Publications

Ragland DA, Nalivaika EA, Nalam MN, Prachanronarong KL, Cao H, Bandaranayake RM, Cai Y, Kurt Yilmaz N, Schiffer CA. “Drug Resistance Conferred by Mutations Outside the Active Site Through Alterations in the Dynamic and Structural Ensemble of HIV-1 Protease.” J Am Chem Soc. 2014 Aug 4.[PubMed]

Cai Y, Myint W, Paulsen, J.L., Ishima R, Schiffer CA, Yilmaz NK. “Drug Resistance Mutations Alter Dynamics of Inhibitor-Bound HIV-1 Protease” J. Chem. Theory Comput. 2014 10(8):3438-3448.[PubMed]

Kolli M, Ozen A, Kurt-Yilmaz N, Schiffer CA. “HIV-1 Protease substrate co-evolution in Nelfinavir resistance” J Virol. 2014 Jul 1;88(13):7145-54.[PubMed]

Hilbert BJ, Grossman SR, Schiffer CA, Royer WE Jr. “Crystal structures of human CtBP in complex with substrate MTOB reveal active site features useful for inhibitor design.” FEBS Lett. 2014 2;588(9):1743-8  [PubMed]

Foll M, Poh YP, Renzette N, Ferrer-Admetlla A, Bank C, Shim H, Malaspinas AS, Ewing G, Liu P, Wegmann D, Caffrey DR, Zeldovich KB, Bolon DN, Wang JP, Kowalik TF, Schiffer CA, Finberg, RW, Jensen JD. "Influenza virus drug resistance: a time-sampled population genetics perspective." PLoS Genet. 2014 10(2):e1004185.[PubMed]

Cheng N, Lee SK, Donover PS, Reichman M, Schiffer CA. Hull-Ryde EA, Swanstrom R, Janzen WP. “Development of a Novel Screening Strategy Designed to Discover a New Class of HIV Drugs” J Lab Autom. 2013 Dec 4.[PubMed]

Renzette N, Caffrey DR, Zeldovich KB, Liu P, Gallagher GR, Aiello D, Porter AJ, Kurt-Jones EA, Bolon DN, Poh YP, Jensen JD, Schiffer CA, Kowalik TF, Finberg RW, Wang JP. “Evolution of the influenza A virus genome during development of oseltamivir resistance in vitro.” J Virol. 2014 88(1):272-81.[PubMed]

Aydin C, Mukherjee S, Hanson AM, Schiffer CA. "The Interdomain Interface in Hepatitis C Virus (HCV) Bifunctional Enzyme Non-Structural Protein 3/4A (NS3/4A) Regulates Protease and Helicase Activities." Protein Science 2013 22(12):1786-98.[PubMed]

Silver N, King B, Nalam M, Cao H, Ali A, Sai G, Reddy K, Rana T, Schiffer C, Tidor B. "Efficient Computation of Small-Molecule Configurational Binding Entropy and Free Energy Changes by Ensamble Enumeration." J Chem Theory Comput. 2013 9(11):5098-5115.[PubMed]

Ozen A, Sherman W, Schiffer CA. "Improving the Resistance Profile of Hepatitis C NS3/4A Inhibitors: Dynamic Substrate Envelope Guided Design." J Chem Theory and Comput. 9(12), 5693-5705 (2013). [PubMed]

Shen Y, Altman MD, Ali A, Nalam MN, Cao H, Rana TM, Schiffer CA, Tidor B. "Testing the Substrate-Envelope Hypothesis with Designed Pairs of Compounds." ACS Chem Biol. Epub ahead of print (2013). [PubMed]

Nalam MN, Ali A, Reddy GS, Cao H, Anjum SG, Altman MD, Yilmaz NK, Tidor B, Rana TM, Schiffer CA. "Substrate Envelope-Designed Potent HIV-1 Protease Inhibitors to Avoid Drug Resistance." Chem Biol. 20(9), 1116-24 (2013). [PubMed]

Lee SK, Cheng N, Hull-Ryde E, Potempa M, Schiffer CA, Janzen W, Swanstrom R. "A Sensitive Assay Using a Native Protein Substrate for Screening HIV-1 Maturation Inhibitors Targeting the Protease Cleavage Site between the Matrix and Capsid." Biochemistry. Epub ahead of print (2013). [PubMed]

