Well-qualified Research Scientist in Computational Biology and Bioinformatics/Statistics with more than9 years of experience. Experience in Designing, Developing, and Applying Computational Approaches in Structure-based Drug Design (SBDD). Working experience and knowledgeable in Machine learning (Supervised and Unsupervised) using Artificial Neural Networks, Clustering, Dimensionality Reduction, Hidden Markov Models, Support Vector Machine. Extensive experience in Algorithm Development in Computational Biology and large-scale Biological Data Analysis. Working knowledge in Statistical Methods and analysis software (R, Matlab, JMP). Strong background in Statistics (Baysian Statistics, Probabilities, Principal Component Analysis) Well-versed and working experience in Statistical Data Analysis and Large-scale Comparative Studies in Biological Sciences. Strong knowledge in Molecular Genetics, Genomics, and Next-generation sequencing (NGS). Experience in method development for pharmaceutical industry (Merck) in modeling complex molecular systems. Strong Computer Science background with programming and scripting (perl, python, C/C++, Java) experience.
tools and Biopython, Pipeline Pilot, Gene Expression and Cell Models, Genomics, Copy Number Variation (CNV),
Concepts Next-Generation Sequencing (NGS). Protein structure and dynamics, Statistical thermodynamics, Molecular Dynamics, Chemo-informatics, Ligand Based Drug Design, Structure Based Drug Design, QSAR, Molecular Modeling, Conformational
Concepts and Analysis, 3-D Structure Determination, Molecular Docking, Pharmacophore Modeling, Chemical Library
interests Design, Homology Modeling, Virtual Screening, Lead Identification, Binding Energy Determinations, Cancer Research, Large-scale Genomic Data Analysis, Rotamer Libraries. Data Structures, Evolutionary Programming, Genetic Algorithms, Artificial Intelligence, Simulation of Complex Systems, Artificial Neural Networks, Hidden Markov Model, Design and Analysis of Algorithms, Object Oriented Methodologies, Project Management and Planning, Software Development
Software Life Cycle, Quality Assurance, Module Testing and Debugging, Risk Management, Relational Databases,
Engineering Probability and statistical Methods, Design Patterns, compilers, debuggers and editors (g++, gcc, Eclipse, gdb, Vim, Emacs, Java builder), GPGPU, WAP, OLAP (OnLine Analytical Processing), Linear Algebra PACKage (LAPACK), LAMP (Linux, Apache, MySQL, PHP) environment, CackPHP, ModPerl, MS FrontPage, Model View Controller (MVC) architecture pattern, VXML, XML, CSS, HTML.
Databases and Oracle, MySQL, MS Access, ER WIN (database design), Oracle Developer, Windows, Database Design
operating systems and Implementation, command based Linux environment. R, Matlab, JMP, SAS, Principal Component Analysis, Statistics and Probability, Baysian Statistics, Machine learning (Supervised and Unsupervised), Artificial Neural Networks, Clustering,
Statistical Dimensionality Reduction, Hidden Markov Models, Support Vector Machine, Linear Regression,
Binding MOAD (Mother Of All Databases) website (www.bindingmoad.org): Designed and developed new website that
incorporates new features for browse, search and filter Binding MOAD database with improved user interface.
University of MichiganApril 2012 to CurrentPostdoctoral Research Associate Ann Arbor, MI
University of ArizonaOctober 2009 to March 2012Postdoctoral Research Associate Tucson, AZ
J. W. Goethe University Merck KGaASeptember 2005 to June 2009Research Assistant Frankfurt, Germany
Computational Method development Designed and developed computational methods like NMSim and RCNMA for investigating the receptor flexibility and mobility in structure-based drug design.
These softwares are being used at Merck KGaA.
Designed and Developed NMSim Web Server (www.nmsim.de) for protein conformation generation and analysis.
Redesigned and Implemented new Binding MOAD website (Mother of All Databases: a Comprehensive Protein-Ligand Database; www.bindingmoad.org) from scratch to overcome technological limitations and to improve user interface.
Modified and incorporated database schema (MySQL) into the new binding MOAD website.
Developed and applied computational approaches that integrate experimental data such as Cryo-EM, FRET, and SAXS for large macromolecular assemblies' structure prediction.
