Teaching
AMS-532 (fall and spring):
Laboratory Rotations and Journal Club in Computational Biology
Syllabus
Description: This is a two semester course in which students spend at least 8 weeks in each of three different laboratories actively participating in the research of participating Computational Biology faculty in the AMS graduate track ( http://compbio.ams.sunysb.edu ). In addition, students will attend and actively participate in research discussions at weekly Journal Club meetings on topics from the current literature using the skills and knowledge acquired during the rotations. Students who have already joined a research group are fully welcome to participate in the Journal Club .
AMS-535 (fall):
Introduction to
Computational Structural Biology and Drug Design
Course Announcement (pdf)
Syllabus
Description: This course will provide an introduction to Computational Structural Biology with application to Drug Design. Methods and applications that use computation to model biological systems involved in human disease will be emphasized. The course aims to foster collaborative learning and will consist of presentations by the instructor, guest lecturers, and by course participants with the goal of summarizing key methods, topics, and papers relevant to Computational Structural Biology. All are welcome to attend.
Topics:
- Drug Discovery and Biomolecular Structure (Chemistry Review, Proteins, Carbohydrates, Nucleic acids, Molecular Interactions and Recognition, Experimental Techniques for Elucidating Structure)
- Molecular Modeling (Thermodynamics, Classical Force Fields, Molecular Mechanics, Solvent Models, Parameter Development)
- Sampling Methods (Conformational Space, Molecular Dynamics, Monte Carlo, Sampling Techniques, Predicting Protein Structure, Protein Folding)
- Lead Discovery (Docking as a Lead Generation Tool, Algorithms, Discovery Methods, Applications)
- Lead Refinement (Free Energy Perturbation, Linear Response and Extended Linear Response, MM-PBSA and MM-GBSA , Properties of Known Drugs , Property Prediction)
Companion Course AMS-536 (see below):
A companion course taught in the Spring (AMS-536, "Molecular Modeling of Biological Molecules") gives hands-on experience in using computational methods discussed in the introductory Fall course. Students interested in taking the two-semester sequence should plan accordingly since AMS-535 (Fall) is a prerequisite for AMS-536 (Spring).
AMS-536 (spring):
Molecular Modeling of Biological Molecules
Course Announcement (pdf)
Syllabus
Description: This course is designed for students who wish to gain hands on experience modeling biological molecules at the atomic level. In conjunction with individual interests, Molecular Mechanics, Molecular dynamics, Monte Carlo, Docking (virtual screening), or Quantum Mechanics software packages can be used to study relevant biological systems(s). Projects will include setup, execution, and analysis. Course participants will give literature presentations relevant to the simulations being performed and a final project report will be required. Familiarity with Unix (Linux) is desirable.
Project Examples From Prior Semesters:
- Molecular Dynamics Simulations of A-DNA to B-DNA Transition with AMBER
- Comparative Homology Modeling of the Catalytic Domains of mTOR and DNA-PK for the Design of Anti-Cancer Agents
- Simulating Botulinum Neurotoxin Type A with Constant pH Molecular Dynamics in Generalized Born Implicit Solvent
- Protein Folding of Trpcage Using Generalized Born and Explicit Solvent Molecular Dynamics
- Building a Docking Test Set
- Docking Botulinum Neurotoxin Type E Light Chain with Phosphoramidon: A Structure Based Rational Drug Design Study for Developing Drug Targets for Botulism
- Pharmacophore Searching in HIV protease
- Docking of Sustiva Analogues as HIV-1 Reverse Transcriptase Inhibitors
- Statistical Study of QSPR of Blood-Brain Partitioning for a Large Set of Drugs