Varghese V, Mitsuya Y, Fessel WJ, Liu TF, Melikian GL, Katzenstein DA, Schiffer CA, Holmes SP, Shafer RW. "Prototypical Recombinant Multi-Protease Inhibitor Resistant Infectious Molecular Clones of Human Immunodeficiency Virus Type-1." Antimicrob Agents Chemother. Epub ahead of print (2013). [PubMed]

Bohn MF, Shandilya SM, Albin JS, Kouno T, Anderson BD, McDougle RM, Carpenter MA, Rathore A, Evans L, Davis AN, Zhang J, Lu Y, Somasundaran M, Matsuo H, Harris RS, Schiffer CA. "Crystal structure of the DNA cytosine deaminase APOBEC3F: the catalytically active and HIV-1 Vif-binding domain." Structure. 21(6), 1042-50 (2013). [PubMed]

Ali A, Aydin C, Gildemeister R, Romano KP, Cao H, Ozen A, Soumana D, Newton A, Petropoulos CJ, Huang W, Schiffer CA. "Evaluating the Role of Macrocycles in the Susceptibility of Hepatitis C Virus NS3/4A Protease Inhibitors to Drug Resistance." ACS Chem Biol. Epub ahead of print (2013). [PubMed]

Mittal S, Bandaranayake RM, King NM, Prabu-Jeyabalan M, Nalam MN, Nalivaika EA, Yilmaz NK, Schiffer CA. "Structural and thermodynamic basis of amprenavir/darunavir and atazanavir resistance in HIV-1 protease with mutations at residue 50." J Virol. 87(8), 4176-84 (2013). [PubMed]

Foulkes-Murzycki JE, Rosi C, Kurt Yilmaz N, Shafer RW, Schiffer CA. "Cooperative effects of drug-resistance mutations in the flap region of HIV-1 protease." ACS Chem Biol. 8(3), 513-8 (2013). [PubMed]

Babrzadeh F, Varghese V, Pacold M, Liu TF, Nyrén P, Schiffer C, Fessel WJ, Shafer RW. "Collinearity of protease mutations in HIV-1 samples with high-level protease inhibitor class resistance." J Antimicrob Chemother. 68(2), 414-8 (2013). [PubMed]

Cai Y, Yilmaz NK, Myint W, Ishima R, Schiffer CA. "Differential Flap Dynamics in Wild-type and a Drug Resistant Variant of HIV-1 Protease Revealed by Molecular Dynamics and NMR Relaxation." J Chem Theory Comput. 8(10), 3452-62 (2012). [PubMed]

Carpenter MA, Li M, Rathore A, Lackey L, Law EK, Land AM, Leonard B, Shandilya SM, Bohn MF, Schiffer CA, Brown WL, Harris RS. "Methylcytosine and normal cytosine deamination by the foreign DNA restriction enzyme APOBEC3A." J Biol Chem. 287(41), 34801-8 (2012). [PubMed]

King NM, Prabu-Jeyabalan M, Bandaranayake RM, Nalam MN, Nalivaika EA, Özen A, Haliloğlu T, Yilmaz NK, Schiffer CA. “Extreme entropy-enthalpy compensation in a drug-resistant variant of HIV-1 protease.” ACS Chem Biol. 7(9), 1536-46 (2012). [PubMed]

Mruk K, Shandilya SM, Blaustein RO, Schiffer CA, Kobertz WR. “Structural insights into neuronal K+ channel-calmodulin complexes.” PNAS. 109(34), 13579-83 (2012). [PubMed]

Parai MK, Huggins DJ, Cao H, Nalam MN, Ali A, Schiffer CA, Tidor B, Rana TM. “Design, synthesis, and biological and structural evaluations of novel HIV-1 protease inhibitors to combat drug resistance.” J Med Chem. 55(14), 6328-41 (2012). [PubMed]

Alvizo O, Mittal S, Mayo SL, Schiffer CA. “Structural, kinetic, and thermodynamic studies of specificity designed HIV-1 protease.” Protein Sci. 21(7), 1029-41 (2012). [PubMed]

Myint W, Cai Y, Schiffer CA, Ishima R. “Quantitative comparison of errors in 15N transverse relaxation rates measured using various CPMG phasing schemes.” J Biomol NMR. 53(1), 13-23 (2012). [PubMed]

