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Thomas Charles Terwilliger

Thomas Terwilliger

Capabilities

  • Biosciences
  • Biosecurity
  • Vaccines and therapeutics for infectious diseases
  • Computational Physics and Applied Mathematics
  • Numerical modeling
  • Algorithms

Expertise

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Macromolecular X-ray crystallography - Development of algorithms and software for determining crystal structures of macromolecules such as proteins and RNA.

Our group is part of the collaborative PHENIX project, an effort led by Paul Adams at LBL that is producing a comprehensive software package for macromolecular structure determination. The PHENIX package includes my SOLVE/RESOLVE software as well as many additional powerful algorithms, including maximum-likelihood molecular replacement (Randy Read's Phaser software), full maximum-likelihood refinement (Paul Adams, Ralf Grosse-Kunstleve, and Pavel Afonine's phenix.refine), model improvement and validation (the Richardson laboratory's Molprobity software) and many other useful tools. The PHENIX software is available free for academic users..

Structural Biology of Bacterial Efflux Pumps

We are part of a multidisciplinary team focused on understanding how bacteria can pump antibiotics out of the cell and prevent the antibiotics from working. We hope that this understanding may help in developing new drugs that will restore the efficacy of existing antibiotics by blocking these pumps. Our role in this project is to determine structures of the bacterial efflux pumps and their components, focusing on pumps from the pathogenic bacteria Burkholderia pseudomallei but also including other related pumps. As a preliminary part of this work we recently determined the structure of an E. coli AcrB pump component bound to the antibiotic Linezolid (Hung et al., 2013).

Structural Genomics - Determination of structures of proteins from Mycobacterium tuberculosis to form a foundation for rational drug design.

Proteins are the molecular machines of life, and a knowledge of their three-dimensional structures is crucial for understanding how they work. A main focus of our laboratory is determining and analyzing the structures of proteins. Our group, along with structural biologists around the world, recognized in the late 1990s that a large-scale effort to determine structures of thousands of proteins could have a profound effect on the understanding of biology. The U.S. Department of Energy and later the National Institutes of Health (the NIH Protein Structure Initiative) have funded our Los Alamos structural genomics team and others around the US to develop and apply technologies for large-scale structure determination. Structural genomics was a major worldwide effort over the past 15 years, and in 2001 our group helped found the International Structural Genomics Organization (ISGO) in order to promote international cooperation in structural genomics.

The TB Structural Genomics Consortium (TB SGC)

The TB Structural Genomics Consortium is a worldwide consortium of scientists from around the world devoted to determining structures of proteins from the pathogenic organism M. tuberculosis. Our group founded and led the TB SGC for its first 5 years as part of phase 1 of the NIH Protein Structure Initiative. Now the TB SGC continues as an NIAID-funded project led by Jim Sacchettini at Texas A&M University, with Los Alamos as an active member. The TB Structural Genomics Consortium has solved over a hundred structures of M. tuberculosis proteins already. We hope that these structures will form a foundation for drug discovery that will lead to improved anti-TB therapy.
 

Education

A. B., Physics, magna cum laude, Harvard College, 1978 
Ph.D., Molecular Biology, University of California at Los Angeles, 1981 

 

LANL Positions

Laboratory Fellow, Los Alamos National Laboratory, 2001

Structural Genomics Thrust Leader, Los Alamos National Laboratory, 1999 - 2001

Group Leader, Structural Biology Group, Los Alamos National Laboratory, 1995 - 1999

Technical Staff Member, Genomics and Structural Biology Group, Los Alamos National Laboratory, 1992 - 1995

 

Professional Societies

Association for the Advancement of Science
American Crystallographic Association
American Society of Biological Chemists
The Protein Society

 

Awards

Bronze Award, Michigan Mathematics Prize Competition, 1976
Harvard Scholarship, 1976
NSF Graduate Fellowship, 1978 - 1981
Helen Hay Whitney Postdoctoral Fellowship, 1982 - 1985
Presidential Young Investigator Award, 1985 - 1990
R&D100 award, 1998
Los Alamos Distinguished Copyright Award, 1999
AAAS Fellow, 2000
Los Alamos Platinum licensing award, 2001
Los Alamos National Laboratory Fellow, 2001
Los Alamos Distinguished Patent Award, 2004
Federal Laboratory Consortium Award for Excellence in Technology Transfer, 2005
Fellow, American Crystallographic Association, 2012
Trueblood Award, American Crystallographic Association, 2013

 

Patents

Wise, A. A., Kuske, C. R., Terwilliger, T. C. (2004). Detection of phenols using engineered bacteria. US Patent No. 6,773,918
Terwilliger, T. C. (2004). Maximum likelihood density modification by pattern recognition of structural motifs. US Patent No. 6,721,664
Terwilliger, T. C.(2005). Likelihood-based modification of experimental crystal structure electron density maps. US Patent No. 6,931,329
Terwilliger, T. C. (2006) . Method for removing atomic-model bias in macromolecular crystallography. US Patent No. 7,085,653
 

 

Publications

Cabantous, S., Nguyen, H. B., Pedelacq, J. D., Koraïchi, F., Chaudhary, A., Ganguly, K., Lockard, M. A., Favre, G., Terwilliger, T.C., Waldo, G. S. (2013). A New Protein-Protein Interaction Sensor Based on Tripartite Split-GFP Association. Scientific reports, 3 [doi:  10.1038/srep02854]

Nwachukwu, J. C., Southern, M. R., Kiefer, J. R., Afonine, P. V., Adams, P. D., Terwilliger, T. C., Nettles, K. W. (2013). Improved Crystallographic Structures Using Extensive Combinatorial Refinement. Structure,epub ahead of print [PMID: 24076406]

DiMaio, F., Echols, N., Headd, J. J., Terwilliger, T. C., Adams, P. D., & Baker, D. (2013). Improved low-resolution crystallographic refinement with Phenix and Rosetta. Nature methods 10, 1102-1104.

