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Researchers
  • Prof.  Amiram Goldblum
 
Research Interest  
The laboratory of molecular modeling and drug design develops algorithms and computer techniques and employs them, as well as other computational methods, for research in structural biology, modeling, and drug design.
 
A central activity in the laboratory is the development of novel optimization methods for solving the complex combinatorial problems that are an integral part of structural biology and drug design. A large scope of issues has already been addressed by our core technology, called “Iterative Stochastic Elimination” (ISE) which was used to search for optimal solutions to the construction of conformational ensembles, multiple loops in proteins, protein-ligand docking, protein design, cheminformatics and others.
 
 
 
Research Projects  
The combinatorial optimization technology, Iterative Stochastic Elimination (ISE) was recently devised in our lab, and is now extended by PhD and MSc students to issues such as :
 
        Modeling the conformations of large (>8 amino acids) loops and multiple loops
        Studying the preexisting ensembles of protein loop conformations
        Constructing conformational populations for computing properties of large ligands
        Structure based design from molecular scaffolds and fragments
        Predicting molecular properties from database comparisons
        Assigning Drug likeness and molecular bioactivity to molecules
        Ligand docking to proteins
        Design of new functions in proteins
        Designing protein sequences for inhibiting protein – protein interactions
        Differentiating between folding and non-folding sequences
        Constructing a new physical force field for proteins
 
A different development in our lab is a result of the application of sequence and structure alignments in protein kinases, which led to the finding of a new binding site in many kinases: a fatty acid, most probably myristoyl, binding pocket, which was previously shown to exist in c-Abl only. We have shown by several computational methods its existence in other kinases and its ability to bind fatty acid (myristoyl) derivatives.
 
Some of the MSc thesis in our lab are dealing with:
 
        Designing inhibitors for the MBP of Abl
        Designing inhibitors for the MBP in Src family kinases
        Selectivity in the MBPs of kinases
        Designing inhibitors for the substrate binding site in IGF1-R
        Mechanism of differential aging of inhibited acetylcholinesterase
 
 
 
Chapters in Books  
Goldblum, A., On the mechanisms of proteinases, In: Computational Approaches to Biochemical Reactivity (Naray-Szabo, G. and Warshel, A.,eds.), pp. 295-340.
 
Computational Biology
Structural Biology
Combinatorial Optimization Technology
Protein Kinase Inhibition
Molecular Bioactivity Indexes
Focused Molecular Libraries
Homology Modeling
Large Loop prediction
Conformational ensembles
Ligand Docking
Protein-protein interactions
Protein Design
Drug Design
 
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