Li M, Shandilya SM, Carpenter MA, Rathore A, Brown WL, Perkins AL, Harki DA, Solberg J, Hook DJ, Pandey KK, Parniak MA, Johnson JR, Krogan NJ, Somasundaran M, Ali A, Schiffer CA, Harris RS. “First-in-class small molecule inhibitors of the single-strand DNA cytosine deaminase APOBEC3G.” ACS Chem Biol. 7(3), 506-17 (2012). [PubMed]

Mittal, S., Cai, Y., Nalam, MNL., Bolon, DNA., Schiffer, C.A. “Hydrophobic Core Flexibility Modulates Enzyme Activity in HIV-1 Protease.” J Am Chem Soc. 134(9), 4163-68 (2012). [PubMed]

Ozen, A., Haliloğlu, T., Schiffer, C.A. “HIV-1 Protease and Substrate Coevolution Validates the Substrate Envelope As the Substrate Recognition Pattern.”J Chem Theory Comput. 8(2), 703-14 (2012). [PubMed]

Lee, SK., Potempa, M., Kolli, M., Ozen, A., Schiffer, C., Swanstrom, R. “Context Surrounding Processing Sites is Crucial in Determining Cleavage Rate of a Subset of the Processing Sites in the HIV-1 Gag and Gag-Pro-Pol precursors by the viral protease.” J Biol Chem. [Epub ahead of print] (2012). [PubMed]

Dierynck, I., Van Marck, H., Van Ginderen, M., Jonckers, T.H., Nalam, M.N., Schiffer, C.A., Raoof, A., Kraus, G., Picchio, G. “TMC310911, a Novel Human Immunodeficiency Virus Type-1 Protease Inhibitor shows in Vitro an Improved Resistance Profile and Higher Genetic Barrier to Resistance Compared with Current Protease Inhibitors.” Antimicrobial Agents and Chemotherapy. Epub ahead of print (2011). [PubMed]

Anderson, A.C., Pollastri, M.P., Schiffer, C.A., Peet, N.P. “The Challenge of Developing Robust Drugs to Overcome Resistance.” Drug Discovery Today. 16(17-18), 755-61 (2011). [PubMed]

Ozen, A., Haliloğlu, T., Schiffer, C.A. “Dynamics of Preferential Substrate Recognition in HIV-1 Protease: Redefining the Substrate Envelope.” J of Molecular Biology. 410(4), 726-44 (2011). [PubMed]

Romano, K.P., Laine, J.M., Deveau, L.M., Cao, H., Massi, F., Schiffer, C.A. “Molecular Mechanisms of Viral and Host Cell Substrate Recognition by Hepatitis C Virus NS3/4A Protease.” J Virology. 85(13), 6106-16 (2011). [PubMed]

Parry, C.M., Kolli M., Myers, R.E., Cane, P.A., Schiffer, C.A., Pillay, D. “Three Residues in HIV-1 Matrix Contribute to Protease Inhibitor Susceptibility and Replication Capacity.” Antimicrobial Agents and Chemotherapy. 55(3), 1106-13 (2011). [PubMed]

Ali, A., Bandaranayake, R.M., Cai Y., King, N.M., Kolli, M., Mittal, S., Murzycki, J.F., Nalam, M.N., Nalivaika, E.A., Özen, A., Prabu-Jeyabalan, M.M., Thayer, K., Schiffer, C.A. “Molecular Basis for Drug Resistance in HIV-1 Protease.” Viruses. 2(11), 2509-2535 (2010). [PubMed]

Ali, A., Reddy, G.S., Nalam, M.N., Anjum, S.G., Cao, H., Schiffer, C.A., Rana, T.M. “Structure-Based Design, Synthesis and Structure-Activity Relationship Studies of HIV-1 Protease Inhibitors Incorporating Phenyloxazolidinones.” J. Med. Chem. 53(21):7699-708 (2010). [PubMed]

Romano, K.P., Ali, A., Royer, W.E., Schiffer, C.A. “Drug resistance against HCV NS3/4A inhibitors is defined by the balance of substrate recognition versus inhibitor binding.” PNAS. 107(49):20986-91 (2010). [PubMed]

Straza, M.W., Paliwal, S., Kovi, R.C., Rajeshkumar, B., Trehn, P., Parker, D., Whalen, G.F., Lyle, S., Schiffer, C.A., Grossman, S.R. “Therapeutic targeting of C-terminal binding protein in human cancer.” Cell Cycle. 9(18): 3740-3750 (2010). [PubMed]

