A5015244397- Monoclonal and Polyclonal Antibodies Research
- Glycosylation and Glycoproteins Research
- vaccines and immunoinformatics approaches
- Protein purification and stability
- Biosimilars and Bioanalytical Methods
- T-cell and B-cell Immunology
- RNA and protein synthesis mechanisms
- Advanced Proteomics Techniques and Applications
- Lung Cancer Research Studies
- Viral Infectious Diseases and Gene Expression in Insects
- Multiple and Secondary Primary Cancers
- Lung Cancer Treatments and Mutations
- Mass Spectrometry Techniques and Applications
- Metabolomics and Mass Spectrometry Studies
- Protein Structure and Dynamics
- Neuroendocrine Tumor Research Advances
- Biochemical and Structural Characterization
- Chronic Lymphocytic Leukemia Research
- SARS-CoV-2 and COVID-19 Research
- Colorectal Cancer Treatments and Studies
- Microbial Metabolic Engineering and Bioproduction
- Peptidase Inhibition and Analysis
- Cancer Treatment and Pharmacology
- Biomedical Text Mining and Ontologies
- Advanced Biosensing Techniques and Applications
University of Southern Denmark
2021-2024
Social Neuroscience Lab
2021
University of Oxford
2013-2019
Science Oxford
2015-2017
Kingston University
2015
Kingston University
2015
UCB Pharma (United Kingdom)
2013-2014
Chinese Academy of Sciences
2014
Shanghai Institute of Applied Physics
2014
Roche (United Kingdom)
2013
Structural antibody database (SAbDab; http://opig.stats.ox.ac.uk/webapps/sabdab) is an online resource containing all the publicly available structures annotated and presented in a consistent fashion. The data are with several properties including experimental information, gene details, correct heavy light chain pairings, antigen details and, where available, antibody-antigen binding affinity. user can select structures, according to these attributes as well structural such complementarity...
Therapeutic mAbs must not only bind to their target but also be free from "developability issues" such as poor stability or high levels of aggregation. While small-molecule drug discovery benefits Lipinski's rule five guide the selection molecules with appropriate biophysical properties, there is currently no in silico analog for antibody design. Here, we model variable domain structures a large set post-phase-I clinical-stage therapeutics (CSTs) and calculate metrics estimate typical...
Abs are immune system proteins that recognize noxious molecules for elimination. Their sequence diversity and binding versatility have made the primary class of biopharmaceuticals. Recently, it has become possible to query their immense natural using next-generation sequencing Ig gene repertoires (Ig-seq). However, Ig-seq outputs currently fragmented across repositories tend be presented as raw nucleotide reads, which means nontrivial effort is required reuse data analysis. To address this...
SAbPred is a server that makes predictions of the properties antibodies focusing on their structures. Antibody informatics tools can help improve our understanding immune responses to disease and aid in design engineering therapeutic molecules. single platform containing multiple applications which can: number align sequences; automatically generate antibody variable fragment homology models; annotate such models with estimated accuracy alongside sequence structural including potential...
Motivation: Antibodies are currently the most important class of biopharmaceuticals. Development such antibody-based drugs depends on costly and time-consuming screening campaigns. Computational techniques as antibody–antigen docking hold potential to facilitate process by rapidly providing a list initial poses that approximate native complex. Results: We have developed new method identify epitope region antigen, given structures antibody antigen—EpiPred. The combines conformational matching...
The Structural T-cell Receptor Database (STCRDab; http://opig.stats.ox.ac.uk/webapps/stcrdab) is an online resource that automatically collects and curates TCR structural data from the Protein Data Bank. For each entry, database provides annotations, such as α/β or γ/δ chain pairings, major histocompatibility complex details, where available, antigen binding affinities. In addition, orientation between variable domains canonical forms of complementarity-determining region loops are also...
Nanobodies are a subclass of immunoglobulins, whose binding site consists only one peptide chain, bestowing favorable biophysical properties. Recently, the first nanobody therapy was approved, paving way for further clinical applications this antibody format. Further development nanobody-based therapeutics could be streamlined by computational methods. One such methods is infilling-positional prediction biologically feasible mutations in nanobodies. Being able to identify possible positional...
