Molecular Structure and Modeling Core

The Molecular Structure and Modeling Core (MSM Core) provides advanced molecular modeling techniques and X-ray crystallography services to support biomedical research, particularly in cancer research and related drug design projects. MSM core service can accelerate lead molecule identification, assist drug design and development process, and improve our understanding of the principles underlying biological processes.

The main goal of this core is to support both ligand-based and structure-based drug design projects at any stage, as well as to provide small molecule X-ray crystallographic services to assist drug design projects. Towards this goal we offer the following services:

Ligand based drug design:

Quantitative Structure activity relationship (QSAR): Identify structure patterns related to activity and obtain insights into the nature of interactions between drug molecules and libraries

Pharmacophore modeling: Determine structure requirements for activity, aids in design of novel ligands/inhibitors and develop pharmacophore based 3D database search strategies

Structure based drug design:

Docking & Virtual screen: Understand ligand-receptor interactions and identify potential agonists or antagonists through virtual screening of chemical libraries

Homology modeling: Construct a reasonable model of target protein from amino acid sequence and related crystal structures. Find ligand binding sites on homology model, design agonists-antagonists.

Molecular dynamics simulations: Determine time dependent behavior of a molecular system and molecular level insight into structure and function of biological molecules.

DFT calculations: Obtain structural, energetic and electronic properties of isolated small molecules. Very useful for both basis research and structure based drug design.

Small Molecule X-ray Crystallography: Identify structure and reference information useful in the process of drug design and the determination of pharmacophore, QSAR and docking studies.

Professional services are provided by a well experienced Molecular Modeling Scientist. Dr. Mottamal has over 15 years of research experience on molecular modeling, which includes working towards finding small molecules to treat various types of cancers, constructing drug-target complex models and extracting molecular level interactions responsible for binding, building homology models, etc. Dr. Mottamal can also assist faculty in writing the molecular modeling part of a project in their manuscripts and/or grants.  

RCMI MSM Core Pamphlet
Full List of Services Offered with general pricing (PDF).

To request services please follow the MSM Core's iLab Solutions link below.


Research Scientist:

Madhu Mottamal, Ph.D.

Email: mmottama@xula.edu

Phone: 504-520-5084

Important Information for Core Users:

We hope the RCMI Molecular Structure and Modeling Core is serving your research needs.  As you are writing manuscripts, preparing presentations, and drafting grant applications that have resulted from core usage, please keep in mind the importance of citing the RCMI grant and following the NIH Public Access Policy.  In order for a publication or presentation to be counted as productivity towards the RCMI Grant, it must be cited with the grant number and a publication must be deposited into PubMed Central. 


Citations must credit NCRR's support.  Please use the statements below when citing research that was completed with the assistance of an RCMI Core facility.  If you are writing RCMI instrumentation into a grant, or using preliminary results obtained with the assistance of an RCMI Core facility, please cite RCMI in the grant application.

“This publication was made possible by NIH Grant Number 8G12MD007595-04 from the National Center for Research Resources.  Its contents are solely the responsibility of the authors and do not necessarily represent the official views of the NIH.”

Obtaining a PubMed Central (PMCID) (This is different than a PMID!)

As a result of NIH's Public Access Policy , the final, peer reviewed author manuscripts of journal articles that are supported by NIH funding must be deposited into PMC via the NIH Manuscript Submission System (NIHMSS) , as soon as the articles have been accepted for publication.  Specifically, the final manuscript supplied to PMC is the version that the journal has accepted for publication, including any revisions that the author has made during the peer review process.

You may deposit your final, peer reviewed manuscript through the Manuscript Submission System http://www.nihms.nih.gov/ , using your eRA Commons login, NIH login, HHMI login, or My NCIB login.  There are FAQs at the bottom of the webpage and submission tutorials are also available.  If you do not have access to one of these logins, please contact Michelle Soliman for assistance with submission.

Helpful links:

PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/

NIH Manuscript Submission System: http://www.nihms.nih.gov/

NIH Public Access Policy: http://publicaccess.nih.gov/

Thank you for helping us stay in compliance with the RCMI Grant and the NIH Public Access Policy. Should you have any questions, please contact the Core Manager, Erica Severan or Guangdi Wang.


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