Bandaranayake, R.M., Kolli, M., King, N.M., Nalivaika, E.A., Heroux, A., Kakizawa, J., Sugiura, W., Schiffer, C.A. “The Effect of Clade Specific Sequence Polymorphisms on HIV-1 Protease Activity and Inhibitor Resistance Pathways.” J Virology. 84(19):9995-10003 (2010). [PubMed]

Ozer, N., Schiffer, C.A., Haliloglu, T. “Rationale for more diverse inhibitors in competition with substrates in HIV-1 protease.” Biophysical Journal. 99(5):1650-9 (2010). [PubMed]

Cai, Y., Schiffer, C.A. “Decomposing the energetic impact of drug resistant mutations in HIV-1 protease on binding Darunavir.” J. Chem. Theory Comput.6(4):1358-1368 (2010). [PubMed]

Nalam MN, Ali A, Altman MD, Reddy GS, Chellappan S, Kairys V, Ozen A, Cao H, Gilson MK, Tidor B, Rana TM, Schiffer, CA. “Evaluating the Substrate-Envelope Hypothesis: Structural Analysis of Novel HIV-1 Protease Inhibitors Designed to be Robust against Drug Resistance.” J. Virology. 84(10):5368-78 (2010). [PubMed]

Shandilya SM, Nalam MN, Nalivaika EA, Gross PJ, Valesano JC, Shindo K, Li M, Munson M, Royer WE, Harjes E, Kono T, Matsuo H, Harris RS, Somasundaran M, Schiffer, CA. “Crystal structure of the APOBEC3G catalytic domain reveals potential oligomerization interfaces.” Structure. 18(1):28-38 (2010). [PubMed]

Kolli, M., Strawiski, E., Chappey, C., Schiffer, C.A., “Human Immunodeficiency Virus Type 1 Protease-Correlated Cleavage Site Mutations Enhance Inhibitor Resistance.” J Virology. 83 (21):11027-11042 (2009). [PubMed]

Kairys, V., Gilson, M.K., Schiffer, C.A., Fernandes, M.X. “Toward the Design of Mutation-Resistant Enzyme Inhibitors: Further Evaluation of the Substrate Envelope Hypothesis.” Chem Biol Drug Des. 74(3):234-245 (2009). [PubMed]

Jorissen RN, Reddy GS, Ali A, Altman MD, Chellappan S, Anjum SG, Tidor B, Schiffer CA, Rana TM, Gilson MK. “Additivity in the analysis and design of HIV protease inhibitors.” J Med Chem. 52(3):737-54 (2009). [PubMed]

Anderson, J., Schiffer, C., Lee, S.K., Swanstrom, R. “Viral Protease Inhibitors.” Handbook Experimental Pharmacology. (189):85-110 (2009). [PubMed]

Chen W, Lam SS, Srinath H, Jiang, Z, Correia, JJ, Schiffer CA, Fitzgerald, KA, Lin, K, Royer WE Jr. “Insights into interferon regulatory factor activation from the crystal structure of dimeric IRF5.” Nature Structural & Molecular Biology. 15(11):1213-20 (2008). [PubMed]

Nalam, M.N., Schiffer, C.A. “New approaches to HIV protease inhibitor drug design II: testing the substrate envelope hypothesis to avoid drug resistance and discover robust inhibitors.” Current Opinion in HIV and AIDS. 3(6):642-646 (2008). [PubMed]

Lefebvre, E., Schiffer, C.A. “Resilience to resistance of HIV-1 protease inhibitors: profile of darunavir.” AIDS Reviews. 10(3):131-142 (2008). [PubMed]

Bandaranayake, R.M., Prabu-Jeyabalan, M., Kakizawa, J., Sugiura, W., Schiffer, C.A. “Structural analysis of human immunodeficiency virus type 1 CRF01_AE protease in complex with the substrate p1-p6.” Journal of Virology. 82(13):6762-6766 (2008). [PubMed]

Chen, W., Srinath, H., Lam, S.S., Schiffer, C.A., Royer, W.E. Jr., Lin, K., “Contribution of Ser386 and Ser396 to Activation of Interferon Regulatory Factor 3.” J Mol Biol. 379(2):251-60 (2008). [PubMed]