Edayathumangalam, R., Wu, R., Garcia, R., Wang, Y., Wang, W., Kreinbring, C. A., Bach, A., Liao, J., Stone, T., Terwilliger, T.C., Hoang, Q.Q., Belitsky, B.R., Petsko, G.A., Liu, D. (2013). Crystal structure of Bacillus subtilis GabR, an autorepressor and transcriptional activator of gabT. Proceedings of the National Academy of Sciences,110, 17820-17825.

Terwilliger, T. C. (2013). Model-Building and Reduction of Model Bias in Electron Density Maps. In Advancing Methods for Biomolecular Crystallography, pp. 193-203.

Uervirojnangkoorn, M., Hilgenfeld, R., Terwilliger, T. C., & Read, R. J. (2013). Improving experimental phases for strong reflections prior to density modification. Acta Crystallographica Section D: Biological Crystallography, 69, 2039-2049.

Terwilliger, T. C., Read, R. J., Adams, P. D., Brunger, A. T., Afonine, P. V.,  Hung, L. W. (2013). Model morphing and sequence assignment after molecular replacement. Acta Crystallographica Section D: Biological Crystallography, 69, 2244-2250.

Hung, L.-W., Kim, H.-B., Murakami, S., Gupta, G., Kim, C.-Y., Terwilliger, T.C. (2013). Crystal structure of AcrB complexed with linezolid at 3.5 Å resolution. J. Struct. Func. Genomics 14, 71-75.

Terwilliger, T.C. (2013). Finding non-crystallographic symmetry in density maps of macromolecular structures. J. Struct. Funct. Genomics 14, 91-95.

Adams P.D., Baker D., Brunger A.T., Das R., Dimaio F., Read R.J., Richardson D.C., Richardson J.S., Terwilliger T.C. (2013). Advances, Interactions, and Future Developments in the CNS, Phenix, and Rosetta Structural Biology Software Systems.  Annual Reviews of Biophysics, 42: 265-287.

Buchko, G.W., Kim, H., Myler, P. J., Terwilliger, T. C., Kim, C. Y. (2012).  Chemical shift assignments for Rv0577, a putative glyoxylase associated with virulence from Mycobacterium tuberculosis. Biomolecular NMR Assignments 6., 43-46.

Grosse-Kunstleve R.W., Terwilliger T.C., Sauter N.K., Adams P.D. (2012). Automatic Fortran to C++ conversion with FABLE. Source Code Biol Med. 7:5.

Adams, Paul D., Afonine, Pavel V., Bunkoczi, Gabor, Chen, Vincent B., Echols, N., Headd, J. J., Hung, L.-W., Jain, S., Kapral, G. J., Grosse-Kunstleve, R. W., McCoy, A. J., Moriarty, N. W., Oeffner, R. D., Read, R. J., Richardson, D. C., Richardson, J. S., Terwilliger, T. C., Zwart, P. H. (2012).  The Phenix software for automated determination of macromolecular structures. Methods 55, 94-106.

Echols, N., Grosse-Kunstleve, R.W., Afonine, Pavel V., Bunkoczi, Gabor, Chen, Vincent B., Headd, J.J., McCoy, A.J., Moriarty, N.W., Read, R.J., Richardson, D.C., Richardson, J.S., Terwilliger, T.C., Adams, P.D. (2012). Graphical tools for macromolecular crystallography in PHENIX.  J. Appl. Cryst. 45, 581-586.

Terwilliger, T. C., DiMaio, F., Read, R. J., Baker, D., Bunkóczi, G., Adams, P. D., Grosse-Kunstleve, R. W., Afonine, P. V., Echols, N. (2012). phenix.mr_rosetta: Molecular replacement and model rebuilding with Phenix and Rosetta. J. Struct. Funct. Genomics 13, 81-90.

Terwilliger, T. C., Read, R. J., Adams, P. D., Brunger, A. T., Afonine, P. V., Grosse-Kunstleve, R. W., Hung, L.-W. (2012). Improved crystallographic models through iterated local density-guided model deformation and reciprocal space refinement. Acta Cryst. D68, 861-870.

Afonine, P. V., Echols, N. Grosse-Kunstleve, R. W., Headd, J. J., Moriarty, N. W., Mustyakimov, M., Terwilliger, T. C. Urhumtsev, A., Zwart, P. H., Adams, P. D. (2012). Towards automated crystallographic structure refinement with phenix.refine. Acta Cryst. D68, 352-367.

Brunger, A. T., Das, D., Deacon, A. M., Grant, J., Terwilliger, T. C., Read, R. J., Adams, P. D., Levitt, M., Schröder, G. F. (2012). Application of DEN refinement and automated model building to a difficult case of molecular-replacement phasing:the structure of a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum. Acta Cryst. D68, 391-403.

Pedelacq, J.D., Nguyen, H., Cabantous, S., Mark, B., Listwan, P., Bell, C., Friedland, N., Lockard, M., Faille, A., Mourey, L., Terwilliger, T., Waldo, G. (2011). Experimental mapping of soluble protein domains using a hierarchical approach. Nucleic Acids Res. 39, e125.

Lockard, M. A., Listwan, P., Pedelacq, J.D., Cabantous, S., Nguyen, H., Terwilliger, T.C., Waldo, G.S. (2011). A high-throughput immobilized bead screen for stable proteins and multi-protein complexes. Protein Engineering, Design, and Selection 24, 565-578.

Buchko, G.W., Phan, I., Myler, P.J., Terwilliger, T.C., Kim, C.-Y. (2011). Inaugural structure from the DUF3349 superfamily of proteins, Mycobacterium tuberculosis Rv0543c. Arch. Biochem. Biophys. 506, 150-156.

