NRBSC Staff Publications


  • Abbas UL, Hood G, Wetzel AW, Mellors JW, 2011. Factors Influencing the Emergence and Spread of HIV Drug Resistance Arising from Rollout of Antiretroviral Pre-Exposure Prophylaxis (PrEP). PLoS ONE 6(4): e18165. doi:10.1371/journal.pone.0018165

  • Bock DD, Lee WC, Kerlin AM, Andermann ML, Hood G, Wetzel AW, Yurgenson S, Soucy ER, Kim HS, Reid RC. Network anatomy and in vivo physiology of visual cortical neurons. Nature. 2011 Mar 10;471(7337):177-82. PubMed PMID: 21390124; PubMed Central PMCID: PMC3095821.

  • Kleinekathöfer U, Isralewitz B, Dittrich M, Schulten K. Domain motion of individual F1-ATPase β-subunits during unbiased molecular dynamics simulations. J Phys Chem A. 2011 Jun 30;115(25):7267-74. Epub 2011 Apr 1. PubMed PMID: 21452901; PubMed Central PMCID: PMC3121902.

  • Luo F, Dittrich M, Stiles JR, Meriney SD. Single-pixel optical fluctuation analysis of calcium channel function in active zones of motor nerve terminals. J Neurosci. 2011 Aug 3;31(31):11268-81. PubMed PMID: 21813687.

  • Szarecka A, Lesnock KR, Ramirez-Mondragon CA, Nicholas HB Jr, Wymore T. The Class D beta-lactamase family: residues governing the maintenance and diversity of function. Protein Eng Des Sel. 2011 Oct;24(10):801-9. Epub 2011 Aug 22. PubMed PMID: 21859796; PubMed Central PMCID: PMC3170078.

  • Zhang X, Badea C, Hood G, Wetzel A, Qi Y, Stiles J, Johnson GA. High-resolution reconstruction of fluorescent inclusions in mouse thorax using anatomically guided sampling and parallel Monte Carlo computing. Biomed Opt Express. 2011 Sep 1;2(9):2449-60. Epub 2011 Jul 29. PubMed PMID: 21991539; PubMed Central PMCID: PMC3184855.


  • DeStefino NR, Pilato AA, Dittrich M, Cherry SV, Cho S, Stiles JR, Meriney SD. (2010). (R)-roscovitine prolongs the mean open time of unitary N-type calcium channel currents. Neuroscience, 167(3):838-849.

  • Ropelewski AJ, Nicholas HB, Gonzalez Mendez RR. MPI-PHYLIP: parallelizing computationally intensive phylogenetic analysis routines for the analysis of large protein families. PLoS One. 2010 Nov 15;5(11):e13999. PubMed PMID: 21085574; PubMed Central PMCID: PMC2981553.

  • Zhang X, Badea CT, Hood G, Wetzel AW, Stiles JR, Johnson GA. Free-space fluorescence tomography with adaptive sampling based on anatomical information from microCT. Proc Soc Photo Opt Instrum Eng. 2010;7757(775706). pii: 755706 (2010). PubMed PMID: 21743784; PubMed Central PMCID: PMC3132136


  • Czech J, Dittrich M, Stiles JR. (2009). Rapid Creation, Monte Carlo Simulation, and Visualization of Realistic 3D Cell Models. Methods in Molecular Biology, Systems Biology, ed. Maly, Ivan V. Humana Press, Clifton, NJ, 237-287.

  • Hempel J, Kraut A, Wymore T. Gamma glutamyl semialdehyde dehydrogenase: simulations on native and mutant forms support the importance of outer shell lysines. Chem Biol Interact. 2009 Mar 16;178(1-3):75-8. Epub 2008 Oct 18. PubMed PMID: 19000660.


  • Kerr R, Bartol TM, Kaminsky B, Dittrich M, Chang JCJ, Baden S, Sejnowski TJ, Stiles JR. (2008). Fast Monte Carlo Simulation Methods for Biological Reaction-Diffusion Systems in Solution and on Surfaces. SIAM J. Sci. Comput., 30(6):3126-3149.

  • Liu J, Louie S, Hsu W, Yu KM, Nicholas HB Jr, Rosenquist GL. Tyrosine sulfation is prevalent in human chemokine receptors important in lung disease. Am J Respir Cell Mol Biol. 2008 Jun;38(6):738-43. Epub 2008 Jan 24. PubMed PMID: 18218997; PubMed Central PMCID: PMC2396251.


  • Baden, SB, Sejnowski, TJ, Bartol, TM, and Stiles, J (2007) Toward petascale simulation of cellular microphysiology. Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering:628-634.

  • Bostick, DL & Brooks, CL, III. Deprotonation by Dehydration: The Origin of Ammonium Sensing in the AmtB Channel. PLoS Comput Biol 3: e22 (2007).

