Chinh Tran-To Su
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View article: Epi4Ab: a data-driven prediction model of conformational epitopes for specific antibody VH/VL families and CDRs sequences
Epi4Ab: a data-driven prediction model of conformational epitopes for specific antibody VH/VL families and CDRs sequences Open
Antibodies recognize antigens via complementary and structurally dependent mechanisms. Therefore, inclusion of antibody inputs is crucial for accurate epitope prediction. Given the limited availability of antibody-antigen complex structure…
View article: Epi4Ab: A data-driven prediction model of conformational epitopes for specific antibody VH/VL families and CDR H3/L1 sequences
Epi4Ab: A data-driven prediction model of conformational epitopes for specific antibody VH/VL families and CDR H3/L1 sequences Open
Antibodies recognize antigens via complementary and structurally dependent mechanisms. Therefore, inclusion of antibody inputs is crucial for accurate epitope prediction. Given limited availability of antibody-antigen complex structures, i…
View article: Gene Identification for Phototropin-dependent Photoprotection in Chlamydomonas Reinhardtii
Gene Identification for Phototropin-dependent Photoprotection in Chlamydomonas Reinhardtii Open
Photosynthetic organisms convert solar energy into chemical energy through photosynthesis, generating carbohydrates and lipids that are valuable for biofuels. Algae, renowned for their rapid growth and efficiency, have developed mechanisms…
View article: epiTCR-KDA: Knowledge Distillation model on Dihedral Angles for TCR-peptide prediction
epiTCR-KDA: Knowledge Distillation model on Dihedral Angles for TCR-peptide prediction Open
Motivation: Antigen recognition by T-cell receptors (TCRs) triggers cascades of immune responses. Successful predictions of the TCR and antigen (as peptide) bindings therefore signify the advancements in immunotherapy. However, most of cur…
View article: Targeting the GPI transamidase subunit GPAA1 abrogates the CD24 immune checkpoint in ovarian cancer
Targeting the GPI transamidase subunit GPAA1 abrogates the CD24 immune checkpoint in ovarian cancer Open
CD24 is frequently overexpressed in ovarian cancer and promotes immune evasion by interacting with its receptor Siglec10, present on tumor-associated macrophages, providing a "don't eat me" signal that prevents targeting and phagocytosis b…
View article: epiTCR-KDA: knowledge distillation model on dihedral angles for TCR-peptide prediction
epiTCR-KDA: knowledge distillation model on dihedral angles for TCR-peptide prediction Open
Motivation The prediction of the T-cell receptor (TCR) and antigen bindings is crucial for advancements in immunotherapy. However, most current TCR-peptide interaction predictors struggle to perform well on unseen data. This limitation may…
View article: Inhibiting the GPI Transamidase Subunit GPAA1 Abolishes CD24 Surface Localization and Enhances Macrophage-Mediated Phagocytosis of Ovarian Cancer Cells
Inhibiting the GPI Transamidase Subunit GPAA1 Abolishes CD24 Surface Localization and Enhances Macrophage-Mediated Phagocytosis of Ovarian Cancer Cells Open
SUMMARY The CD24-Siglec10 signaling axis is an immune checkpoint pathway that shields ovarian cancer cells from phagocytosis by tumor-associated macrophages (TAMs), making it an appealing immunotherapeutic target. Here, we investigate fact…
View article: Engaging the ‘A’ Class Antibody: Variable-Heavy (VH) region influencing IgA1&2 engagement of FcαRI and superantigen proteins G, A, and L
Engaging the ‘A’ Class Antibody: Variable-Heavy (VH) region influencing IgA1&2 engagement of FcαRI and superantigen proteins G, A, and L Open
Interest in IgA as an alternative therapeutic and diagnostic antibody has increased over the years, yet much remains to be investigated especially given their importance in activating immune cells in blood and in mucosal immunity. Recent w…
View article: Molecular Insights of Nickel Binding to Therapeutic Antibodies as a Possible New Antibody Superantigen
Molecular Insights of Nickel Binding to Therapeutic Antibodies as a Possible New Antibody Superantigen Open
The binding of nickel by immune proteins can manifest as Type IV contact dermatitis (Ni-specific T cells mediated) and less frequently as Type I hypersensitivity with both mechanisms remaining unknown to date. Since there are reports of pa…
View article: An Alternative HIV-1 Non-Nucleoside Reverse Transcriptase Inhibition Mechanism: Targeting the p51 Subunit
An Alternative HIV-1 Non-Nucleoside Reverse Transcriptase Inhibition Mechanism: Targeting the p51 Subunit Open
The ongoing development of drug resistance in HIV continues to push for the need of alternative drug targets in inhibiting HIV. One such target is the Reverse transcriptase (RT) enzyme which is unique and critical in the viral life cycle—a…
