively. The framework and HCDR loops are visually distinguished in the structure: HC
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Structure of the Variable Light Domain Based on the Gelfand Numbering Schem...
Published: 01 April 2025
Figure 6
Structure of the Variable Light Domain Based on the Gelfand Numbering Scheme. The structure of the variable light domain from a Fab (PDB: 4NYL) is shown, with the domain defined according to the Gelfand numbering scheme. Two structural perspectives are shown: the outer β-sheet ( Left ) and the inne
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Consensus Structure and Main-Chain Hydrogen Bonding Pattern of Immunoglobul...
Published: 01 April 2025
Figure 7
Consensus Structure and Main-Chain Hydrogen Bonding Pattern of Immunoglobulin Variable Domains. Residues are numbered according to the AHo numbering scheme. Arrows indicate hydrogen bonds that are conserved across the majority of immunoglobulin variable domain structures. Regions corresponding to l
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Graphical Abstract Created with BioRender.com
Published: 01 April 2025
Graphical Abstract
Graphical Abstract Created with BioRender.com
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Structures of antibody and antibody fragments. The structure of a typical ...
Published: 01 April 2025
Figure 1
Structures of antibody and antibody fragments. The structure of a typical IgG molecule with four polypeptide chains joined by disulfide bonds. The four polypeptide chains consist of two heavy chains (denoted by subscript H) and two light chains (denoted by subscript L). Each heavy chain is composed
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A representation of the CDR definition based on different numbering schemes...
Published: 01 April 2025
Figure 4
A representation of the CDR definition based on different numbering schemes. The 2D map of the residues in the CDR loops are defined based on the IMGT, Kabat, Chothia, and Consensus Chothia (CC) numbering schemes respectively. The number in the box represents the residue number based on the Kabat n
Journal Article
CDRxAbs: antibody small-molecule conjugates with computationally designed target-binding synergy Get access
Protein Engineering, Design and Selection, Volume 38, 2025, gzaf004, https://doi.org/10.1093/protein/gzaf004
Published: 21 March 2025
Includes: Multimedia
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Computationally-designed nanobody-biotin conjugates. (A) Schematic represen... Get access
Published: 21 March 2025
Figure 1
Computationally-designed nanobody-biotin conjugates. (A) Schematic representation of workflow. (B) Final model of 4NBX.B-biotin103 in complex with mSA WT streptavidin. mSA WT shown in green (left side of figures); nanobody shown in cyan (right side of figures); Biotin103 side chain shown as stick.
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Framework design for reduced aggregation. (A) SEC traces normalized by mono... Get access
Published: 21 March 2025
Figure 3
Framework design for reduced aggregation. (A) SEC traces normalized by monomer peak height of 4NBX.B-biotin103 (biological triplicates – blue traces) and 4NBX.B WT (orange trace) (top panel), v119 (second panel), v149 (third panel), v186 (fourth panel) and v186_Fr (bottom panel). ‘*’ indicates instr
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Summary of results and design workflow. (A and B) Summary of SPR determined... Get access
Published: 21 March 2025
Figure 5
Summary of results and design workflow. (A and B) Summary of SPR determined binding affinities and kinetic parameters for the various complexes studied in this report. Setups for the SPR binding experiments are depicted by the cartoon above the lanes Individual data points are from biological tripli
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Design models and SPR binding for CDR sequence designs v119 and v149. (A) v... Get access
Published: 21 March 2025
Figure 2
Design models and SPR binding for CDR sequence designs v119 and v149. (A) v119 design showing potential inter-protein hydrogen bonds (left and middle -- mSA WT , green (bottom of figures); v119, cyan (top of figures); Biotin103 thick sticks) and SPR measurement of v119/mSA WT binding (right). (B) v
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MD simulation analysis of various models. (A) Solvent accessible surface ar... Get access
Published: 21 March 2025
Figure 4
MD simulation analysis of various models. (A) Solvent accessible surface area distribution from 100 ns MD simulations for two hydrophobic residue clusters shown as red spheres in the left and right panels. Data for v186 shown in blue; data for v186_Fr shown in red. (B) Analysis of CA backbone RMSD t
Journal Article
Tuning ProteinMPNN to reduce protein visibility via MHC Class I through direct preference optimization
Protein Engineering, Design and Selection, Volume 38, 2025, gzaf003, https://doi.org/10.1093/protein/gzaf003
Published: 18 March 2025
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Stable designs with reduced isoelectric point: this figure depicts the same...
Published: 18 March 2025
Figure 5
Stable designs with reduced isoelectric point: this figure depicts the same information as Fig. 4 , but focusing only on 1M40 .
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Trade-off between visibility and structural validity on validation data: ea...
Published: 18 March 2025
Figure 1
Trade-off between visibility and structural validity on validation data: each data-point in these two plots represents a checkpoint. The red one is the original ProteinMPNN network. The blue ones represent checkpoints that were created during the hyper-parameter search (after 2, 10, and 20 epochs)