  • Bostick, DL & Brooks, CL, III. Selectivity in K+ Channels is Due to Topological Control of the Permeant Ion's Coordinated State. Proc Natl Acad Sci, USA in the press (2007).

  • Bostick, DL & Brooks, CL, III. On the equivalence point for ammonium (de)protonation during its transport through the AmtB channel. Biophys J in the press (2007).

  • Marko AC, Stafford K, Wymore T. Stochastic pairwise alignments and scoring methods for comparative protein structure modeling. J Chem Inf Model. 2007 May-Jun;47(3):1263-70. Epub 2007 Mar 29. PubMed PMID: 17391002.

  • Cannon, RC, Gewaltig, MC, Gleeson, P, Bhalla, U, Cornelis, H, Hines, ME, Howell, FW, Muller, E, Stiles, JR, Wils, S, De Schutter, E (2007) Interoperability of neuroscience modeling software: current status and future directions. Neuroinformatics 5:127-138.

  • Davis CH, Deerfield D 2nd, Wymore T, Stafford DW, Pedersen LG. A quantum chemical study of the mechanism of action of Vitamin K epoxide reductase (VKOR) II. Transition states. J Mol Graph Model. 2007 Sep;26(2):401-8. Epub 2006 Nov 6. PubMed PMID: 17182266.

  • Davis CH, Deerfield D 2nd, Wymore T, Stafford DW, Pedersen LG. A quantum chemical study of the mechanism of action of Vitamin K carboxylase (VKC) III. Intermediates and transition states. J Mol Graph Model. 2007 Sep;26(2):409-14. Epub 2006 Nov 6. PubMed PMID: 17182265.

  • Wymore T, Deerfield DW 2nd, Hempel J. Mechanistic implications of the cysteine-nicotinamide adduct in aldehyde dehydrogenase based on quantum mechanical/molecular mechanical simulations. Biochemistry. 2007 Aug 21;46(33):9495-506. Epub 2007 Jul 27. PubMed PMID: 17655326; PubMed Central PMCID: PMC2529467.


  • Patel, S & Brooks, CL, III. Fluctuating charge force fields: Recent developments and applications from small molecules to macromolecular biological systems. Molec Simul 32: 231-49 (2006).


  • Munshi, R, Coalson, RD, Ermentrout, GB, Madura, JD, Meirovitch, H, Stiles, JR, and Bahar, I. (in press) An introduction to simulation and visualization of biological systems at multiple scales: a summer training program for interdisciplinary research. Biotech. Prog.

  • Deerfield, D., Hood, G. An Experiment in Using the Access Grid for Distance Education. Journal of Science Education and Technology. 2005.

  • Nicholas, H. B., Hempel, J., Stanley, S., Perozich, J., Wymore, T. Residue Conservations in Aldehyde Dehydrogenase Gene Fusion Products Reemphasize Functional Interpretations. Purdue University Press. 2005.

  • Luo, F., Stiles, JR, Meriney, SD. Variance analysis of action-potential-evoked calcium influx reveals low opening probability of presynaptic calcium channels at the frog neuromuscular junction. Soc. Neurosci. Abst.

  • Coggan, JS, Bartol, TM, Esquenazi, E, Stiles, JR, Lamont, S, Martone, ME, Berg, DK, Ellisman, M, Sejnowski, TJ. Evidence for ectopic neurotransmission at a neuronal synapse. Science 309:446-451.


  • Kerr, R, Bartol, TM, Stiles, JR, Kennedy, MB, and Sejnowski, TJ. MCell3: A next-generation simulator of cellular microphysiology. Soc. Neurosci. Abst.

  • Pattillo, JM, Meriney, SD, and Stiles, JR. Spatially realistic Monte Carlo simulations predict calcium dynamics underlying transmitter release at a neuromuscular active zone. Soc. Neurosci. Abst.

  • Stiles, JR, Ford, WC, Pattillo, JM, Deerinck, TE, Ellisman, MH, Bartol, TM, and Sejnowski, TJ. Spatially realistic computational physiology: past, present, and future. In: Parallel Computing: Software Technology, Algorithms, Architectures & Applications, ed. Joubert, G, et al. Elsevier, Amsterdam, pp. 685-694.

  • Wachman, ES, Poage, RE, Stiles, JR, Farkas, DL, and Meriney, SD. Spatial distribution of calcium entry evoked by single action potentials within the presynaptic active zone. J. Neurosci. 24:2877-2885.

  • Casanova, H, Bartol, T, Berman, F, Birnbaum, A, Dongarra, J, Ellisman, M, Faerman, M, Gokcay, E, Miller, M, Obertelli, G, Pomerantz, S, Sejnowski, T, Stiles, J, and Wolski, R. The Virtual Instrument: Support for Grid-enabled MCell Simulations. Intern. J. High Performance Computing Applications 18:3-18.