Chim, N., Habel, J.E.,  Johnston, J.M., Kireger, I., Mialluo, L., Sankaranarayanan, R., Morse, R.P., Bruning, J., Swanson, S., Kim, H., Kim, C.-Y., Li, H., Bulloch, E.M., Payne, R.J., Manos-Turvey, A., Hung, L.-W., Baker, E.N., Lott, J.S., James, M.N.G., Terwilliger, T.C., Eisenberg, D.S., Sacchettini, J.C., Goulding, C.W. (2011)  The TB Structural Genomics Consortium: A decade of progress, Tuberculosis, 91: 155-172.

DiMaio, F., Terwilliger, T.C., Read, R.J., Wlodawer, A., Oberdorfer, G., Wagner, U., Valkov, E., Alon, A., Fass, D., Axelrod, H.L., Das, D., Vorobiev, S.M., Iwai, H., Pokkuluri, P.R., D. Baker (2011). Improving molecular replacement by density and energy guided protein structure optimization Nature 473, 540-543.

Habel, J. E., Bursey, E. H., Rho, B.-S., Kim, C.-Y., Segelke, B. W., Rupp, B., Park, M. S., Terwilliger, T. C., Hung, L.-W. (2010). Structure of Rv1848 (UreA), the Mycobacterium tuberculosis urease gamma subunit. Acta Cryst. F66, 781-786.

Buchko, G.W., Kim, C.-Y. Terwilliger, T.C., Myler, P. (2010) Solution structure of Rv2377c-founding member of the MbtH-like protein family.  Tuberculosis, 90, 245-251.

Terwilliger, T. C. (2010). Rapid chain-tracing of polypeptide backbones in electron density maps. Acta Cryst. D66, 285-294.

Terwilliger, T. C. (2010). Rapid model-building of β-sheets in electron density maps. Acta Cryst. D66, 276-284.

Terwilliger, T. C. (2010). Rapid model-building of α-helices in electron density maps. Acta Cryst. D66, 268-275.

Adams, P. D., Afonine, P. V., Bunkóczi, G., Chen, V. B., Davis, I. W., Echols, N., Headd, J. J., Hung, L.-W., Kapral, G. J., Grosse-Kunstleve, R. W., McCoy, A. J., Moriarty, N. W., Oeffner, R., Read, R. J., Richardson, D. C., Richardson, J. S., Terwilliger, T. C., Zwart, P. H (2010). PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Cryst. D66, 213-221.

Chim N., Riley R., The J., Im S., Segelke B., Lekin T., Yu M., Hung L.W., Terwilliger T., Whitelegge J.P., Goulding C.W. (2010). An extracellular disulfide bond forming protein (DsbF) from Mycobacterium tuberculosis: Structural, biochemical and gene expression analysis. J. Mol. Biol. 396, 1211- 1226.

Kim, C.-Y., Webster, C., Roberts, J. K. M, Moon, J. H., Alipio Lyon, E. Z., Kim, H., Yu, M., Hung, L.-W., Terwilliger, T. C. (2009). Analysis of nucleoside-binding proteins by ligand-specific elution from dye resin: application to Mycobacterium tuberculosis aldehyde dehydrogenases. J. Struct. Funct. Genomics 10, 291-301.

Adams, P.D., Afonine, P. V., Grosse-Kunstleve, R. W., Read, R.J., Richardson, J. S., Richardson, D. S., Terwilliger, T. C. (2009). Recent developments in phasing and structure refinement for macromolecular crystallography. Current Opinion in Structural Biology 19, 566–572.

Terwilliger, T.C., Adams, P.D., Read, R.J., McCoy, A. J., Moriarty, N.W., Grosse-Kunstleve, R.W., Afonine, P.V., Zwart, P., Hung, L.-W. (2009). Decision-Making in Structure Solution using Bayesian Estimates of Map Quality: The PHENIX AutoSol Wizard. Acta Cryst D65, 582-601.

Listwan, P., Terwilliger, T.C., Waldo, G.S. (2009). Automated, high-throughput platform for protein solubility screening using and split-GFP system. J. Struct. Funct. Genomics 10, 47-55.

Roberts, J.K.M., Webster, C., Terwilliger, T.C., and Kim, C.-Y. (2009) High-throughput analysis of nucleoside-and nucleotide-binding by proteins. In Systems Chemistry, Martin G. Hicks & Carsten Kettner (Eds.) Proceedings of the Beilstein-Institut Workshop, May 26th – 30th, 2008, Bozen, Italy.

Kim, K.H., Yang, J.K., Waldo, G.S. ; Terwilliger, T.C. ; Suh, S.W. (2008). From no expression to high-level soluble expression in Escherichia coli by screening a library of the target proteins with randomized N-termini. Methods in Molecular Biology, Vol. 426 ( B. Kobe, M. Guss and T. Huber, Eds.).

Zwart, P. H., Afonine, P. V., Grosse-Kunstleve, R. W., Hung, L.-W., Ioerger, T. R., McCoy, A. J., Mckee, E., Moriarty, N. W., Read, R. J., Sacchettini, J., C., Sauter, N. K., Storoni, L. C., Terwilliger, T. C., Adams, P. D (2008). Automated Structure Solution with the PHENIX Suite. Methods in Molecular Biology, Vol. 426 ( B. Kobe, M. Guss and T. Huber, Eds.).

Cabantous S, Rogers Y, Terwilliger T, Waldo GS (2008). New Molecular Reporters for Rapid Protein Folding Assays. PLoS ONE 3(6): 1-10 (e2387).

Terwilliger, T.C., Grosse-Kunstleve, R.W., Afonine, P.V., Moriarty, N.W., Adams, P.D., Read, R.J., Zwart, P., Hung, L.-W. (2008). Iterative-build OMIT maps: map improvement by iterative model building and refinement without model bias. Acta Cryst D, 64, 515-524.

