Junzhuo Liao
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View article: A Method for Treating Significant Conformational Changes in Alchemical Free Energy Simulations of Protein–Ligand Binding
A Method for Treating Significant Conformational Changes in Alchemical Free Energy Simulations of Protein–Ligand Binding Open
Relative binding free energy (RBFE) simulation is a rigorous approach to the calculation of quantitatively accurate binding free energy values for protein-ligand binding in which a reference binder is gradually converted to a target binder…
View article: Development of Phenyl‐substituted Isoindolinone‐ and Benzimidazole‐type Cereblon Ligands for Targeted Protein Degradation
Development of Phenyl‐substituted Isoindolinone‐ and Benzimidazole‐type Cereblon Ligands for Targeted Protein Degradation Open
Thalidomide, pomalidomide and lenalidomide, collectively referred to as immunomodulatory imide drugs (IMiDs), are frequently employed in proteolysis‐targeting chimeras (PROTACs) as cereblon (CRBN) E3 ligase‐recruiting ligands. However, the…
View article: Free Energy Perturbation Calculations of Mutation Effects on SARS-CoV-2 RBD::ACE2 Binding Affinity
Free Energy Perturbation Calculations of Mutation Effects on SARS-CoV-2 RBD::ACE2 Binding Affinity Open
The strength of binding between human angiotensin converting enzyme 2 (ACE2) and the receptor binding domain (RBD) of viral spike protein plays a role in the transmissibility of the SARS-CoV-2 virus. In this study we focus on a subset of R…
View article: Development of Substituted Phenyl Dihydrouracil as the Novel Achiral Cereblon Ligands for Targeted Protein Degradation
Development of Substituted Phenyl Dihydrouracil as the Novel Achiral Cereblon Ligands for Targeted Protein Degradation Open
Glutarimides such as thalidomide, pomalidomide, and lenalidomide are the most frequently used ligands to recruit E3 ubiquitin ligase cereblon (CRBN) for the development of proteolysis-targeting chimeras (PROTACs). Due to the rapid and spon…
View article: In Silico Modeling and Scoring of PROTAC-Mediated Ternary Complex Poses
In Silico Modeling and Scoring of PROTAC-Mediated Ternary Complex Poses Open
Proteolysis targeting chimeras (PROTACs) are bifunctional molecules that induce ubiquitination and subsequent degradation of proteins via formation of ternary complexes between an E3 ubiquitin ligase and a target protein. Rational design o…
View article: Structures, Scripts and Outputs for In Silico Modeling and Scoring of PROTAC-Mediated Ternary Complex Poses
Structures, Scripts and Outputs for In Silico Modeling and Scoring of PROTAC-Mediated Ternary Complex Poses Open
The input structures, run and analysis scripts, and output files for the PROTAC modeling work as reported in the paper.
View article: Structures, Scripts and Outputs for In Silico Modeling and Scoring of PROTAC-Mediated Ternary Complex Poses
Structures, Scripts and Outputs for In Silico Modeling and Scoring of PROTAC-Mediated Ternary Complex Poses Open
The input structures, run and analysis scripts, and output files for the PROTAC modeling work as reported in the paper.
View article: In Silico Modeling and Scoring of PROTAC-Mediated Ternary Complex Poses
In Silico Modeling and Scoring of PROTAC-Mediated Ternary Complex Poses Open
Proteolysis targeting chimeras (PROTACs) are bifunctional molecules that can induce the ubiquitination of targeted proteins via the formation of ternary complexes between an E3 ubiquitin ligase and a target protein. The poly-ubiquitinated …
View article: In Silico Modeling and Scoring of PROTAC-Mediated Ternary Complex Poses
In Silico Modeling and Scoring of PROTAC-Mediated Ternary Complex Poses Open
Proteolysis targeting chimeras (PROTACs) are bifunctional molecules that can induce the ubiquitination of targeted proteins via the formation of ternary complexes between an E3 ubiquitin ligase and a target protein. The poly-ubiquitinated …
View article: Dataset for MD and MM/GBSA-Based Evalulation of Ternary Complexes Induced by Proteolysis Targeting Chimeras (PROTACs) for Targeted Protein Degradation
Dataset for MD and MM/GBSA-Based Evalulation of Ternary Complexes Induced by Proteolysis Targeting Chimeras (PROTACs) for Targeted Protein Degradation Open
This is the dataset for all input files, output files/results, and submit script or its templates for running the MD and MMGBSA calculations in the paper. Four compressed archives represent the 4 systems we ran our simulations on. The gene…
View article: Dataset for MD and MM/GBSA-Based Evalulation of Ternary Complexes Induced by Proteolysis Targeting Chimeras (PROTACs) for Targeted Protein Degradation
Dataset for MD and MM/GBSA-Based Evalulation of Ternary Complexes Induced by Proteolysis Targeting Chimeras (PROTACs) for Targeted Protein Degradation Open
This is the dataset for all input files, output files/results, and submit script or its templates for running the MD and MMGBSA calculations in the paper. Four compressed archives represent the 4 systems we ran our simulations on. The gene…