  • Nicholas, H. B., Wymore, T., Cho, S. S., MacKerell, A. D., Deerfield, D. W.. 2004 Molecular recognition of aldehydes by aldehyde dehydrogenase and mechanism of nucleophilic activation. Proteins Structure Function Bioinformatics. 57:758-771. 2004.

  • Brothers EN, Suarez D, Deerfield DW II, Merz KM Jr. PM3-compatible zinc parameters optimized for metalloenzyme active sites. J. Comput. Chem., 25(14):1677-92.

  • Ropelewski, A.J., Nicholas, H.B. Jr, Deerfield, D.W. II, 2004. Mathematically Complete Nucleotide and Protein Sequence Searching Using Ssearch. in Current Protocols in Bioinformatics, Volume I, Baxevanis, A., and Davison, D. ed., pp 3.10.1 - 3.10.13

  • Wachman, ES, Poage, RE, Stiles, JR, Farkas, DL, and Meriney, SD. 2004. Spatial distribution of calcium entry evoked by single action potentials within the presynaptic active zone. J. Neurosci. 24:2877-2885.

  • Liu, Z., Xu, Y., Saladino, A.C., Wymore, T., Tang, P. 2004. Parametrization of 2-Bromo-2-Chloro-1,1,1-Trifluoroethane (Halothane) and Hexafluoroethane for Nonbonded Interactions. J. Phys. Chem. A 108(5):781-786.

  • Ropelewski, A.J., Nicholas, H.B. Jr, Deerfield, D.W. II. 2004. "Mathematically Complete Nucleotide and Protein Sequence Searching Using Ssearch", in Current Protocols in Bioinformatics, Volume I, Baxevanis, A., and Davison, D. ed., pp 3.10.1 - 3.10.13

  • Carley, K., Altman, N., Kaminsky, B., Nave, D., Yahja, A. 2004. BioWar: A City-Scale Multi-Agent Network Model of Weaponized Biological Attacks, Technical Report (CMU-ISRI-04-101). Pittsburgh, PA: CASOS, Carnegie Mellon University.


  • Chrisochoides, N., Nave, D. 2003. Parallel Delaunay mesh generation kernel. In Special Issue of Int'l Journal for Numerical Methods in Engineering (IJNME), 58(2):161-176.

  • Carley, K.M., Fridsma, D., Casman, E., Altman, N., Chang, J., Kaminski, B., Nave, D., & Yahja, A. 2003. BioWar: Scalable Multi-Agent Social and Epidemiological Simulation of Bioterrorism Events. NAACSOS conference proceedings, Pittsburgh, PA

  • Wetzel, A.W., Nieder, G.L., Durka-Pelok, G. Gest, T.R., Pomerantz, S.M. Nave, D., Czanner, S., Wagner, L., Shirey, E., Deerfield II, D.W.. 2003. Photo-Realistic Representation of Anatomical Structures for Medical Education by Fusion of Volumetric and Surface Image Data Proceedings of 32nd Applied Imagery and Pattern Recognition Workshop: Image Data Fusion, Oct 15-17 2003, Washington DC, IEEE Computer Society Press, pp 131-138

  • Nicholas, H.B. Jr., Deerfield, D.W. II, Ropelewski, A.J. 2003. Strategies for Searching Sequence Databases in "Biocomputing: Computer Tools for Biologists", Eaton Publishing, ed. S.M.Brown., pp 209-231..

  • Chrisochoides, N., Nave, D.. 2003. Parallel Delaunay mesh generation kernel. International Journal for Numerical Methods in Engineering 58:161-176.

  • J. A. Beckstead, R. Dawson, P. A. Feineigle, J. Gilbertson, C. Hauser, T. McVaugh, F. Palmieri, D. Sholehvar, A. Wetzel, 2003. High-throughput high-resolution microscopic slide digitization for pathology. InterScope Technologies, Inc. Photonics West 2003, Conference 4958, San Jose, California, Jan 25-31.

  • Arst, H.N.,Jr., Nicholas, H.B.,Jr., Caddick, M.X. 2003. Re: Watts et al., Proteins 2002;48:161-168. Editor's Corner. Proteins: Structure, Function, and Genetics. (in press).

  • Wymore, T., Deerfield II, D.W., Field, M.J., Nicholas, H.B. Hempel, J.. Initial Events in class 3 Aldehyde Dehydrogenase: MM and QM/MM simulations Chemico-Biological Interactions, 2003, 143-144: 75-84.

  • Hempel, J., Perozich, J., Wymore, T. Nicholas, H.B.. An Algorithm for the Identification and Ranking of Family-Specific Residues Applied to the ALDH3 Family Chemico-Biological Interactions, 2003, 143-144:23-28.


  • A.W. Wetzel, S.M. Pomerantz, D. Nave, A. Kar, J. Sommerfield, M. Mathis, D.W. Deerfield II, F.L. Bookstein, W.D. Green, A. Ade, B. Athey, "A Networked Environment for Interactively Viewing and Manipulating Visible Human Datasets", Proceedings of the 4th Visible Human Conference, Keystone, Colorado, Oct 17-19, 2002.