Structural Genomics Consortium; China Structural Genomics Consortium; Northeast Structural Genomics Consortium, Gräslund S., Nordlund P., Weigelt J., Bray J., Gileadi O., Knapp S., Oppermann U., Arrowsmith C., Hui R., Ming J., dhe-Paganon S., Park H.W., Savchenko A., Yee A., Edwards A., Vincentelli R., Cambillau C., Kim R., Kim S.H., Rao Z., Shi Y., Terwilliger T.C., Kim C.Y., Hung L.W., Waldo G.S., Peleg Y., Albeck S., Unger T., Dym O., Prilusky J., Sussman J.L., Stevens R.C., Lesley S.A., Wilson I.A., Joachimiak A., Collart F., Dementieva I., Donnelly M.I., Eschenfeldt W.H., Kim Y., Stols L., Wu R., Zhou M., Burley S.K., Emtage J.S., Sauder J.M., Thompson D., Bain K., Luz J., Gheyi T., Zhang F., Atwell S., Almo S.C., Bonanno J.B., Fiser A., Swaminathan S., Studier F.W., Chance M.R., Sali A., Acton T.B., Xiao R., Zhao L., Ma .LC., Hunt J.F., Tong L., Cunningham K., Inouye M., Anderson S., Janjua H., Shastry R., Ho C.K., Wang D., Wang H., Jiang M., Montelione G.T., Stuart D.I., Owens R.J., Daenke S., Schütz A., Heinemann U., Yokoyama S., Büssow K., Gunsalus K.C. Protein production and purification. Nature Methods. 2008, 135-46.

Murillo, A.C. , Li, H.Y. , Alber, T., Baker, E.N. , Berger, J.M. , Cherney, L.T. , Cherney, M.M. , Cho, Yoon Song , Eisenberg, D., Garen, C.R. , Goulding, C.W. , Hung, L.W. , Ioerger, T.R., Jacobs, W.R. , James, M.N.G. , Kim, C. , Krieger, I. , Lott, J.S. , Sankaranarayanan, R. , Segelke, B.W. , Terwilliger, T.C. , Wang, F. , Wang, S. , Sacchettini, J.C. (2007). High throughput crystallography of TB drug targets. Infectious Disorders - Drug Targets; 7, 127-139.

Terwilliger, T.C., Grosse-Kunstleve, R.W., Afonine, P.V., Moriarty, N.W., Zwart, .PH., Hung, L.W., Read, R.J., Adams, P.D. (2007). Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard. Acta Cryst D, 64, 61-69.

Kim, S.M., Bowers, P.M., Pal, .D, Strong, M., Terwilliger, T.C., Kaufmann, M., Eisenberg, .D. (2007). Functional linkages can reveal protein complexes for structure determination. Structure 15, 1079-1089.

Bursey E., Kim C.-Y., Terwilliger T.C., Hung L.-W.(2007) An Automated High-throughput Screening Method for the Identification of High-yield, Soluble Protein Variants.  J. Struc. Func. Gen. 7, 139-147.

Friedland, N., Mack, T.R., Yu, M., Hung, L.-W., Terwilliger, T.C., Waldo, G.S., Stock, A.M. (2007). Domain orientation in the inactive response regulator Mycobacterium tuberculosis MtrA provides a barrier to activation. Biochemistry 46, 6733-6743.

Terwilliger, T.C., Grosse-Kunstleve, R.W., Afonine, P.V., Adams, P.D., Moriarty, N.W., Zwart, P., Read, R.J., Turk, D., Hung, L.-W. (2007). Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models. Acta Cryst. D63, 597-610.

Terwilliger, T.C., Adams, P.D., Moriarty, N.W., Cohn, J.D. (2007). Ligand identification using electron-density map correlations Acta Cryst.. D63, 101-107.

Goulding, C.W., Bowers, P.M., Segelke, B., Lekin, T., Kim, C.-Y., Terwilliger, T.C., Eisenberg, D. (2007). The Structure and Computational Analysis of Mycobacterium tuberculosis Protein CitE Suggest a Novel Enzymatic Function J. Mol Biol. 365, 275-283.

Terwilliger, T.C., Klei, H., Adams, P.D., Moriarty, N.W., Cohn, J.D. (2006). Automated ligand fitting by core-fragment fitting and extension into density. Acta Cryst. D62, 915-922.

Rho, B.-S., Hung, L.-W., Holton, J.M., Vigil, D., Kim, S.-I., Park, M.S., Terwilliger, T.C., Pedelacq, J.D. (2006). Functional and structural characterization of a thiol peroxidase from Mycobacterium tuberculosis. J. Mol Biol. 361, 850-863.

Buchko, G. W., Kim, C.–Y., Terwilliger, T. C.., Kennedy, M. A. (2006). Solution Structure of the Conserved Hypothetical Protein Rv2302 from Mycobacterium tuberculosis. J. Bacteriol. 188, 5993-6001.

Prabu, J. R., Thamotharan, S., Khanduja, J. S., Alipio, E. Z., Kim, C.-Y., Waldo, G.S., Terwilliger, T. C., Segelke, B., Lekin, T., Toppani, D., Hung, L.-W., Yu, M., Bursey, E., Muniyappa, K., Chandara, N.R., Vijayan, M. (2006). Structure of Mycobacterium tuberculosis RuvA, a protein involved in recombination. Acta Cryst F62, 731-734.

Pédelacq, J.D., Rho, B. S., Kim, C.-Y., Waldo, G. S.,  Lekin, T. P., Segelke, B. W., Rupp, B., Hung, L.-W., Kim, S.-I., Terwilliger, T. C. (2006) Crystal structure of a putative pyridoxine 5'-phosphate oxidase (Rv2607) from Mycobacterium tuberculosis. Proteins. 62:563-569.

Furnham, N., Blundell, T. L., DePristo, M. A., Terwilliger, T.C. (2006). Is one solution good enough? Nature Structural & Molecular Biology 13, 184 – 185.

Pédelacq, J.-D., Cabantous, S., Tran, T., Terwilliger, T.C., Waldo, G. S. (2006). Engineering and characterization of a superfolder green fluorescent protein. Nature Biotechnology, 24, 79-88.