Altman, M.D., Ali, A., Reddy, G.S., Nalam, M.N., Anjum, S.G., Cao, H., Chellappan, S., Kairys, V., Fernandes, M.X., Gilson, M.K., Schiffer, C.A., Rana, T.M., Tidor, B. “HIV-1 Protease Inhibitors from Inverse Design in the Substrate Envelope Exhibit Subnanomolar Binding to Drug-Resistant Variants” J Am Chem Soc.130(19):6099-113(2008). [PubMed]

Schiffer, C.A. “Combating Drug Resistance – Identifying Resilient Molecular Targets and Robust Drugs” Royal Society of Chemistry, Computational and Structural Approaches to Drug Discovery. Chapter 7, pages 127-133 (2008).

Altman, M.D., Nalivaika, E.A., Prabu-Jeyabalan, M., Schiffer, C.A., Tidor, B. “Computational design and experimental study of tighter binding peptides to an inactivated mutant of HIV-1 protease.” Proteins: Structure, Function and Bioinformatics. 70(3):678-694 (2008). [PubMed]

Reddy, G.S., Ali, A., Nalam, M.N., Anjum, S.G., Cao, H., Nathans, R.S., Schiffer, C.A., Rana, T.M. “Design and synthesis of HIV-1 protease inhibitors incorporating oxazolidinones as P2/P2' ligands in pseudosymmetric dipeptide isosteres.” J Med Chem. 50(18):4316-28 (2007). [PubMed]

Nalam, M.N., Peeters, A., Jonckers, T.H., Dierynck, I., Schiffer, C.A.. “Crystal structure of lysine sulfonamide inhibitor reveals the displacement of the conserved flap water molecule in human immunodeficiency virus type 1 protease.” J. Virol. 81(17):9512-8 (2007). PMID 17596316

Chellappan, S., Kiran Kumar Reddy, G.S., Ali, A., Nalam, M.N., Anjum, S.G., Cao, H., Kairys, V., Fernandes, M.X., Altman, M.D., Tidor, B., Rana, T.M., Schiffer, C.A., Gilson, M.K. “Design of Mutation-Resistant HIV Protease Inhibitors with the Substrate Envelope Hypothesis.” Chem. Biol. And Drug Design. 69(5):298-313 (2007). PMID 17539822

Auclair, J.R., Green, K.M., Shandilya, S., Evans, J.E., Somasundaran, M., Schiffer, C.A. “Mass Spectrometry analysis of HIV-1 Vif reveals an increase in ordered structure upon oligomerization in regions necessary for viral infectivity.” Proteins: Structure, Function and Bioinformatics. 69(2):270-84 (2007). PMID 17598142

Chellappan, S., Kairys, V., Fernandes, M.X., Schiffer, C.A., Gilson, M.K. “Evaluation of the Substrate Envelope Hypothesis for Inhibitors of HIV-1 Protease.”Proteins: Structure, Function and Bioinformatics. 68(2):561-7 (2007). PMID 17474129

Chen, W., Lam, S.S., Srinath, H. Schiffer, C.A., Royer, W.E. Jr., Lin, K. “Competition between Ski and CREB-binding protein for binding to Smad proteins in transforming growth factor-beta signaling.” J. Biol. Chem. 282(15):11365-76 (2007). PMID 17283070

Foulkes-Murzycki, J.E., Scott, W.R., Schiffer, C.A. “Hydrophobic Sliding: A Possible Mechanism for Drug Resistance in Human Immunodeficiency Virus Type 1 Protease.” Structure. 15(2):225-33 (2007). PMID 17292840

Mitsuya, Y., Winters, M.A., Fessel, W.J., Rhee, S.Y., Hurley, L., Horberg, M., Schiffer, C.A., Zolopa, A.R., Shafer, R.W. “N88D Facilitates the Co-Occurrence of D30N and L90M and the Development of Multidrug Resistance in HIV type 1 Protease Following Nelfinavir Treatment Failure.” AIDS Research and Human Retroviruses. 22(12):1300-5 (2006). PMID 17209774

Ali, A., Reddy, G.S., Cao, H., Anjum, S.G., Nalam, M.N., Schiffer, C.A., Rana, T.M. “Discovery of HIV-1 Protease Inhibitors with Picomolar Affinities Incorporating N-Aryl-Oxazolidinone-5-Carboxamides as Novel P2 Ligands.” J Med Chem. 49(25):7342-56 (2006). PMID 17149864