Biostatistical Analysis Performed comparative statistical study of several Hsp90 protein/ligand structures.
Designed and constructed ligand binding decoy sets for 58 protein-ligand complexes in CSAR benchmark 2012 release.
Used statistical analysis, R, JMP, Diversity measure.
Statistically compared and analyzed methods for fitting atomic structures into Cryo-electron microscopy (cryo-EM) maps for variety of systems like ribosomes, viruses and other molecular assemblies.
Performed a large-scale comparative study of protein motions using Statistics and Principal Component Analysis, and R.
Conducted and analyzed 2013 benchmark exercise in the CSAR using docking decoys of engineered protein in collaboration.
Used Receiver Operating Characteristic (ROC), Correlations, Statistical Tests, and JMP.
Modeling, Prediction and Supervised Learning Involved in analysis and predictions of Conformational Changes, Allosteric Binding Sites, Flexible Docking, Flexible Regions and Transient Pockets in proteins.
Performed modeling and simulation of the bug's society of different species that can see, hear, walk, mate, attack, and can make noises.
Their survival is the fitness criterion which is based on eating food.
The idea was to analyze the characteristics of best Dr.
Aqeel Ahmed Faburary, 2014 Page 1 of 3 evolved specie.
Acquired extensive experience in multi-scale modeling of receptor Flexibility and Dynamics.
Extensively studied speech recognition using Hidden Markov Model.
Developed, trained, and used Artificial Neural Networks for classification of patient's data (academic).
Developed and studied similar binding site interaction network of proteins in Binding MOAD database using statistical analysis.
Successfully build homology models and performing conformational analysis, and molecular docking using Clustering, and Principal Component Analysis.
Modeled soluble guanylyl cyclase structure using a combination of experimental (SAXS and chemical cross-linking) and computational approaches (MD and docking).
Biological Systems Investigated Macromolecules like Kinases, Antibodies, Integrin avb3, and Hsp90 important target for important diseases including cancer.
Working experience in computer-aided drug design including docking, molecular dynamics, ligand based drug design, QSAR, and chemo-informatics.
Investigated flexibility/mobility characteristics of kinases in active/inactive states.
Actively involved in the Community Structure-Activity Resource (CSAR; www.csardock.org) that provides datasets of crystal structures and binding affinities for diverse complexes.
J. W. Goethe University2009Ph.D: Structural bioinformatics/BiologyFrankfurt, GermanyStructural bioinformatics/Biology "Development of a geometric simulation approach for investigating the intrinsic mobility of proteins"
Advisor: Prof. Dr. Holger Gohlke
Chalmers University of Technology2005M.Sc: Complex Adaptive Systems (Computational Biology)Gothenburg, SwedenComplex Adaptive Systems (Computational Biology) "Multi-scale modeling of receptor flexibility in structure based drug design"
University of Karachi2003B.S: Computer ScienceKarachi, PakistanComputer Science "Speech recognition using Hidden Markov Model"
Participated in Workshop on Computational Biophysics at the Max Planck Institute of Biophysics, Frankfurt, Germany, in March 2006.
Oral presentation at the 19th Darmstadt Molecular Modeling Workshop, organized by Computer Chemistry Center, Erlangen, Germany, in May 2005.
Oral presentation at the 13th All Pakistan Software Competition and Exhibition organized by Khan Research Laboratories, Islamabad, Pakistan in Sept.
Fellowships and Supervisions/Teaching: Achieved stipend from Merck KGaA, Darmstadt, Germany, in 2006, for the duration of 3 years.
Achieved fellowship from the "Stiftung zur Förderung der internationalen wissenschaftlichen Beziehungen der Goethe Universität", Germany, in 2005, for the duration of 9 months.
Designed, developed, and taught practical courses at undergraduate/graduate levels: Protein-protein and protein-ligand docking, Protein flexibility/rigidity analysis, and Protein dynamics.
Supervised graduate level students: Thesis: A large-scale comparison between essential dynamics (ED) of molecular dynamics (MD) and normal modes.