  • S.M. Pomerantz, A.W. Wetzel, D. Nave, D.W. Deerfield II "A Natural Plane Anatomical Segmentation Interface", Proceedings of the 4th Visible Human Conference, Keystone, Colorado, Oct 17-19, 2002.

  • D. Nave, S.M. Pomerantz, A.W. Wetzel, D.W. Deerfield II "Semi-Automated Reconstruction of Biological Surfaces from Few Contours in the Visible Female Dataset", Proceedings of the 4th Visible Human Conference, Keystone, Colorado, Oct 17-19, 2002.

  • T. Weymouth, G. Durka-Pelok, T. Gest, J. Huang, S.M. Pomerantz, A.W. Wetzel, C. Burger, B. Athey, "Using a Knowledge Base: The University of Michigan Visible Human Project", Proceedings of the 4th Visible Human Conference, Keystone, Colorado, Oct 17-19, 2002.

  • G. Durka-Pelok, S.M. Pomerantz, C. Gadd, T. Weymouth, T. Gest, J. Huang, D. Nave, A.W. Wetzel, S. Lee, B. Athey "Evaluation of a Volume Browser: PSC-VB", Proceedings of the 4th Visible Human Conference, Keystone, Colorado, Oct 17-19, 2002.

  • G. Durka-Pelok, T. Gest, G. Nieder, T. Weymouth, Jie Huang, A.W. Wetzel, S.M. Pomerantz, D. Nave, B. Athey, "Creation of an educational visual module: integration of QTVR and the Visible Human Data Set", Proceedings of the 4th Visible Human Conference, Keystone, Colorado, Oct 17-19, 2002.

  • G. Durka-Pelok, T. Weymouth, T. Gest, S.M. Pomerantz, D. Nave, A.W. Wetzel, S. Lee, B. Athey, "Bookmarking the Visible Human Dataset", Proceedings of the 4th Visible Human Conference, Keystone, Colorado, Oct 17-19, 2002.

  • Yu, K.M., Liu, J., Moy, R., Lin, H, Nicholas, Jr., H.B., Rosenquist, G.L. 2002. Prediction of tyrosine sulfation in seven-transmembrane receptors. Endocrine. 19:333-337.

  • Gomez, CM, Maselli, R, Vohra, BPS, Navedo, M, Stiles, J, Charnet, P, Schott, K, Rojas, L, Keesey, J, Verity, A, Wollmann, RW, Lasalde-Dominicci, J. A Novel Delta Subunit Mutation in Slow-Channel Syndrome Causes Severe Weakness by Novel Mechanisms. Annals of Neurology. Ann Neurol. 2002 51:102-12

  • Nicholas Jr., H.B., Ropelewski, A.J., Deerfield II, D.W. 2002. Strategies for Multiple Sequence Alignment. Biotechniques, 32:592-603.

  • Lee, I., Athey, B.D., Wetzel, A.W. Meixner, W., Baker, J.R. Jr.. 2002. Structural Molecular Dynamics Studies on Polyamidoamine Dendrimers for a Therapeutic Application: the Effects of pH and Generation. Macromolecules. 35:4510-4520.

  • Wetzel, A.W., Feineigle, P.A., Gilbertson, J.R.. 2002. Design of a High-Speed Slide Imaging System for Pathology Proceedings of IEEE International Symposium on Biomedical Imaging: Macro to Nano, July 7-10, pp 305-308.


  • Lee, I., Athey, B.D., Wetzel A.W., Baker, J.R. Jr., Molecular Dynamics Studies on Folic Acid and Fluorescein-Derivatized PAMAM Dendrimers Technical Proceedings of the 2001 International Conference on Computational Nanoscience and Nanotechnology, pp13-16

  • Wetzel, A.W., Pomerantz, S.M., Nave, D., Meixner, W., Johnson, A. Distributed Multiuser Visualization of Time Varying Anatomical Data 30th AIPR Workshop: Analysis and Understanding of Time Varying Imagery, Oct 10-12 2001, Washington DC, IEEE Computer Society Press, pp 109-114

  • Goddard, N., Hood, G., Howell, F., Hines, M., and De Schutter, E. 2001. NEOSIM: Portable large-scale plug and play modelling. Neurocomputing 38-40 (1-4): 1657-1661.

  • Casanova, H., Bartol, Jr., T.M., Stiles, J., and Berman , F. 2001. Distributing MCell Simulations on the Grid. The International Journal of High Performance Computing Applications 15:243-257.

  • Wagner, M.H., Tsui, F.-C., Espino, J.U., Dato, V.M., Sittig, D.F., Caruana, R.A., McGinnis, L.F., Deerfield, D.W. Druzdzel, M.J., and Fridsma, D.B. 2001. The Emerging Science of Very Early Detection of Disease Outbreaks J. Public Health Management Practice 7:51-59.

