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View article: Prediction of Antibody Non-Specificity using Protein Language Models and Biophysical Parameters
Prediction of Antibody Non-Specificity using Protein Language Models and Biophysical Parameters Open
The development of therapeutic antibodies requires optimizing target binding affinity and pharmacodynamics, while ensuring high developability potential, including minimizing non-specific binding. In this study, we address this problem by …
View article: Molecular Representations in Machine-Learning-Based Prediction of PK Parameters for Insulin Analogs
Molecular Representations in Machine-Learning-Based Prediction of PK Parameters for Insulin Analogs Open
Therapeutic peptides and proteins derived from either endogenous hormones, such as insulin, or de novo design via display technologies occupy a distinct pharmaceutical space in between small molecules and large proteins such as antibodies.…
View article: Modeling conformational flexibility of kinases in inactive states
Modeling conformational flexibility of kinases in inactive states Open
Kinase structures in the inactive “DFG‐out” state provide a wealth of druggable binding site variants. The conformational plasticity of this state can be mainly described by different conformations of binding site‐forming elements such as …
View article: From Cancer to Pain Target by Automated Selectivity Inversion of a Clinical Candidate
From Cancer to Pain Target by Automated Selectivity Inversion of a Clinical Candidate Open
Elimination of inadvertent binding is crucial for inhibitor design targeting conserved protein classes like kinases. Compounds in clinical trials provide a rich source for initiating drug design efforts by exploiting such secondary binding…
View article: Mol2vec: Unsupervised Machine Learning Approach with Chemical Intuition
Mol2vec: Unsupervised Machine Learning Approach with Chemical Intuition Open
Inspired by natural\nlanguage processing techniques, we here introduce\nMol2vec, which is an unsupervised machine learning approach to learn\nvector representations of molecular substructures. Like the Word2vec\nmodels, where vectors of cl…
View article: Mol2vec: Unsupervised Machine Learning Approach with Chemical Intuition
Mol2vec: Unsupervised Machine Learning Approach with Chemical Intuition Open
Inspired by natural language processing techniques we here introduce Mol2vec which is an unsupervised machine learning approach to learn vector representations of molecular substructures. Similarly, to the Word2vec models where vectors of …
View article: Kinome‐Wide Profiling Prediction of Small Molecules
Kinome‐Wide Profiling Prediction of Small Molecules Open
Extensive kinase profiling data, covering more than half of the human kinome, are available nowadays and allow the construction of activity prediction models of high practical utility. Proteochemometric (PCM) approaches use compound and pr…
View article: Additional file 1: of KinMap: a web-based tool for interactive navigation through human kinome data
Additional file 1: of KinMap: a web-based tool for interactive navigation through human kinome data Open
(KinMap_Examples.zip) contains the input CSV files used to generate the annotated kinome trees in Fig. 1 (Example_1_Erlotinib_NSCLC.csv), Fig. 2a (Example_2_Sunitinib_Sorafenib_Cancer.csv), and Fig. 2b (Example_3_Kinase_Stats.csv). (ZIP 5 …
View article: Putative histidine kinase inhibitors with antibacterial effect against multi-drug resistant clinical isolates identified by in vitro and in silico screens
Putative histidine kinase inhibitors with antibacterial effect against multi-drug resistant clinical isolates identified by in vitro and in silico screens Open
Novel antibacterials are urgently needed to address the growing problem of bacterial resistance to conventional antibiotics. Two-component systems (TCS) are widely used by bacteria to regulate gene expression in response to various environ…
View article: Complex long-distance effects of mutations that confer linezolid resistance in the large ribosomal subunit
Complex long-distance effects of mutations that confer linezolid resistance in the large ribosomal subunit Open
The emergence of multidrug-resistant pathogens will make current antibiotics ineffective. For linezolid, a member of the novel oxazolidinone class of antibiotics, 10 nucleotide mutations in the ribosome have been described conferring resis…