Cabantous, S, Pédelacq, J.-D., Mark, B. L., Naranjo, C., Terwilliger, T.C., Waldo, G.S. (2005). Recent Advances in GFP Folding Reporter and Split-GFP Solubility Reporter Technologies. Application to Improving the Folding and Solubility of Recalcitrant Proteins from Mycobacterium tuberculosis.  J. Struct. Func. Genomics 6, 113-119.

Pedelacq, J.D., Waldo, G.S., Cabantous, S., Liong, E.C, Terwilliger, T.C. (2005). Structural and functional features of an NDP kinase from the hyperthermophile crenarchaeon Pyrobaculum aerophilum. Protein Science 14, 2562-2573.

Kantardjieff, K.A.; Vasquez, C., Castro, P., Warfel, N.M., Rho, B.S., Lekin, T., Kim, C.Y., Segelke, B.W., Terwilliger, T.C., Rupp, B.  (2005). Structure of pyrR (Rv1379) from Mycobacterium tuberculosis: a persistence gene and protein drug target. Acta Cryst D 61, 355-364.

Cabantous, S., Terwilliger, T. C., Waldo, G. S. (2005). Protein tagging and detection with engineered self-assembling fragments of green fluorescent protein. Nature Biotechnology 23, 102-107.

Terwilliger, T. C. (2005). Harvesting should be a complete and repeatable record of experiment. Acta Cryst A61, c129

Terwilliger, T. C. (2004) Using prime-and-switch phasing to reduce model bias in molecular replacement. Acta Cryst. D60, 2144-2149.

Terwilliger, T. C. (2004) Structures and technology for biologists. Nature Structural and Molecular Biology 11, 296-297.

Wang, J. W., Chen, J. R., Gu, Y. X., Zheng, C. D., Jiang, F., Fan, H. F., Terwilliger, T.C., Hao, Q. (2004).  SAD phasing by combination of direct methods with the SOLVE/RESOLVE procedure.  Acta Cryst. D60, 1244-1253.

Kantardjieff, K. A., Kim, C.-Y., Naranjo, G., Waldo, G. S, Lekin, T., Segelke, B. W., Zemla, A., Park, M. S., Terwilliger, T. C. and Rupp, B. (2004). Mycobacterium tuberculosis rmlC epimerase (Rv3465): a promising drug-target structure in the rhamnose pathway.  Acta Cryst. D60, 895-902.

Adams, P. D., Gopal, K., Grosse-Kunsteleve, R. W., Hung, L.-W., Ioerger, T. R., McCoy, A. J., Moriarty, N. W., Pai, R. K., Read, R. J., Romo, T. D., Sacchettini, J. C., Sauter, N. K., Storoni, L. C. and Terwilliger, T. C. (2004). Recent developments in the PHENIX software for automated crystallographic structure determination.  J. Synchrotron Rad.  11, 53-55.

Terwilliger, T. C. (2004). SOLVE and RESOLVE: Automated structure solution, density modification, and model building.  J. Synchrotron Rad.  11, 49-52.

Terwilliger, T. C. (2003). Statistical density modification using local pattern matching. Acta Cryst. D59, 1688-1701.

Mou, T. C.,  Shen, M. C.,  Terwilliger, T. C. Gray, D. M. (2003) Binding and reversible denaturation of double-stranded DNA by Ff gene 5 protein. Biopolymers 70, 637-648.

Weeks, C. M., Adams, P. D., Berendzen, J., Brunger, A. T., Dodson, E. J., Grosse-Kunstleve, R. W., Schneider, T. R., Sheldrick, G. M., Terwilliger, T. C., and Turkenburg, M. (2003). Automatic solution of heavy-atom substructures.  Methods Enzymol. 374, 37-82.

Terwilliger, T. C. (2003). SOLVE and RESOLVE: Automated structure solution and density modification.  Methods Enzymol.  374, 22-36

Terwilliger, T. C., Park, M. S., Waldo, G. S., Berendzen, J., Hung, L.-W., Kim, C.-Y., Smith, C. V., Sacchettini, J. C., Bellinzoni, J., Bossi, R., De Rossi, E., Mattevi, A., Milano, A., Riccardi, G., Rizzi, M., Roberts, M. M., Coker, A. R., Fossati, G., Mascagni, P., Coates, A. R. M., Wood, S. P., Goulding, C. W., Apostol, M., Anderson, D. H., Gill, H. S., Eisenberg, D. S., Taneja, B., Mande, S., Pohl, E., Lamzin, V., Tucker, P., Wilmanns, M., Colovos, C., Meyer-Klaucke, W., Munro, A. W., McLean, KI. J., Marshall, K. R., Leys, D., Yang, J. K., Yoon, H.-J., Lee, B. I., Lee, M. G., Kwak, J. E., Han, B. W., Lee, J. Y, Baek, S.-H., Suh, S. W., Komen, M. M., Arcus, V. M. L., Baker, E. N., Lott, J. S., Jacobs, W., Jr., Alber, T., Rupp, B. (2003). The TB Structural Genomics Consortium: A resource for TB biology. Tuberculosis 83, 223-249.

Chaudhuri, B. N., Sawaya, M. R., Kim, C.-Y., Waldo, G. S., Park, M. S., Terwilliger, T. C. & Todd O. Yeates, T. O. The Crystal Structure of the First Enzyme in the Pantothenate Biosynthetic Pathway, Ketopantoate Hydroxymethyltransferase, from M. tuberculosis (2003).   Structure, 11, 753-764

Terwilliger, T. C. (2003). Improving macromolecular atomic models at moderate resolution by automated iterative model building, statistical density modification and refinement. Acta Cryst. D59, 1174-1182.

Terwilliger, T. C. (2003). Automated side-chain model-building and sequence assignment by template-matching. Acta Cryst. D59, 45-49.

Terwilliger, T. C. (2003). Automated main-chain model-building by template-matching and iterative fragment extension. Acta Cryst. D59, 38-44.

Terwilliger, T. C. (2002). Rapid Automatic NCS identification Using Heavy-Atom Substructures. Acta Cryst. D58, 2213-2215.