  • Deerfield, D.W. II, Carter, C.W. Jr., Pedersen, L.G. 2001. Models for Protein-Zinc Ion Binding Sites. II. The Catalytic Sites. J. Quantum Chem. 83, 150-165.

  • Hempel, J., Kuo, I., Perozich, J., Wang, B-C., Lindahl, R., and Nicholas, H. 2001. Aldehyde dehydrogenase: Maintaining critical active site geometry at motif 8 in the class 3 enzyme. European Journal of Biochemistry Vol. 268, pp. 722-726.

  • Hempel J, Lindahl R, Perozich J, Wang BC, Kuo I, Nicholas H 2001. Beyond the catalytic core of ALDH: a web of important residues begins to emerge. Chem-Biol Interact 130:39-46.

  • Nicholas, H.B.Jr., Arst, H.N.Jr., and Caddick, M.X. 2001. Evaluating low level sequence identity: are Aspergillus Quta and Arom homologous? European Journal of Biochemistry. Vol. 268. pp. 414- 419.

  • Stiles, JR, and Bartol, TM. 2001. Monte Carlo methods for simulating realistic synaptic microphysiology using MCell. In: Computational Neuroscience: Realistic Modeling for Experimentalists, ed. De Schutter, E. CRC Press, Boca Raton, pp. 87-127. CD-ROM material available at

  • Stiles, JR, Bartol, TM, Salpeter, MM, Salpeter, EE, and Sejnowski, TJ. 2001. Synaptic variability: new insights from reconstructions and Monte Carlo simulations with MCell. In: Synapses, ed. Cowan, WM, Stevens, CF, and Sudhof, TC. Johns Hopkins Univ. Press, Baltimore, pp. 681-731.

  • Wymore T, Nicholas HB, Hempel, J. 2001. Molecular dynamics simulation of class 3 aldehyde dehydrogenase. Chem-Biol Interact 130: 201-207.


  • A.W. Wetzel, John Gilbertson, Lei Zheng, John Gilespie, Jennifer Swallwell,Yukako Yagi, Sujin Kim, Mike Emmert-Buck, Michael Becich, Three-dimensional reconstruction for genomic analysis of prostate cancer, 28th AIPR Workshop: 3D Visualization for Data Exploration and Decision Making, Oct 13-15 1999, Washington DC, Proceedings of the SPIE Vol. 3905 (2000), pp204-212.

  • Becich, M. Feldman, M., Foran, D., Grygotis, A., Saltz, J., Wetzel, A.W. 2000. The HUBS Telemicroscopy Project CD-ROM Proceedings of the World Congress on Medical Physics and Biomedical Engineering, July 23-28, 2000"

  • Bookstein, F.L., Athey, B.D., Wetzel, A.W., Green, W.D. 2000. Navigating solid medical images by pencils of sectioning planes, SPIE 45th Annual Meeting, July 30 to August 4, 2000, San Diego Proceedings of SPIE Vol. 4121.

  • Hood, G., Burkardt, J., Foss, G., 2000. Visualizing the Visual System Neurocomputing, 32-33:801- 808.

  • Nicholas, H.B. Jr., Chan, S.S., and Rosenquist, G.L. 2000. A re-evaluation of the determinants of tyrosine. Endrocrine 11:285-292.

  • Nicholas, H.B. Jr., Deerfield, D.W. II, Ropelewski, A.J. 2000. Strategies for Searching Sequence Databases. Biotechniques 28:1174-1191.

  • Tiraboschi, G., Gresh, N., Giessner-Prettre, C., Pedersen, L.G., Deerfield, D.W. II. 2000. A joint ab initio and molecular mechanics investigation of polycoordinated Zn(II) complexes with model hard and soft ligands. Variations of the binding energy and of its components with the number and the charges of the ligands. J. Comp. Chem. 21:1011-1039.

  • Wetzel, A.W., Ade, A., Bookstein, F.L., Green, W., Athey, B.D. 2000. Representation and Performance Issues in Navigating Visible Human Datasets, The Third Visible Human Project Conference, Oct 4-5, 2000, National Institutes of Health, Bethesda, Maryland USA

  • Wymore, T. and Wong, T. 2000. The Structure and Dynamics of ACTH(1-10) on the surface of a Sodium Dodecylsulfate (SDS) micelle: A molecular dynamics study. Journal of Biomolecular Structure and Dynamics 18:461-476.

  • Crowley, M.F., Deerfield III, D.W., Darden, T.A., Cheatham III, T.E. 2000. Molecular dynamics simulations using particle-mesh Ewal methods. In: Industrial Strength Parallel Computing. Koniges, A. (Ed), Morgan Kaufmann. pp. 355 - 388.

