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William McLaughlin

Secretary of Faculty Council
Associate Professor of Computational Biology
Department of Basic Sciences
Geisinger Commonwealth Research Department
North Campus

Geisinger Commonwealth School of Medicine
Medical Sciences Building
525 Pine St.
Office 3040
Scranton, PA 18509
Fax: 570-504-9639

Research interests

William McLaughlin, PhD, is an associate professor of computational biology in the Department of Basic Sciences. He completed graduate work in the joint program in computational biochemistry at Rutgers, the State University of New Jersey/University of Medicine and Dentistry of New Jersey. His postdoctoral training was done at the University of California, San Diego, where he was a Ruth L. Kirschstein National Research Service Award Fellow and a member of the Center of Theoretical Biological Physics. Dr. McLaughlin is currently a contributing member of the Protein Society, The International Society for Computational Biology, American Medical Informatics Association and the American Chemical Society. His research interests include the energetics of macromolecular association (protein/DNA and protein/protein), protein/drug interactions, high throughput molecular biological experiments, data mining and drug repositioning.

Dr. McLaughlin’s laboratory aims to help bring together advances in biomedical science regarding our knowledge of proteins in living systems. Descriptions of the biological functions of protein are being assembled. Connections are made between protein functions and the characteristics of proteins with regard to their primary amino acid sequences and their three-dimensional structures. As an overview of the functions that are attributed to protein structures, see such descriptions in chart format.

The laboratory is developing online search tools which connect proteins with their biological functions, disease associations, and their interactions with medications. You are welcome to initiate an interactive query. One application is to identify known and putative medications for a queried disease. The laboratory is applying the search tools to identify and prioritize medications which may be used to treat dementia with the goal of improving clinical outcomes.

The laboratory’s research is supported in part by the Marquardt Foundation for research to advance the treatments for Alzheimer’s disease.

Student research opportunities

Members of Dr. McLaughlin’s laboratory study the large scale elucidation of protein structure to function relationships. Connections between health conditions, proteins and medications are made with attention paid to their quality and completeness. Query tools are being developed which enable the retrieval of known and putative therapeutics for a queried disease. Predictions are made regarding the functional and phenotypic associations of proteins. Also, accuracy estimates of protein structural models are being derived. To better enable individualized care for those with dementia, associations between drug treatments and genetic variations are being identified. Students gain training in the fields of structural bioinformatics, pharmacogenomics and translational bioinformatics.

Recent publications

  • Farrell MS, Wallace SJ, Clarke SM, Tarafder MR, McLaughlin WA. Implementation of the Connective Tissue Screening Questionnaire in northeast Pennsylvania to identify comorbidities of connective tissue diseases in subjects with systemic lupus erythematosus. J Prim Care Community Health. 2014 Apr 1;5(2):134-8. Full Text
  • DePietro PJ, Julfayev ES, McLaughlin WA. Quantification of the impact of PSI:Biology according to the annotations of the determined structures. BMC Struct Biol. 2013 Oct 21;13:24. Full Text
  • Julfayev ES, McLaughlin RJ, Tao YP, McLaughlin WA. KB-Rank: efficient protein structure and functional annotation identification via text query. J Struc Funct Genomics. 2012 Jan 21. Full Text
  • Gabanyi MJ, Adams PD, Arnold K, Bordoli L, Carter LG, Flippen-Andersen J,Gifford L, Haas J, Kouranov A, McLaughlin WA, Micallef DI, Minor W, Shah R, Schwede T, Tao YP, Westbrook JD, Zimmerman M, Berman HM. The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods. J Struct Funct Genomics. 2011 Apr 7. Full Text
  • Julfayev ES, McLaughlin RJ, Tao YP, McLaughlin WA. A new approach to assess and predict the functional roles of proteins across all known structures. J Struct Funct Genomics. 2011 Mar 29. Full Text         
  • McLaughlin, W.A., Hou, T., Taylor, S., Wang W. The identification of novel A-kinase anchoring proteins using bioinformatic filters and peptide arrays. Protein Eng Des Sel. 2011 Mar;24(3):333-9. Epub 2010 Nov 29.
  • Julfayev, E., McLaughlin, R., Westbrook, J.D., Tao, W.Y., Shah, R. Gabanyi, M., and Berman, H.M., and McLaughlin, W.A. Using the PSI Structural Biology Knowledgebase to predict novel functions of under-characterized proteins. Journal of Structural and Functional Genomics.
  • Hou, T., Xu, Z., Zhang, W., McLaughlin, W.A., Case, D. A., Xu, Y., Wang, W., Characterization of domain-peptide interaction interface: a generic structure-based model to decipher the binding specificity of SH3 domains, Mol Cell Proteomics, 8(4):639-649, (2009).
  • Chang CA*, McLaughlin WA*, Baron R, Wang Q, McCammon JA. Entropic contributions and the influence of the hydrophobic environment in promiscuous protein-protein association. Proc Natl Acad Sci U S A. 2008 May 27;105(21):7456-61. PMID: 18495919.
  • Hou T, McLaughlin WA, Wang W. Evaluating the potency of HIV-1 protease drugs to combat resistance. Proteins: Structure, Function, and Bioinformatics. 2007 Nov 14. PMID: 18004760.
  • McLaughlin WA, Chen K, Hou T, Wang W. On the detection of functionally coherent groups of protein domains with an extension to protein annotation. BMC Bioinformatics. 2007, 8:390. PMID: 17937820.
  • McLaughlin WA, Hou T, Wang W. Prediction of binding sites of peptide recognition domains: an application on Grb2 and SAP SH2 Domains. J Mol Biol. 2006 Apr 7;357(4):1322-34. PMID: 16476443.
  • Hou T, Chen K, McLaughlin WA, Lu B, Wang W. Computational analysis and prediction of the binding motif and protein interacting partners of the Abl SH3 domain. PLoS Comput Biol. 2006 Jan;2(1). PMID: 16446784.
  • Hou T, McLaughlin WA, Lu B, Chen K, Wang W. Prediction of binding affinities between the human amphiphysin-1 SH3 domain and its peptide ligands using homology modeling, molecular dynamics and molecular field analysis. J Proteome Res. 2006 Jan;5(1):32-43. PMID: 16396493.
  • McLaughlin WA, Kulp DW, de la Cruz J, Lu XJ, Lawson CL, Berman HM. A structure-based method for identifying DNA-binding proteins and their sites of DNA-interaction. J Struct Funct Genomics. 2004;5(4):255-65. PMID: 15704013.
  • McLaughlin WA, Berman HM. Statistical models for discerning protein structures containing the DNA-binding helix-turn-helix motif. J Mol Biol. 2003 Jun 27;330(1):43-55. PMID: 12818201.
  • Binder-Macleod SA, McLaughlin WA. Effects of asynchronous stimulation on the human quadriceps femoris muscle. Arch Phys Med Rehabil. 1997 Mar;78(3):294-7. PMID: 9084353.


Bachelor of Arts in Biology – University of Delaware, Newark, Del.
Bachelor of Science in Chemistry – University of Delaware, Newark, Del.
Doctor of Philosophy in Biochemistry – Rutgers, The State University of New Jersey/The University of Medicine and Dentistry of New Jersey, Piscataway, NJ
Postdoctoral training – University of California, San Diego