Dr Karami en

Resume

 

Personal Information

Full name:Leila Karami

Date of Birth:September 2 1983

Address: Department of Cell and Molecular Biology

                                   Faculty of Biological Siences
Kharazmi University
Tehran, Iran

Phone:    +98 9193155894

Email:l_karami@khu.ac.ir

karami.leila1@gmail.com
 

Education

Postdoctoral Fellow, Computational Biophysics                     

  • University of Tehran, (2015-2017)

Postdoctoral Fellow, Computational Physical Chemistry

  • K. N. Toosi University of Technology(2013-2014)

Doctor of Philosophy, Computational Physical Chemistry

  • K. N. Toosi University of Technology (2008-2012)

Master of Science, Computational Physical Chemistry

  • TarbiatModares University (2006-2008)

Bachelor of Science, Pure Chemistry  

  • ShahidBeheshti University    (2002-2006)

 

 

Research Experience

Postdoctoral research:

  • Study of the interaction between some new inhibitors with soluble epoxide hydrolase by molecular docking and molecular dynamics simulations.

Postdoctoral research:

  • Study of the interaction of anticancer drug (Cytarabine) with the lipid membranes using molecular dynamics simulations.

 

Doctoral thesis research:

  • Study of the interaction of Proline-Rich Homeodomain with DNA using molecular dynamics simulation.

Masters' thesis research:

  • Investigation of effects of hydrogen bonds on amyloid-beta structure by DFT quantum calculation of electric field gradient and chemical shielding tensors.

 

Teaching Experience

Islamic Azad University, Shahre Qods Branch, Tehran, Iran

  • Instructor: General Chemistry I and II, Physical Chemistry Laboratory, Principles of Industrial chemistry calculations, Technical language.          (2011-2016)

Shahid Beheshti University of Medical Sciences, Tehran, Iran

  • Instructor: molecular dynamics simulation workshop (Gromacs)                         (Jun 2012)

Amirkabir university of Technology

  • Instructor: molecular dynamics simulation workshop (Gromacs)                         (Dec 2014)

 

Participation in workshops

  • Molecular Docking, University of Tehran (IBB)(Jun 2014)
  • Computational Drug Design, University of Tehran (IBB)   (Jun 2014)
  • Quantum Espresso, K. N. Toosi University of Technology(Nov 2014)
  • High Performance Computing (IPM)(Dec 2014)

 

Memberships

Member, Iranian Chemical Society                                                                         (2009-present)

Member, Iranian Bioinformatics Society (2014-present)

 

Technical Skills

  • Operating Systems: Windows, Linux
  • Programming Language: C, Python,
  • Scripting Language:Shell
  • Molecular Viewer: Gauss view, VMD, S-pdbV, Pymol,Chimera, ArgosLab, ICM-Browser                                          
  • Computational Software: HyperChem, Gaussian, Gromacs, Amber
  • Docking Software: AutoDock, AutoDockVina
  • Drug Design & QSAR: Discovery Studio, Sybyl

 

Research Interests

  • Molecular dynamics simulation of the biological systems to study structure-function relationship.
  • Molecular modeling &molecular docking
  • QSAR
  • Computational drug design
  • Quantum mechanics calculations

 

Publications

  1. L.karami, H. Behzadi, N.L. Hadipour, M. Mousavi-khoshdel, Study of C=O···H–N Hydrogen bond interactions in Amyloid beta (Aβ): A DFT study of the electric field gradient

and CS tensors and NBO analysis, Computational and Theoretical Chemistry. 965,2011, 137–145.

 

  1. S. Jalili, L. Karami,Study of Intermolecular Contacts in the (Proline-Rich Homeodomain) PRH-DNA Complex Using Molecular Dynamics Simulations,European Biophysics Journal. 41,2012, 329–340.

 

  1. S. Jalili, L. Karami, J. Schofield, Study of base pair mutations in proline-rich homeodomain (PRH)–DNA complexes using molecular dynamics, European Biophysics Journal. 42,2013, 427-440.

 

  1. L. Karami, S. Jalili, Effects of Cholesterol Concentration on the Interaction of the Cytarabine with Lipid Membranes: A Molecular Dynamics Simulation Study,Journal of Biomolecular Structure & Dynamics,33, 2014, 1254-1268.