  • Goddard, N.H., Hood G., Cohen, J.D., Eddy, W.F., Genovese, C.R., Noll, D.C. and Nystrom, L.E. 2000. Functional magnetic resonance imaging dataset analysis. In: Industrial Strength Parallel Computing. Koniges, A. (Ed), Morgan Kaufmann. pp. 431 - 452.

  • Ropelewski, A.J., Nicholas Jr., H.B., Deerfield II, D.W. 2000. Selective and Sensitive Comparison of Genetic Sequence Data. In: Industrial Strength Parallel Computing. Koniges, A. (Ed), Morgan Kaufmann. pp. 453 - 479.


  • Perozcih, J., Nicholas, H.B., Lindahl, R. & Hempel, J. 1999 The big book of aldehyde dehydrogenase sequences. An overview of the extended family. In: Advances in Experimental Medicine and Biology, 463:1-8. Enzymology and Molecular Biology of Carbonyl Metabolism 7. (Weinger, H., Maser, E., Crabb, D.W., and Lindahl, R. Eds.).

  • Perozich, J., Nicholas, H.B., Wang, B.-C., Lindahl, R. & Hempel, J., Relationships within the aldehyde dyhdrogenase extended family. Protein Science. 8:137-146, 1999.

  • Welling, J., Foss, G., Deerfield II, D.W., The Biomedical Supercomputing Initiative at the Pittsburgh Supercomputing Center. SIG-Bio Newsletter 19:17-19, 1999.


  • Goddard, N.H. and Hood. G. Large-Scale Simulation using Parallel GENESIS in The Book of GENESIS, 2nd ed., Bower, J.M. and Beeman, D. (Eds), Springer-Verlag, 1998

  • Wetzel, A.W., Crowley, R., Dawson, R., Gilbertson, J., Kim, S.J., Yagi, Y., Zheng, L., Gadd, C., Joo, Y.M., Deerfield, D.W., and Becich, M.J. Evaluation of prostate tumor grades by content based image retrieval. 27th Applied Imagry and Pattern Workshop: Advances in Computer Assisted Recognition Washington D.C., Oct 16, 1998, and SPIE Proceedings volume 3584, pages 244-252, 1998.


  • Beeman, D., Bower, J.M., DeSchutter, E., Efthimiadis, E.N., Goddard, N., and Leigh, J., The GENESIS Simulator-based Neuronal Database''. In Neuroinformatics : An Overview of the Human Brain Project (Progress in Neuroinformatics Research) Huerta, M. (Eds.), Lawrence Earlbaum Associates, 1997

  • Cho, B., Taylor, D.C., Nicholas Jr., H.B., Schmidt, F.J. Interacting RNA Species Identified by Combinatorial Selection. Biorganic and Medincinal Chemistry, 5:1107-1113, 1997.

  • Cheatham III, T.E., Crowley, M.F., Fox, T., and Kollman, P.A. 1997. A molecuilar level picture of the stabilization of A-DNA in mixed ethanol-water solutions. Proc. Nat. Acad Sci. 94, 9626-9630.

  • Crowley, M.F., Darden, T.A., Cheatham, T.E. III, Deerfield, D.W. II Adventures in Improving the Scaling and Accuracy of a Parallel Molecular Dynamics Program J. Supercomputing, 11:255-278, 1997

  • Deerfield, D.W., II, Pedersen,L.G. 1997. Structure and Relative Acidity for a Zinc Finger. J. Mol. Struct. (THEOCHEM), 416:221-226.

  • Deerfield II, D.W., Holland-Minkley, A.M., Geigel, J., Nicholas Jr., H.B., Classification of the Environment of Protein Residues J. Prot. Chem. 16:441-447, 1997.

  • Wetzel, A. W.. 1997. Computational Aspects of Pathology Image Classification and Retrieval J. Supercomputing, 11:279-293.

  • Goddard, N.H., Hood G., Cohen, J.D., Eddy, W.F., Genovese, C.R., Noll, D.C. and Nystrom, L.E., Online Analysis of Functional {MRI} Datatsets on Parallel Platforms J. Supercomputing,
    11:295-318, 1997

  • Goddard, N.H. and Hood, G., Parallel Genesis for Large Scale Modeling, Computational Neuroscience: Trends in Research 1997. Plenum Publishing, NY, 1997, pp 911--917.

  • Goddard, N.H. Human Activity Recognition in Motion-Based Recognition (Computational Imaging and Vision, V. 9), Shah, M. and Jain, R. (Eds.), Kluwer Academic Publishers, 1997. pp 147--170.

  • Nicholas, K.B., Nicholas Jr, H.B., Deerfield II, D.W., GeneDoc: Analysis and Visualization of Genetic Variation 4:1-4, 1997.

  • Ropelewski, A.J., Nicholas Jr., H.B., Deerfield II, D.W. Implementation of Genetic Sequence Alignment Programs on Supercomputers J. Supercomputing, 11:237-253, 1997


  • Deerfield, D.W., II, Pedersen, L.G. Enol and Deprotonated Forms of Acetic and Malonic Acid J. Mol. Struct. (THEOCHEM) 368:163-196, 1996.