Terwilliger, T. C. (2002). Statistical density modification with non-crystallographic symmetry. Acta Cryst. D58, 2082-2086.

Adams, P. D., McCoy, A. J., Grosse-Kunsteleve, R. W., Hung, L.-W., Ioerger, T. R., Moriarty, N. W., Read, R. J., Sacchettini, J. C., Sauter, N. K. & Terwilliger, T. C (2002). PHENIX: Developing new software for automated crystallographic structure determination. Acta Cryst. D Acta Cryst. D58, 1948-1954.

Terwilliger, T. C. (2002) Automated structure solution, density modification, and model-building. Acta Cryst. D58, 1937-1940.

Goulding, C. W., Apostol, M.,. Anderson, D. H. , Gill, H. S., Smith, C. V., Kuo, M. R., Yang, J. K., Waldo. G. S., Suh, S. W., Chauhan, R., Kale, A., Bachhawat, N., Mande, S. C. , Johnston, J. M., Lott, J. S., Baker, E. N., Arcus, V. L., Leys, D., McLean, K. J., Munro, A. W., Berendzen, J., Sharma, V., Park, M. S., Eisenberg, D.,Sacchettini, J., Alber, T., Rupp. B., Jacobs,W. Jr. and Terwilliger, T. C. (2002). The TB Structural Genomics Consortium: Providing a Foundation for TB Drug Discovery. Current Drug Targets-Infectious Disorders 2, 121-141.

Pédelacq, J.-D., Piltch, E., Liong, E. E., Berendzen, J., Kim, C.-Y., Rho, B.-S., Park, M. S., Terwilliger, T. C. & Waldo, G. S (2002). Engineering soluble proteins for structural genomics.  Nature Biotechnology, 20, 927-932.

Mou, T.-C., Sreerma, N., Terwilliger, T. C., Woody, R. W. & Gray, D. M. (2002). Independent tyrosyl contributions to the CD of Ff gene 5 protein and the distinctive effects of Y41H and Y41F mutants on protein-protein cooperative interaction. Protein Science, 11, 601-613.

Terwilliger, T. C. (2001). Map-likelihood phasing. Acta Crystallographica D57, 1763-1775.

Terwilliger, T. C. (2001). Maximum likelihood density modification by pattern recognition of structural motifs. Acta Crystallographica D57, 1755-1762.

Mou, T. C., Gray, C. W., Terwilliger, T. C. & Gray, D. M. (2001). Ff gene 5 protein has a high binding affinity for single-stranded phosphorothioate DNA. Biochemistry 40, 2267-2275.

Cort, J. R., Mariappan, S. V., Kim, C. Y., Park, M. S., Peat, T. S., Waldo, G. S., Terwilliger, T. C. & Kennedy, M. A. (2001). Solution structure of Pyrobaculum aerophilumDsrC, an archael homologue of the gamma subunit of dissimilatory sulfite reductase. Eur. J. Biochem. 268, 1-10.

Terwilliger, T.C. (2000) Maximum-likelihood density modification for X-ray crystallography. Proceedings of SPIE 4123, 243-248.

Terwilliger, T. C. (2000). Structural Genomics in North America. Nature Structural Biology 7, 935-939.

Terwilliger, T. C.  (2000). Maximum-likelihood density modification. Acta Crystallographica, D55, 965-972.

Newman, J., Peat, T. S., Richard, R., Kan, L., Swanson, P. E., Affholter, J. A., Holmes, I. H., Schindler, J. F., Unkefer, C. J., and Terwilliger, T. C. (1999).  Haloalkane dehalogenases: Structure of a Rhodococcus enzyme.  Biochemistry, 38, 16105-16114.

Terwilliger, T. C.  (1999). Reciprocal-space solvent flattening. Acta Crystallographica, D55, 1863-1871

Terwilliger, T. C. and Berendzen, J.  (1999). Evaluation of macromolecular electron density map quality using the correlation of local rms density. Acta Crystallographica, D55, 1872-1877.

Chang, C.-H., Schindler, J. F., Unkefer, C. J., Vanderberg, L. A., Brainard, J. R., & Terwilliger, T. C.  (1999) In vivo screening of haloalkane dehalogenase mutants.  Chemistry and Biology, 2175-2181.

Terwilliger T.C., Berendzen J.  (1999) Exploring structure space: A protein structure initiative. Genetica106, 141-147.

Waldo, G., Standish, B. M., Berendzen, J. & Terwilliger, T. C. (1999) Rapid protein-folding assay using green fluorescent protein.  Nature Biotechnology 17, 691-695.

Terwilliger, T. C.  (1999).Sigma-squared-R, a reciprocal-space measure of the quality of macromolecular electron density maps. Acta Crystallographica, D55, 1174-1178.

Terwilliger, T. C. and Berendzen, J.  (1999). Automated MAD and MIR structure solution. Acta Crystallographica, D55, 849-861.

Terwilliger, T. C. and Berendzen, J.  (1999).  Discrimination of solvent from protein regions in native Fouriers as a means of evaluating heavy-atom solutions in the MIR and MAD methods.  Acta Crystallographica, D55, 501-505.

Chen, C.-B., Landgraf, R., Walts, A. D., Chan, L., Schlunk, P. M., Terwilliger, T. C., Sigman, D. S.  (1998). Scission of DNA at a preselected sequence using a single-strand specific chemical nuclease.  Chemistry and Biology 5,283-292.

Ruscetti, T., Newman, J., Peat, T.S., Francis, J., Nolan, R., Terwilliger, T.C., Peterson, S. R., Lehnert, B. E.  (1998). A non-denaturing purification scheme for the DNA binding domain of poly (ADP-ribose) polymerase: a structure-specific DNA binding protein. Protein Expression and Purification, 14, 79-86.

Terwilliger, T. C., Waldo, G., Peat, T. S., Newman, J. M., Chu, K., & Berendzen, J.  (1998).  Class-directed structure determination: Foundation for a Protein Structure Initiative.  Protein Science, 7, 1851-1856.