A multi-level approach for macromolecular geometric simulation (J. Chem. Inf. Model. 2011; 51: 160422): Successfully applied to proteins showing functionally important conformational changes. Currently being used as an important computational tool at the Department of Bio- and Chemoinformatics, Merck KGaA. RCNMA: A multi-scale approach for macromolecular flexibility prediction (Proteins 2006, 63, 1038-1051): Cited in more than 60 research articles in different journals. Currently being used as an important computational tool at the Department of Bio- and Chemoinformatics, Merck KGaA. NMSim Web Server (Nucl. Acids Res. 2012; 40: W310W316; www.nmsim.de): An easy to use webserver for efficiently generating and analyzing conformations of proteins. Dr. Aqeel Ahmed Faburary, 2014 Page 2 of 3 Peer-reviewed publications: 1. Ahmed, A.; Gohlke, H. Multiscale Modeling of Macromolecular Conformational Changes Combining Concepts from Rigidity and Elastic Network Theory. Proteins 2006, 63, 1038-1051. 2. Ahmed, A.; Kazemi, S.; Gohlke, H. Protein flexibility and mobility in structure-based drug design. Front. Drug Des. Discov. 2007, 3, 455-476. 3. Ahmed, A.; Gohlke, H. Multiscale modeling of macromolecular conformational changes. in: "Proceedings of the 1st International Conference on Computational & Mathematical Biomedical Engineering (CMBE09)", P. Nithiarasu, R. Löhner, R. van Loon (eds.), Swansea 2009, 219-222. 4. Ahmed, A.; Villinger, S.; Gohlke, H. Large-scale comparison of protein essential dynamics from molecular dynamics simulations and elastic networks models. Proteins 2010, 78, 3341-3352. 5. Ahmed, A.; Rippmann, F.; Barnickel, G.; Gohlke, H. A normal mode-based geometric simulation approach for exploring biologically relevant conformational transitions in proteins. J. Chem. Inf. Model. 2011; 51: 160422. 6. Ahmed, A.; Whitford, P.; Sanbonmatsu, K; Tama, F. Consensus among flexible fitting approaches improves the interpretation of cryo-EM data. J. Struct. Biol. 2012; 177(2):561-70. 7. Whitford, P.; Ahmed, A.; Yu, Y.; Hennelly, S.; Tama, F.; Spahn, C.; Onuchic, J.; Sanbonmatsu, K. Excited states of ribosome translocation revealed through integrative molecular modeling. Proc. Nat. Acad. Sci. USA 2011; 108:18943-8. 8. Krüger, D.; Ahmed, A.; Gohlke, H. NMSim webserver: normal mode-based geometric simulations for exploring biologically relevant conformational transitions in proteins. Nucl. Acids Res. 2012; 40: W310W316 (http://www.nmsim.de). 9. Fritz, B.; Roberts, S.; Ahmed A.; Breci, L.; Li, W.; Weichsel, A.; Brailey, J.; Wysocki, V.; Tama, F.; Montfort, W. Molecular model of soluble guanylyl cyclase determined by small-angle X-ray scattering and chemical cross-linking. Biochemistry 2013, 52: 156882. 10. Ahmed, A.; Tama, F. Consensus among multiple flexible fitting approaches as a measure of reliable fitting into cryo-EM data. J. Struct. Biol. 2013; 182: 67-77. 11. Dunbar, J. Jr. B.; Smith, R. D.; Damm-Ganamet, K. L.; Ahmed, A.; Esposito, E. X.; Delproposto, J.; Chinnaswamy, K.; Kang, Y.; Kubish, G.; Gestwicki, J. E.; Stuckey, J. A.; Carlson, H. A. CSAR Dataset Release 2012: Ligands, affinities, complexes, and docking decoys. J. Chem. Inf. Model 2013, DOI: 10.1021/ci4000486 12. Ahmed, A.; Tama, F. Automated consensus approach to predict correct orientation for flexible fitting into cryo-EM data. To be Submitted 2013. Selected communications and presentations: Poster presentation at the 4th German Conference on Chemoinformatics, organized by Gesellschaft Deutscher Chemiker (GDCH), Goslar, Germany, in Nov. 2008. Poster presentation at the MMS07 (Methods of Molecular Simulation), organized by Computational Molecular Biophysics Group, Heidelberg, Germany, in Sept. 2007. Poster presentation at the 9th International Symposium on "Protein structure function relationship" organized by HEJ Research Institute of Chemistry, Karachi, Pakistan, in Jan. 2007. Poster awarded 3rd prize.