  • James L. McClelland and Nigel H. Goddard, Considerations Arising from a Complementary Learning Systems Perspective on Hippocampus and Neocortex , Hippocampus 6(6):654-665, 1996.

  • Wimberly, F.C., Lambert, M.H., Nystrom, N.A., Ropelewski, A.J., and Young,W.S., Porting Third-Party Applications Packages to the Cray T3D: Programming Issues and Scalability Results Parallel Computing, Volume 22, 1073-1089, 1996


  • S.Cabaniss, D.W. Deerfield II, D.M. Monroe, R.G. Hiskey, and L.G. Pedersen. Is Ca(II) ion binding to prothrombin fragment 1 intrinsically cooperative, or is the cooperative binding accounted for by self-association? Blood Coagulation and Fibrinolysis: 6:464-473 (1995) Medline Abstract

  • D.W. Deerfield II, D.J. Fox, M. Head-Gordon, R.G. Hiskey, and L.G. Pedersen. The first Solvation Shell of Magnesium Ion in a Model Protein Environment with Formate, Water and X=NH3, H2S, Imidazole, Formaldehyde and Chloride as Ligands: An ab initio Study. Proteins: Structure, Function and Genetics: 21:244-255 (1995) Medline Abstract

  • Deerfield, D.W., II, Pedersen, L.G., An ab initio Quantum Mechanical Study of Thioesters., J. Mol. Struct. (THEOCHEM) 358:99-106 (1995).

  • Deerfield, D.W., II, Pedersen, L.G., The First Solvation Shell of Magnesium Ions in a Model Nucleic Acid Environment: An ab initio Study., J. Biomol. Struct. Dynam., 13:167-180 (1995). Medline Abstract

  • H.W. Kim, T.J. Shen, D. P. Sun, N. T. Ho, M. Madrid and C. Ho, A Low Oxygen Affinity Recombinant Hemoglobin (96Val-->Trp): Switching Quaternary Structure without Changing the Ligation State, J. Mol. Biol, 248: 867-882 (1995). Medline Abstract

  • Hugh B. Nicholas, Jr., William H. McClain. Searching tRNA Sequences for Relatedness to Aminoacyl-tRNA Synthetase Families J. Mol. Evol: 40:482-486 (1995) Medline Abstract

  • H.B. Nicholas Jr., A.J. Ropelewski, D.W. Deerfield II and J.G. Behrmann A Metric Measure for Comparing Sequence Alignments in Methods in Protein Sequence Analysis, Plenum Press, NY, eds. M.Z. Atassi, E. Appella, 515-525, 1995.

  • Nicholas HB Jr, Persson B, Jornvall H, Hempel J Ethanol utilization regulatory protein: profile alignments give no evidence of origin through aldehyde and alcohol dehydrogenase gene fusion. Protein Sci 4 (12): 2621-2624 (Dec 1995) Medline Abstract

  • Patrick, T.B., Springer, G.K., Nicholas, H.B., and Ropelewski, A.J. Information Retrieval Maps for Biomedical Research MEDINFO 8 Pt 2, R.A. Greens ed., 1443-1446, 1995 Medline Abstract


  • Deerfield II, D.W., Holland-Minkley, A., Hempel, J.D., and Nicholas, Jr., H.B. Conformational Flexibility of the Gly-Gly dipeptide within protein structures. J. Prot. Chem, vol. 113, pp. 526 (1994).

  • Goddard, Nigel H., Rochester Connectionist Simulation Environment In Neural Network Simulation Environments, J. Skrzypek, Ed., Kluwer, 1994.

  • Kim, H.W., Shen, T.J., Sun, D.P., Ho, N. T. , Madrid, M., Tam, M.F, Zou, M., Cottam, C. and Ho, C., Restoring Allosterism with Compensatory Mutations in Hemoglobin. Proc. Natl. Acad. Sci. U.S.A., vol. 91, pp. 11547-11551 (1994).

  • Lee, A.K.S., Nicholas Jr., H.B., and Rosenquist, G.L. 1994. Evidence for a helix-turn-helix in the N-termnius of CCK-58. Proceedings of the New York Academy of Sciences, 713, 328-330 (1994) Medline Abstract

  • Leng, B., Buchanan, B., and Nicholas, Jr., H.B., 1994. Protein Secondary Structure Prediction Using Two-Level Case Based Reasoning. Computational Biology, vol. 1, No 1., pp 25-37. Medline Abstract

  • Nicholas, Jr., H.B., Hempel, J.D., Hinich. A., Deerfield II, D.W., Behrmann, J., and Ropelewski, A.J. Quantitative evaluation of different multiple alignment programs. J. Prot. Chem, vol. 113, pp. 535 (1994).

