Machine learning for functional protein design
Recent breakthroughs in AI coupled with the rapid accumulation of protein sequence and
structure data have radically transformed computational protein design. New methods …
structure data have radically transformed computational protein design. New methods …
Adaptive immune receptor repertoire analysis
B cell and T cell receptor repertoires compose the adaptive immune receptor repertoire
(AIRR) of an individual. The AIRR is a unique collection of antigen-specific receptors that …
(AIRR) of an individual. The AIRR is a unique collection of antigen-specific receptors that …
MBE: model-based enrichment estimation and prediction for differential sequencing data
A Busia, J Listgarten - Genome Biology, 2023 - Springer
Characterizing differences in sequences between two conditions, such as with and without
drug exposure, using high-throughput sequencing data is a prevalent problem involving …
drug exposure, using high-throughput sequencing data is a prevalent problem involving …
Investigating the volume and diversity of data needed for generalizable antibody-antigen∆∆ G prediction
Antibody-antigen binding affinity lies at the heart of therapeutic antibody development:
efficacy is guided by specific binding and control of affinity. Here we present Graphinity, an …
efficacy is guided by specific binding and control of affinity. Here we present Graphinity, an …
[HTML][HTML] Accelerating therapeutic protein design with computational approaches toward the clinical stage
Therapeutic protein, represented by antibodies, is of increasing interest in human medicine.
However, clinical translation of therapeutic protein is still largely hindered by different …
However, clinical translation of therapeutic protein is still largely hindered by different …
Biochemical and biophysical characterization of natural polyreactivity in antibodies
To become specialized binders, antibodies undergo a process called affinity maturation to
maximize their binding affinity. Despite this process, some antibodies retain low-affinity …
maximize their binding affinity. Despite this process, some antibodies retain low-affinity …
Reduction of monoclonal antibody viscosity using interpretable machine learning
Early identification of antibody candidates with drug-like properties is essential for
simplifying the development of safe and effective antibody therapeutics. For subcutaneous …
simplifying the development of safe and effective antibody therapeutics. For subcutaneous …
Biophysical cartography of the native and human-engineered antibody landscapes quantifies the plasticity of antibody developability
Designing effective monoclonal antibody (mAb) therapeutics faces a multi-parameter
optimization challenge known as “developability”, which reflects an antibody's ability to …
optimization challenge known as “developability”, which reflects an antibody's ability to …
Prediction of polyreactive and nonspecific single-chain fragment variables through structural biochemical features and protein language-based descriptors
Background Monoclonal antibodies (mAbs) have been used as therapeutic agents, which
must overcome many developability issues after the discovery from in vitro display libraries …
must overcome many developability issues after the discovery from in vitro display libraries …
Developability considerations for bispecific and multispecific antibodies
Bispecific antibodies (bsAb) and multispecific antibodies (msAb) encompass a diverse
variety of formats that can concurrently bind multiple epitopes, unlocking mechanisms to …
variety of formats that can concurrently bind multiple epitopes, unlocking mechanisms to …