Thompson, T. M., Mark, B. L., Gray, C. W., Terwilliger, T. C., Sreerama, N., Woody, R. W., Gray, D. M.  (1998).  Circular dichroism and electron microscopy of a core Y61F mutant of the f1 gene 5 single-stranded DNA binding protein, and theoretical analysis of CD spectra of four Tyr-> Phe substitutions.  Biochemistry 37, 7463-7477.

Peat T.S., Newman J, Waldo G.S, Berendzen J., Terwilliger T.C.  (1998) Structure Of Translation Initiation-Factor 5a From Pyrobaculum-Aerophilum At 1.75 Angstrom Resolution. Structure 6, 1207-1214.

Terwilliger, T. C.  (1997). MAD phasing of macromolecular structures: Analysis of MAD data as Single Isomorphous Replacement with Anomalous Scattering (SIRAS) data using the MADMRG program.  Methods in Enzymology 276, 530-537.

Terwilliger, T. C. and Berendzen, J.  (1997).  Bayesian correlated MAD phasing.  Acta Crystallographica, D53, 571-579.

Su, S., Gao, Y.-G., Zhang, H., Terwilliger, T. C., and Wang, A. H.-J.  (1997) Analyses of the stability and function of three surface mutants (R82C, K69H, and L32R) of the gene V protein from Ff phage by X-ray crystallography.  Protein Science 6, 771-780.

Benevides, J. M., Terwilliger, T. C., Vhonik, S., and Thomas, G. J., Jr.  (1996).  Raman spectroscopy of the Ff gene V protein and complexes with poly(dA): Non-specific DNA recognition and binding.  Biochemistry, 35, 9603-9609.

Terwilliger, T. C. and Berendzen, J.  (1996).  Correlated phasing of multiple isomorphous replacement data. Acta Crystallographica D52, 749-757.

Terwilliger, T. C. and Berendzen, J.  (1996).  Bayesian weighting for macromolecular crystallographic refinement. Acta Crystallographica D52, 743-748.

Terwilliger, T. C. and Berendzen, J.  (1996).  Bayesian difference refinement.  Acta Crystallographica section D52, 1004-1011.

Skinner, M. M. and Terwilliger, T. C.  (1996) Potential use of additivity of mutational effects in simplifying protein engineering.  Proc. Natl. Acad. Sci. USA 93, 10753-10757.

Terwilliger, T. C.  (1996) Gene V protein dimerization and cooperativity of binding to poly(dA) Biochemistry, 51, 16652-16664.

Cheng, X., Hofstadler, S. A., Bruce, J. E., Harms, A. C., Chen, R., Smith, R. D., Terwiliger, T. C., and P. N. Goudreau  (1996) Electrospray ionization with high performance Fourier transform ion cyclotron resonance mass spectrometry for the study of noncovalent biomolecular complexes.  Techniques in Protein Chemistry vol. VII. pp. 13-22. Academic Press (San Diego).

Cheng, X., Harms, A. C., Goudreau, P.N., Terwilliger, T. C. and Smith, R. D  (1996) Direct Measurement of Oligonucleotide Binding Stoichiometry of Gene V Protein by Mass Spectrometry.  Proc. Natl. Acad. Sci. USA 93, 7022-7027.

Zhang, H., Skinner, M. M., Sandberg, W.S, Wang, A. H.-J., and Terwilliger, T. C.  (1996) Context-dependence of mutational effects in a protein: the crystal structures of the V35I, I47V and V35I/I47V gene V protein core mutants. J. Mol Biol. 259, 148-159.

Skinner, M. M. and Terwilliger, T. C.  (1996) An atomic view of additive mutational effects in a protein structure.  Proceedings of the Hanford Symposium on Health and the Environment, 111-121.

Sandberg, W.S., Schlunk, P.M., Zabin, H.B., and Terwilliger, T.C.  (1995). Relationship between in vivo activity and in vitro measures of function and stability of a protein.  Biochemistry 34, 11970-11978.

Terwilliger, T. C.  (1995).  Engineering the stability and function of gene V protein.  Advances in Protein Chemistry 46, 177-215.

Terwilliger, T. C. & Berendzen, J.  (1995).  Difference refinement: Obtaining differences between two related structures.  Acta Crystallographica  D51, 609- 618.

Mark, B.L., Terwilliger, T. C., Vaughan, M.R. and Gray, D.M.  (1995).  Circular dichroism spectroscopy of three tryosine-to-phenylalanine substitutions of fd gene 5 protein.  Biochemistry 34, 12854-12865.

Guan, Y., Zhang, H., Konings, R. N. H., Hilbers, C. W., Terwilliger, T. C., and A. H.- J. Wang  (1994).  Crystal structures of Y41H and Y41F mutants of gene V protein from Ff phage suggest possible protein-protein interactions in the gvp-ssDNA complex.  Biochemistry 33, 7768-7778.

Skinner, M. M., Zhang, H., Leschnitzer, D. H. , Guan, Y., Bellamy, H., Sweet, R. M., Gray, C. W., Konings, R. N. H., Wang, A. H.-J., and T. C. Terwilliger  (1994).  Structure of the gene V protein of bacteriophage f1 determined by multiwavelength X- ray diffraction on the selenomethionyl protein.  Proc. Natl. Acad. Sci. USA 91, 2071-2075. 

Terwilliger, T. C.  (1994) MAD phasing: Bayesian estimates of FA .  Acta Crystallographica D50, 11-16.

Terwilliger, T. C. , Zabin, H. B., Horvath, M. P., Sandberg, W. S. and Schlunk, P. M.  (1994) In vivo characterization of mutants of the bacteriophage f1 gene V protein isolated by saturation mutagenesis.  J. Mol. Biol., 236, 556-571.

Terwilliger, T. C.  (1994)  MAD phasing: Treatment of dispersive differences as isomorphous replacement information. Acta Crystallographica D50, 17-23.