View article: Essentially Leading Antibody Production: An Investigation of Amino Acids, Myeloma, and Natural V-Region Signal Peptides in Producing Pertuzumab and Trastuzumab Variants
Essentially Leading Antibody Production: An Investigation of Amino Acids, Myeloma, and Natural V-Region Signal Peptides in Producing Pertuzumab and Trastuzumab Variants Open
Boosting the production of recombinant therapeutic antibodies is crucial in both academic and industry settings. In this work, we investigated the usage of varying signal peptides by antibody V-genes and their roles in recombinant transien…
View article: Essentially leading antibody production: An investigation of amino acids, myeloma and natural V-region signal peptides in producing Pertuzumab and Trastuzumab variants
Essentially leading antibody production: An investigation of amino acids, myeloma and natural V-region signal peptides in producing Pertuzumab and Trastuzumab variants Open
Boosting the production of recombinant therapeutic antibodies is crucial in both academic and industry settings. In this work, we investigated the usage of varying signal peptides by antibody genes and their roles in recombinant transient …
View article: Signal Peptides and Essential Amino Acids in Antibody Production
Signal Peptides and Essential Amino Acids in Antibody Production Open
Summary Boosting the production of recombinant therapeutic antibodies is crucial in both academic and industry settings. In this work, we investigated the usage of varying signal peptides by antibody genes and their roles in recombinant t…
View article: Antibody Signal peptides and essential amino acid counts on recombinant antibody production
Antibody Signal peptides and essential amino acid counts on recombinant antibody production Open
SummaryBoosting the production of recombinant therapeutic antibodies is crucial in both academic and industry settings. In this work, we investigated the usage of varying signal peptides by antibody genes and their roles in recombinant tra…
View article: Molecular insight into Nickel(II) binding by Her2-specific IgE: a possible mechanistic insight into the pathogenesis of Type I nickel hypersensitivity
Molecular insight into Nickel(II) binding by Her2-specific IgE: a possible mechanistic insight into the pathogenesis of Type I nickel hypersensitivity Open
SUMMARY Nickel (Ni) allergy has been reported in contact dermatitis Type IV (Ni-specific T cells mediated) and asthmatic Type I (IgE-mediated) hypersensitivities. Associations between the two hypersensitivities have been found in some pati…
View article: Structural Modelling of the Lumenal Domain of Human GPAA1, the Metallo-Peptide Synthetase Subunit of the Transamidase Complex, Reveals Zinc-Binding Mode and Two Flaps Surrounding the Active Site
Structural Modelling of the Lumenal Domain of Human GPAA1, the Metallo-Peptide Synthetase Subunit of the Transamidase Complex, Reveals Zinc-Binding Mode and Two Flaps Surrounding the Active Site Open
Background The transamidase complex is a molecular machine in the endoplasmic reticulum of eukaryotes that attaches a glycosylphosphatidylinositol (GPI) lipid anchor to substrate proteins after cleaving a C-terminal propeptide with a defin…
View article: The Determination of HIV-1 RT Mutation Rate, Its Possible Allosteric Effects, and Its Implications on Drug Resistance
The Determination of HIV-1 RT Mutation Rate, Its Possible Allosteric Effects, and Its Implications on Drug Resistance Open
The high mutation rate of the human immunodeficiency virus type 1 (HIV-1) plays a major role in treatment resistance, from the development of vaccines to therapeutic drugs. In addressing the crux of the issue, various attempts to estimate …
View article: The Determination of HIV-1 RT Mutation Rate, Its Possible Allosteric Effects, and Its Implications on Drug Resistance
The Determination of HIV-1 RT Mutation Rate, Its Possible Allosteric Effects, and Its Implications on Drug Resistance Open
The high mutation rate of human immunodeficiency virus type 1 (HIV-1) plays a major role in treatment resistance from the development of vaccines to long-lasting drugs. In addressing the crux of the issue, various attempts to estimate the …
View article: Additional file 8 of Structural modelling of the lumenal domain of human GPAA1, the metallo-peptide synthetase subunit of the transamidase complex, reveals zinc-binding mode and two flaps surrounding the active site
Additional file 8 of Structural modelling of the lumenal domain of human GPAA1, the metallo-peptide synthetase subunit of the transamidase complex, reveals zinc-binding mode and two flaps surrounding the active site Open
Additional file 8: File S2. GPAA1_Zn1Zn2_PEP.pdb - atomic structure coordinates for GPAA1Zn1Zn2.