Antibodies are a class of proteins indispensable for the vertebrate immune system. The general architecture all antibodies is very similar, but they contain hypervariable region which allows millions antibody variants to exist, each can bind different molecules. This binding malleability means that an increasingly important category biopharmaceuticals and biomarkers. We present Antibody i-Patch, method annotates most likely residues be in contact with antigen. show our predictions correlate...
Antibody-based therapeutics must not undergo chemical modifications that would impair their efficacy or hinder developability. A commonly used technique to de-risk lead biotherapeutic candidates annotates liability motifs on sequence. By analyzing sequences from all major sources of data (therapeutics, patents, GenBank, literature, and next-generation sequencing outputs), we find almost antibodies contain an average 3–4 such in paratopes, irrespective the source dataset. This is line with...
Designing effective monoclonal antibody (mAb) therapeutics faces a multi-parameter optimization challenge known as "developability", which reflects an antibody's ability to progress through development stages based on its physicochemical properties. While natural antibodies may provide valuable guidance for mAb selection, we lack comprehensive understanding of developability parameter (DP) plasticity (redundancy, predictability, sensitivity) and how the DP landscapes human-engineered relate...
Nanobodies, a subclass of antibodies found in camelids, are versatile molecular binding scaffolds composed single polypeptide chain. The small size nanobodies bestows multiple therapeutic advantages (stability, tumor penetration) with the first approval 2018 cementing clinical viability this format. Structured data and sequence information will enable accelerated development nanobody-based therapeutics. Though nanobody structure deposited public domain at an accelerating pace, heterogeneity...
Abstract Nanobodies are a subclass of immunoglobulins, whose binding site consists only one peptide chain, bestowing favorable biophysical properties. Recently, the first nanobody therapy was approved, paving way for further clinical applications this antibody format. Further development nanobody-based therapeutics could be streamlined by computational methods. One such methods is infilling - positional prediction biologically feasible mutations in nanobodies. Being able to identify possible...
Antibodies are proteins produced by our immune system that have been harnessed as biotherapeutics. The discovery of antibody-based therapeutics relies on analyzing large volumes diverse sequences coming from phage display or animal immunizations. Identification suitable therapeutic candidates is achieved grouping the their similarity and subsequent selection a set antibodies for further tests. Such groupings typically created using sequence-similarity measures alone. Maximizing diversity in...
Every human possesses millions of distinct antibodies. It is now possible to analyze this diversity via Next Generation Sequencing Immunoglobulins Genes (Ig-seq). This technique produces large volume sequence snapshots B-cell receptors that are indicative the antibody repertoire. In paper we enrich these scale datasets with structural information. Enriching a its data allows better approximation many vital features, such as binding site and specificity. Here, describe Structural Annotation...
The patent literature should reflect the past 30 years of engineering efforts directed toward developing monoclonal antibody therapeutics. Such information is potentially valuable for rational design. Patents, however, are designed not to convey scientific knowledge, but provide legal protection. It obvious whether from documents, such as sequences, useful in conveying know-how, rather than a reference only. To assess utility data therapeutic engineering, we quantified amount sequences...
Recently it has become possible to query the great diversity of natural antibody repertoires using next-generation sequencing (NGS). These methods are capable producing millions sequences in a single experiment. Here we compare clinical-stage therapeutic antibodies ~1b from 60 independent studies Observed Antibody Space database, which includes NGS analysis immunoglobulin gene repertoires. Of 242 post-Phase 1 antibodies, found 16 with sequence identity matches 95% or better for both heavy...
Rational design of therapeutic antibodies can be improved by harnessing the natural sequence diversity these molecules. Our understanding has recently been greatly facilitated through deposition hundreds millions human antibody sequences in next-generation sequencing (NGS) repositories. Contrasting a query to naturally observed similar from NGS provide mutational roadmap for engineers designing biotherapeutics. Because sheer scale datasets, performing queries across them is computationally...