Liang, H., Sandberg, W. S. and T. C. Terwilliger  (1993). Genetic fusion of subunits of a dimeric protein substantially enhances its stability and rate of folding.  Proc. Natl.  Acad. Sci. USA.  90, 7010-7014.

Sandberg, W. S and T. C. Terwilliger  (1993).  Engineering multiple properties of a protein by combinatorial mutagenesis. Proc. Natl. Acad. Sci. USA 90, 8367-8371.

Zabin, H. and T. C. Terwilliger  (1991). Isolation and in vitro characterization of temperature- sensitive mutants of the bacteriophage f1 gene V protein.  J. Mol. Biol 219, 257-275.

Liang, H. and T. C. Terwilliger  (1991).  Reversible unfolding of the bacteriophage f1 gene 5 protein.  Biochemistry 30, 2772-2782.

Sandberg, W. S. and T. C. Terwilliger  (1991).  Repacking Protein Interiors.  Trends in Biotechnology 9, 59-63.

Sandberg, W. S. and T. C. Terwilliger  (1991).  Energetics of repacking a protein interior.  Proc. Natl. Acad. Sci. USA 88, 1706-1710.

Zabin, H., Horvath, M. P. and T. C. Terwilliger  (1991).  Approaches to predicting effects of  single amino acid substitutions on the function of a protein.  Biochemistry 30, 6230- 6240.

Sandberg, W. S. and T. C. Terwilliger  (1989). Influence of interior packing and hydrophobicity on the stability of a protein.  Science 245, 54-57.

Terwilliger, T. C.  (1988).  Simple and highly efficient site-specific mutagenesis, by ligation of an oligodeoxyribonucleotide into gapped heteroduplex DNA in which the template strand contains uridine.  Gene 69, 317-324.

Terwilliger, T. C.  (1988).  Construction of a synthetic variant of the bacteriophage f1 gene 5 by assembling oligodeoxynucleotides corresponding to only one strand of DNA.  Gene 61, 41-47.

Terwilliger, T. C., Fulford, W. D. and H. B. Zabin.  (1988).  A genetic selection for temperature-sensitive variants of the bacteriophage f1 gene 5 protein.  Nucl. Acids Res.  16, 9027-9039.

Terwilliger, T. C. and D. Eisenberg.  (1987).  Isomorphous replacement: effects of errors on the phase probability distribution.  Acta Crystallographica A43, 6-13.

Terwilliger, T. C., Kim, S.-H., and D. Eisenberg.  (1987).  Generalized method of determining heavy-atom positions using the difference Patterson function.  Acta Crystallographica  A43, 1-5. 

Terwilliger, T. C., Wang, J. Y. and D. E. Koshland, Jr.  (1986).  Surface structure recognized for covalent modification of the aspartate receptor in chemotaxis.  Proc. Natl. Acad. Sci.  USA 83, 6707-6710.

Terwilliger, T. C., Bollag, G. E., Sternberg, D. W., Jr. and D. E. Koshland, Jr.  (1986).  S-methyl glutathione synthesis is catalyzed by the cheR methyltransferase in Escherichia coli.  J.  Bacteriol. 165, 958-963.

Terwilliger, T. C., Wang, J. Y. and D. E. Koshland, Jr.  (1986).  Kinetics of receptor modification: the multiply methylated aspartate receptors involved in bacterial chemotaxis.  J. Biol. Chem. 261, 10814-10820.

Eisenberg, D., Weiss, R. M., and T. C.  Terwilliger.  (1984).  The hydrophobic moment detects  periodicity in protein hydrophobicity. Proc. Natl. Acad. Sci. USA 81, 140-144.

Terwilliger, T. C. and D. E. Koshland, Jr.  (1984).  Sites of methyl esterification and deamination on the aspartate receptor involved in chemotaxis.  J. Biol. Chem. 259, 7719-7725.

Terwilliger, T. C. and D. Eisenberg.  (1983).  Unbiased three-dimensional refinement of heavy-atom parameters by correlation of origin-removed Patterson functions.  Acta Crystallographica A39, 813-817.

Terwilliger, T. C., Bogonez, E., Wang, E. A., and D. E. Koshland, Jr.  (1983).  Sites of methyl esterification on the aspartate receptor involved in bacterial chemotaxis.  J. Biol. Chem.  258, 9608-9611.

Terwilliger, T. C. and D. Eisenberg.  (1982).  The structure of melittin. II.  Interpretation of the structure.  J. Biol. Chem.  257, 6016-6022.

Terwilliger, T. C. and D. Eisenberg.  (1982).  The structure of melittin.  I. Structure determination and partial refinement.  J. Biol. Chem.  257, 6010-6015.

Terwilliger, T. C., Weissman, L, and D. Eisenberg.  (1982).  The structure of melittin in the form I crystals and its implication for melittin's lytic and surface activities.  Biophys. J.  37, 353-361.

Eisenberg, D., Weiss, R. M., and T. C. Terwilliger  (1982).  The helical hydrophobic moment: a measure of the amphiphilicity of a helix.  Nature 299, 371-374..

Eisenberg, D., Weiss, R. M., Terwilliger, T. C. and W. Wilcox.  (1982).  Hydrophobic moments and protein structure.  Faraday Symp. Chem. Soc. 17, 109-120.

Terwilliger, T. C. and A. K. Solomon.  (1981).  Osmotic water permeability of human red cells.  J. General Physiol.  77, 549-570.

Terwilliger, T. C. and S. Clarke.  (1981).  Methylation of membrane proteins in human erythrocytes: Identification and characterization of polypeptides methylated in lysed cells.  J. Biol. Chem.  256, 3067-3076.

Anderson, D., Terwilliger, T. C., Wickner, W. and D. Eisenberg.  (1980).  Melittin forms crystals which are suitable for high-resolution x-ray structural analysis and which reveal a molecular 2-fold axis of symmetry.  J. Biol Chem.  255, 2578-2582.