View article: Additional file 7 of Structural modelling of the lumenal domain of human GPAA1, the metallo-peptide synthetase subunit of the transamidase complex, reveals zinc-binding mode and two flaps surrounding the active site
Additional file 7 of Structural modelling of the lumenal domain of human GPAA1, the metallo-peptide synthetase subunit of the transamidase complex, reveals zinc-binding mode and two flaps surrounding the active site Open
Additional file 7: File S1. GPAA1_Zn_PEP.pdb - atomic structure coordinates for GPAA1Zn.
View article: Additional file 6 of Structural modelling of the lumenal domain of human GPAA1, the metallo-peptide synthetase subunit of the transamidase complex, reveals zinc-binding mode and two flaps surrounding the active site
Additional file 6 of Structural modelling of the lumenal domain of human GPAA1, the metallo-peptide synthetase subunit of the transamidase complex, reveals zinc-binding mode and two flaps surrounding the active site Open
Additional file 6: Table S1. Summary of known M28 family 3D structures. Summary of 145 structures of M28 protein family, including 2 Zn-bound aminopeptidase and carboxypeptidase, and 1 Zn-bound cyclotransferase structures, tabulating the c…
View article: Reviewing HIV-1 Gag Mutations in Protease Inhibitors Resistance: Insights for Possible Novel Gag Inhibitor Designs
Reviewing HIV-1 Gag Mutations in Protease Inhibitors Resistance: Insights for Possible Novel Gag Inhibitor Designs Open
HIV protease inhibitors against the viral protease are often hampered by drug resistance mutations in protease and in the viral substrate Gag. To overcome this drug resistance and inhibit viral maturation, targeting Gag alongside protease …
View article: Reviewing HIV-1 Gag Mutations in Protease Inhibitors Resistance: Insights for Possible Novel Gag Inhibitor Designs
Reviewing HIV-1 Gag Mutations in Protease Inhibitors Resistance: Insights for Possible Novel Gag Inhibitor Designs Open
HIV treatment strategies against viral enzymes are continuously hampered by viral drug resistance. Recent findings show that viral substrate Gag contributes to HIV-1 Protease Inhibitor (PI) resistance, leading to demands for new strategies…
View article: Perspective: The promises of a holistic view of proteins—impact on antibody engineering and drug discovery
Perspective: The promises of a holistic view of proteins—impact on antibody engineering and drug discovery Open
The reductionist approach is prevalent in biomedical science. However, increasing evidence now shows that biological systems cannot be simply considered as the sum of its parts. With experimental, technological, and computational advances,…
View article: Allosteric Effects between the Antibody Constant and Variable Regions: A Study of IgA Fc Mutations on Antigen Binding
Allosteric Effects between the Antibody Constant and Variable Regions: A Study of IgA Fc Mutations on Antigen Binding Open
Therapeutic antibodies have shifted the paradigm of disease treatments from small molecules to biologics, especially in cancer therapy. Despite the increasing number of antibody candidates, much remains unknown about the antibody and how i…
View article: Allosteric Effects between the Antibody Constant and Variable Regions: A Study of IgA Fc Mutations on Antigen Binding
Allosteric Effects between the Antibody Constant and Variable Regions: A Study of IgA Fc Mutations on Antigen Binding Open
Therapeutics antibodies have increasingly shifted the paradigm of disease treatments, from small molecules to biologics, especially in cancer therapy. Despite the increasing number of antibody candidates, much remains unknown about the ant…
View article: A computational study for rational HIV-1 non-nucleoside reverse transcriptase inhibitor selection and the discovery of novel allosteric pockets for inhibitor design
A computational study for rational HIV-1 non-nucleoside reverse transcriptase inhibitor selection and the discovery of novel allosteric pockets for inhibitor design Open
HIV drug resistant mutations that render the current Highly Active Anti-Retroviral Therapy (HAART) cocktail drugs ineffective are increasingly reported. To study the mechanisms of these mutations in conferring drug resistance, we computati…