ANIL KORKUT

 

Columbia University

Dept. of Biochemistry & Mol. Biophysics

650W 168th Street BB204

New York NY

Phone: 212 305 1846

ak2048_at_columbia_edu

 
 

 

 

 

EDUCATION

Columbia University, New York, NY

·        Ph.D. Candidate (2001-Expected in 2008)                                                       

      Department of Biochemistry and Molecular Biophysics

      Thesis Advisor: Wayne A. Hendrickson, Ph.D.                                                 

·        Master of Philosophy, (2002-2004)

Department of Biochemistry and Molecular Biophysics, GPA: 4.0/4.0

·        Master of Arts, (2001-2002)

Department of Biochemistry and Molecular Biophysics, GPA: 4.0/4.0

Bogazici University Istanbul-Turkey

·        Bachelor of Arts, (1996-2001)

      Molecular Biology and Genetics, GPA:3.9/4.0 summa cum laude

      Chemistry-Double Major, GPA:3.9/4.0 summa cum laude

RESEARCH AREAS

Computational biology, macromolecular dynamics, collective motions of proteins, molecular biophysics, viral entry proteins, dynamics of helicases, HIV gp120, bioinformatics.

COMPUTATIONAL SKILLS:

Computational biology:

Expert in molecular dynamics and Monte Carlo simulations applied to macromolecular systems, normal mode analysis, homology modeling, coarse grained simulations, energy minimization algorithms, coarse grained force field development, loop modeling and QSAR.

Software:

Expert in CHARMM and TINKER simulation packages, PROTARCH/UNRES ab initio protein structure modeling, Nest for homology modeling, RAPPER loop modeling, MODELLER, Dyndom for molecular domain motion analysis, GRASP and DELPHI, DSSP, various structure visualization software.

Programming languages:

Highly proficient in FORTRAN 77/90, proficient in Python, proficient in Mathematica, MATLAB.

Numerical:

Expert in Fourier analysis, eigenvalue problems, singular value decomposition, principal component analysis, hidden Markov models, iterative mixed-basis diagonalization (DIMB) in normal mode analysis applications, numerical Hessian construction, golden section line search algorithm, n-means clustering, support vector machines, truncated Newton, ABNR  and conjugate gradient optimization algorithms.

EXPERIMENTAL SKILLS:

Expert in molecular cloning, protein expression, protein purification and crystallization, SDS-PAGE and western blotting of proteins, yeast molecular biology techniques and yeast two-hybrid essay.

RESEARCH EXPERIENCE

Columbia University - Graduate Research Assistant (2001-present)

Advisor: Wayne A. Hendrickson, Ph.D.

·        Conformational transition pathway of HIV gp120 between CD4 bound state, b12 antibody bound state and apostate using an iterative normal mode analysis approach

·        Calculation of large scale conformational transition trajectories and transition states of macromolecules using coarse grained approaches.

·        Development of coarse grained force field and minimization algorithms to be used in coarse grained energy minimizations, normal mode analysis and molecular dynamics simulations of proteins.

·        Domain motions, structural plasticity and fusion mechanism of HIV gp120: From coarse grained to full atomic analysis studies.

·        Domain motions and enzymatic mechanism of SF1 helicases: Coarse grained normal mode analysis.

·        Crystallographic studies of Insulin-like peptides from nematodes.

Harvard University - Visiting Scholar (1999-2000)

Advisor: Don C. Wiley, Ph.D.

·        Purification and crystallization studies of gD (Herpes simplex virus entry protein) and cellular gD receptor HveC.

Bogazici University - Undergraduate Student (1996-2000)

Advisor: Ivet Bahar, Ph.D. (now with the University of Pittsburgh)

·        Investigation of dynamics of F1-ATPase using the Gaussian Network Model approach.

Tereza Varnali, Ph.D.

·        Quantitative Structure Activity Relationship (QSAR) of N-Methyl-D-Aspartate (NMDA) Antagonists.

PUBLICATIONS

·        Korkut A, Hendrickson W.A., A novel coarse grained normal mode based method for analysis of large scale conformational transition pathways and intermediate states of macromolecules: An application on the adenylate kinase model system. (Manuscript in preparation).

·        Korkut A, Hendrickson W.A., Development and verification of a novel coarse grained statistical force field (cgff) designed for the analysis of protein dynamics. (Manuscript in preparation).

·        Korkut A, Hendrickson W.A., Conformational plasticity of gp120 and affects of ligand binding: A normal mode analysis study. (Manuscript in preparation).

·        Korkut A, Varnali T., Quantitative Structure Activity Relationship (QSAR) of Competitive N-Methyl-D-Aspartate (NMDA) Antagonists. Molecular Physics, 101:3285-3291(7), 2003.

POSTERS, RESEARCH COURSES

·        Poster: Korkut, A., Hendrickson, W.A, Conformational plasticity of gp120: A normal mode analysis study. Keystone Symposia: Frontiers of Structural Biology, Steamboat, CO, Jan. 2008.

·        Poster: Korkut A, Pyle A.M, Bahar I, Hendrickson W.A., Domain motions of SF1 and SF2 helicases. Biophysical Society 47th Annual Meeting, San Antonio, TX, March 2003.

·        Research Course: “Biomolecular Simulations and Computational Biology” European Molecular Biology Laboratories, Heidelberg-Germany, June 2000.

·        Research Course: “Research on Membrane Proteins” European Molecular Biology Laboratories, Heidelberg-Germany, June 2000.

·        Poster: Korkut A, Varnali T. “Quantitative structure activity relationship (QSAR) of competitive N-Methyl-D-Aspartate (NMDA)” World Congress of Theoretically Oriented Chemists (WATOC 99), Imperial College, London, UK, August 1999

AWARDS:

·        Howard Hughes Medical Institute Pre-Doctoral fellowship. Honorable Mention (2001)

·        Bogazici University President`s Award (The most prestigious award given to Bogazici University Graduates) (2001)

·        Highest GPA of Double Major Program Graduates, Bogazici University (2001)

·        Highest GPA of Faculty of Arts and Sciences Graduates,  Bogazici University (2001)

·        Highest GPA of Molecular Biology & Genetics Graduates, Bogazici University (2001)

·        Highest GPA of Chemistry Graduates, Bogazici University (2001)

·        Turkish Science & Technology Council Fellowship (1996-2000).

·        Bogazici University Undergraduate Merit Fellowship (1996-2000)

·        Turkish Science & Technology Council National Science Olympiads, Silver Medal in Chemistry (1996)

·        Turkish Science & Technology Council  Regional Science Olympiads, Highest Degree in Chemistry (1995)

·        MEF-BAV  National Research Projects Competition, Bronze Medal in Biology (1995)

·        MEF-BAV  National Research Projects Competition, Gold Medal in Chemistry (1994)