Gideon Lapidoth
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View article: StabilizeIT: An Automated Workflow for Protein Stabilization
StabilizeIT: An Automated Workflow for Protein Stabilization Open
The industrial application of enzymes is often hampered by poor stability and low expression yields. While computational tools can predict stabilizing mutations, many are bound by restrictive licenses that hinder their broader adoption. To…
View article: Context-dependent design of induced-fit enzymes using deep learning generates well-expressed, thermally stable and active enzymes
Context-dependent design of induced-fit enzymes using deep learning generates well-expressed, thermally stable and active enzymes Open
The potential of engineered enzymes in industrial applications is often limited by their expression levels, thermal stability, and catalytic diversity. De novo enzyme design faces challenges due to the complexity of enzymatic catalysis. An…
View article: Context-Dependent Design of Induced-fit Enzymes using Deep Learning Generates Well Expressed, Thermally Stable and Active Enzymes
Context-Dependent Design of Induced-fit Enzymes using Deep Learning Generates Well Expressed, Thermally Stable and Active Enzymes Open
The potential of engineered enzymes in practical applications is often constrained by limitations in their expression levels, thermal stability, and the diversity and magnitude of catalytic activities. De-novo enzyme design, though excitin…
View article: <i>AbPredict 2</i>: a server for accurate and unstrained structure prediction of antibody variable domains
<i>AbPredict 2</i>: a server for accurate and unstrained structure prediction of antibody variable domains Open
Summary Methods for antibody structure prediction rely on sequence homology to experimentally determined structures. Resulting models may be accurate but are often stereochemically strained, limiting their usefulness in modeling and design…
View article: Highly active enzymes by automated combinatorial backbone assembly and sequence design
Highly active enzymes by automated combinatorial backbone assembly and sequence design Open
Automated design of enzymes with wild-type-like catalytic properties has been a long-standing but elusive goal. Here, we present a general, automated method for enzyme design through combinatorial backbone assembly. Starting from a set of …
View article: Principles for computational design of binding antibodies
Principles for computational design of binding antibodies Open
Significance Antibodies are the most versatile class of binding molecule known, and have numerous applications in biomedicine. Computational design of antibodies, however, poses unusual difficulties relative to previously designed proteins…
View article: Improved antibody-based ricin neutralization by affinity maturation is correlated with slower off-rate values
Improved antibody-based ricin neutralization by affinity maturation is correlated with slower off-rate values Open
While potent monoclonal antibodies against ricin were introduced over the years, the question whether increasing antibody affinity enables better toxin neutralization was not fully addressed yet. The aim of this study was to characterize t…
View article: High‐accuracy modeling of antibody structures by a search for minimum‐energy recombination of backbone fragments
High‐accuracy modeling of antibody structures by a search for minimum‐energy recombination of backbone fragments Open
Current methods for antibody structure prediction rely on sequence homology to known structures. Although this strategy often yields accurate predictions, models can be stereo‐chemically strained. Here, we present a fully automated algorit…
View article: <i>AbDesign</i>: An algorithm for combinatorial backbone design guided by natural conformations and sequences
<i>AbDesign</i>: An algorithm for combinatorial backbone design guided by natural conformations and sequences Open
Computational design of protein function has made substantial progress, generating new enzymes, binders, inhibitors, and nanomaterials not previously seen in nature. However, the ability to design new protein backbones for function--essent…