  • Nicholas, Jr., H.B., Rosenquist, G.L., Lee, A.K.S., and Phan, T. Sequence Analysis for Hormone and Receptors. Digestive Diseases and Sciences, vol. 39, pp 1824 (1994).


  • Goddard, N. H. Associating What and Where Using Temporal Cues." In: Proceedings of the 15th Annual Conference of the Cognitive Science Society. Hillsdale, NJ: Lawrence Erlbaum Associates, 1993.

  • Hempel, J., H.B. Nicholas Jr. and R. Lindahl. Aldehyde Dehydrogenases: Widespread Structural and Functional Diversity Within a Shared Framework. Protein Science, 2:1890-1900, 1993. Medline Abstract

  • Leng, B., B. G. Buchanan and H. B. Nicholas. Protein Secondary Structure Prediction Using Two-Level Case-Based Reasoning, ISMB 1: 251-259 (1993) Medline Abstract

  • Rosenquist, G.L. and Nicholas Jr., H.B. 1993. Analysis of sequence requirements for protein tyrosine sulfation. Protein Science, 2:215-222. Medline Abstract

  • Shuey, S.W., Deerfield II, D.W., Amburgey, J.C., Cabaniss, S.E., Huh, N.-W., Charifson, P.S., Pedersen, L.G., Hiskey, R.G. Cyclohexanediol Biphosphates as Models for Phospholipid-Metal Ion Binding Sites. (1993) Bioorganic Chemistry, 21:95-108.


  • LLinas, E., LLinas, M. and Madrid, M., Refined Solution Structure and Ligand-binding Properties of PDC-109 Domain b, Journal of Molecular Biology, vol. 223: 281, 1992.

  • Rosenquist, Grace L. and Hugh B. Nicholas Jr. Analysis of Protein Sulfation Sites. Abstract in Reg Peptide 40 (1992): 250.

  • Wang, J., C. V. Rojas, J. Zhou, L. S. Schwartz, H. Nicholas, and E. P. Hoffman, Sequence and Genomic Structure of the Human Adult Skeletal Muscle Sodium Channel alpha Subunit Gene on 17 q., Biochemical and Biophysical Research Communications, 1992, vol. 182, pp. 794-801.

  • York, D.M., Darden, T., Deerfield II, D.W., Pedersen, L.G. The Interaction of Na(I), Ca(II) and Mg(II) Metal Ions with Duplex DNA. (1992) Int. J. Quantum Chem: Biol. Symp, 19:145-166.


  • Deerfield II, D.W., Fox, D.J., Head-Gordon, M., Hiskey, R.G., Pedersen, L.G. The Interaction of Calcium and Magnesium Ions with Malonate and the Role of the Waters of Hydration: A Quantum Mechanics Study. (1991) J. Am. Chem. Soc., 113:1892-1899.

  • Giras, G. , V. Hartonas-Garmhausen, M. Kopko, C. Maher, A. Ropelewski, and Hugh Nicholas, Distributing the Dynamic Programming Algorithm Across Heterogeneous Supercomputers, Supercomputing 1991 Proceedings.

  • Hempel, J., Nicholas, H., and Jornvall, H., Thiol Proteases and Aldehyde Dehydrogenase: Evolution from a Common Thiolesterase Precursor?, Proteins: Structure, Function and Genetics, vol. 11, no. 3, 1991, pp. 176-183.

  • Monroe, D.M., Deerfield II, D.W., , Olson, D.L., Stewart, T.N., Treanor, R.E., Roberts, H.R., Hiskey, R.G., Pedersen, L.G. Calcium Ion binding to Human and Bovine Factor X. (1991) Blood Coagulation and Fibrinolysis, 1:633-640. Medline Abstract

  • Smith, P.R., Ropelewski, A.J., Balog, D.A., Gottesman, Deerfield II, D.W., A Simple Approach for the Distribution of Computationally Intense Tasks in an Heterogeneous Environment: Distribution of the MDPP Image Processing Package. (1991) CABIOS, 7:501-507. Medline Abstract


  • Cain, J.T., Deerfield II, D.W., Hiskey, R.G., Pedersen, L.G. The Divalent Metal Ion Mediated Interaction of Proteins with Negatively Charged Membranes: A Model Study Employing Molecular Mechanics. (1990) Int. J. Peptide Protein Res., 35:111-116. Medline Abstract

  • Lapadat, M.A., Deerfield II, D.W., Pedersen, L.G. Spremulli, L.L. Generation of Potential Structures for the G-Domain of Chloroplast EF-Tu(CHL) using Comparative Molecular Modeling. (1990) Proteins, 8:237-250. Medline Abstract


Search NRBSC

Related Links


Movies and graphics

Software development
and distribution

Online teaching tools


NRBSC projects are made possible by these sponsors:

NIH logo.  Pittsburgh Supercomputing Center logo.  NCRR logo.