 

  1. A. Soltani, Z. Azmoodeh, M. Bezi Javan, E. Tazikeh Lemeski, L. Karami, A DFT study of adsorption of glycine onto the surface of BC2N nanotube, Applied Surface Science, 384, 2016, 230-236.

 

  1. L. Karami, A. A. Saboury, E. Rezaee, S. A. Tabatabai, Investigation of the binding mode of 1, 3, oxadiazole derivatives as amide-based inhibitors for soluble epoxide hydrolase (sEH) by molecular docking and MM-GBSA, European Biophysics Journal, DOI: 10.1007/s00249-016-1188-0

 

  1. E. Tazikeh,L. Karami, A. A. Saboury, A. Soltani, Molecular Dynamics Simulation and Free Energy Studies on the Interaction of Salicylic Acid with Human Serum Albumin (HSA), revised in Physical Chemistry Research.5, 2017, 483-496.

 

 

 

Invited presentations

 

Shahid Beheshti University of Medical Sciences

  • First workshop in Modeling of biological nanosystems                                             (Jun 2012)

Institute of Medicinal Plants and Raw Materials, ShahidBeheshti University, Tehran, Iran

  • Guest Lecturer: Medicinal Chemistry, H. Rafati instructor                     (Nov 2013)

 

 

Presentations, Papers,and Posters

  • L. Karami. (Jul 2008). Density functional theory study of N-H…O=C hydrogen bonding effects in structure of beta amyloid.Paper presented at the 11th Iranian Physical Chemistry Conference, Ardebil, Iran (Poster)

 

  • L. Karami. (Apr 2010). Molecular dynamics analysis of Proline-Rich Homeodomain (PRH) – DNA interaction.Paper presented at the 13th Iranian Physical Chemistry Conference, Shiraz, Iran (Poster)

 

  • L. Karami. (Feb 2010). Study of intermolecular contacts in the (proline-rich homeodomain) PRH – DNA complex using molecular dynamics simulations.Paper presented at the 14th Iranian Physical Chemistry Conference, Tehran, Iran (Poster)

 

  • L. Karami. (Aug 2012). Predicting the effects of basepair mutations in proline-rich homeodomain (PRH)-DNA complex by thermodynamic integration.Paper presented at the 15th Iranian Physical Chemistry Conference, Tehran, Iran (Oral)

 

  • L. Karami. (May 2014).Dynamical and Structural Properties of Cytarabine in a Lipid Bilayer: A Molecular Dynamics Study. Paper presented at the 5th Iranian Bioinformatic Conference, Tehran, Iran (Oral)

 

  • L. Karami. (Oct 2014). Molecular Dynamics Simulation study of charged and uncharged Isoniazid in a DPPC Lipid Bilayer, Paper presented at the 17th Iranian Physical Chemistry Conference, Tehran, Iran (Oral)

 

  • L. Karami. (Oct 2014). Study of Interaction between Human Growth Hormone and Zinc Ions by Molecular Dynamic Simulation, Paper presented at the 17th Iranian Physical Chemistry Conference, Tehran, Iran (Poster)

 

  • L. Karami. (Dec 2015). Molecular docking and molecular dynamics simulation study of the

interaction between new amide-based inhibitors and soluble epoxide hydrolase (sEH), Paper presented at 14th Iranian Pharmaceutical Science Congress & 1st symposium of biopharmaceutics and pharmacokinetics, Tehran, Iran (Poster)

 

  • L. Karami. (Dec 2016). Exploring the complex formation between a mutant DNA and the Wild type Hoxc8 protein: A MD simulation approach. Paper presented at the 6th Iranian Bioinformatic Conference, Tehran, Iran (Poster)

 

  • L. Karami. (Dec 2016) Discovery of Phytochemicals Targeting c-Met Kinase Domain using Consensus Docking and Molecular Dynamics Simulation Studies. Paper presented at the 6th Iranian Bioinformatic Conference, Tehran, Iran (Poster)

 

Book Translation

  • Physical Chemistry for Biological Sciences, G. Hammes (Wiley)

 

 

Thesis Advised

  • Niosha Kalantari, MSc (Islamic Azad University of Gorgan, 2015)