Dr. Masha Niv

The lab

Our lab uses and develops structural bioinformatics techniques. Our goal is to study how protein structure, function and dynamics, as well as protein/protein and protein/ligand interactions mediate cell signaling. We aim to provide insights for rational modulation of biological function and to facilitate innovative in-silico drug design.

Research interests

Bitter taste: molecules, receptors and recognition.
Activation, specificity and dynamics of GPCRs.
Protein kinases: conformational dynamics, molecular recognition, inhibitors design.
Structure, function and flexible docking of peptides and peptidomimetics.

Courses

• Bioinformatics And Structural Biochemistry, 71437
• Methodology of Sensory evaluation of Food, 71451
• Principals in Toxicology and Pharmacology, 71478

Electronic Resources

• BitterDB, a database of bitter compounds http://bitterdb.agri.huji.ac.il/bitterdb
  Ayana Wiener, Marina Shudler, Anat Levit and Masha Y. Niv, accepted in NAR database issue.
• Summary of activation changes in GPCRs http://physiology.med.cornell.edu/GPCRactivation/gpcrindex.html
  Cite: Masha Y. Niv, Lucy Skrabanek, Marta Filizola, Harel Weinstein, Modeling the activated form of GPCRs: The rhodopsin template Journal of Computer-Aided Molecular Design, (GPCR issue), 2006 Jul-Aug;20(7-8):437-48.

Examples of applications to signal modulation and drug design

Design of antidiabetic kinase mimicking peptide
Mack et al., Diabetes/Metabolism Res and Rev,2008

Computational peptide/protein complex structure prediction
Niv and Weinstein JACS 2005, Rubinstein and Niv
Biopolymers 2009

Improvement of proteins functional annotation
Skrabanek and Niv, Proteins 2008

Molecular mechanisms of Differential signaling of related GPCRs