Forget, A.L., Kudron, M.M., McGrew, D.A., Calmann, M.A., Schiffer, C.A., Knight, K.L., “RecA dimers serve as a functional unit for assembly of active nucleoprotein filaments.” Biochemistry. 45(45):13537-42 (2006). PMID 17087507

Foulkes, J.E., Prabu-Jeyabalan, M., Cooper, D., Henderson, G.J., Harris, J., Swanstrom, R., Schiffer, C.A. “Role of invariant Thr80 in human immunodeficiency virus type 1 protease structure, function, and viral infectivity.” J. Virology. 80(14):6906-16 (2006). PMID 16809296

Ozer, N. Haliloglu, T., Schiffer, C.A. “Substrate Specificity in HIV-1 Protease by a Biased Sequence Search Method.” Proteins. 64(2):444-56. (2006). PMID 16741993

Prabu-Jeyabalan, M., King, N.M., Nalivaika, E.A., Heilek-Snyder, G., Cammack, N., Schiffer, C.A. “Substrate Envelope and Drug Resistance: Crystal Structure of RO1 in Complex with Wild-Type Human Immunodeficiency Virus Type 1 Protease.” Antimicrobial Agents and Chemotherapy. 50(4):1518-21 (2006). PMID 16569872

Kolli, M., Lastere, S., Schiffer, C.A. “Co-evolution of Nelfinavir-Resistant HIV-1 Protease and the p1-p6 Substrate.” Virology. 347(2):405 – 409 (2006). PMID 16430939

Prabu-Jeyabalan, M., Nalivaika, E.A., Romano, K., Schiffer, C.A. “Mechanism of substrate recognition by drug-resistant human immunodeficiency virus type 1 protease variants revealed by a novel structural intermediate.” J. Virology. 80(7):3607-16 (2006). PMID 16537628

Liu, F., Wagner, S., Campbell, R.B., Nickerson, J.A., Schiffer, C.A., Ross, A.H. “PTEN enters the nucleus by diffusion.” J Cell Biochem. 96(2):221-34 (2005). PMID 16088943

Surleraux, D.L., de Kock, H.A., Verschueren, W.G., Pille, G.M., Maes, L.J., Peeters, A., Vendeville, S., De Meyer, S., Azijn, H., Pauwels, R., de Bethune, M.P., King, N.M, Prabu-Jeyabalan, M., Schiffer, C.A., Wigerinck, P.B. “Design of HIV-1 Protease Inhibitors Active on Multidrug-Resistant Virus.” J. Med. Chem.48(6):1965-73 (2005). PMID 15771440

Surleraux, D.L., Tahri, A., Verschueren, W.G., Pille, G.M., de Kock, H.A., Jonckers, T.H., Peeters, A., De Meyer, S., Azijn, H., Pauwels, R., de Bethune, M.P., King, N.M., Prabu-Jeyabalan, M., Schiffer, C.A., Wigerinck, P.B. “Discovery and Selection of TMC114, a next generation HIV-1 protease inhibitor.” J. Med. Chem. 48(6):1813-22 (2005). PMID 15771427

Johnston, E., Winters, M.A., Rhee, S.Y., Merigan, T.C., Schiffer, C.A., Shafer, R.W. “Association of a Novel Human Immunodeficiency Virus Type 1 Protease Substrate Cleft Mutation, L23I, with Protease Inhibitor Therapy and In Vitro Drug Resistance.” Antimicrobial Agents and Chemotherapy. 48(12)4864-4868 (2004).PMID 15561868

King, N.M., Prabu-Jeyabalan, M., Nalivaika, E.A., Schiffer, C.A. “Combating susceptibility to drug resistance: lessons from HIV-1 protease” Chemistry and Biology. 11(10): 1333-8 (2004). PMID 15489160

Prabu-Jeyabalan, M., Nalivaika, E.A., King, N.M., Schiffer, C.A. “Structural Basis For Coevolution of a Human Immunodeficiency Virus Type 1 Nucleocapsid-p1 Cleavage Site with a V82A Drug-Resistant Mutation in Viral Protease.” J Virology. 78(22): 12446-54 (2004). PMID 15507631

King, N.M., Prabu-Jeyabalan, M., Nalivaika, E.A., Wigerinck, P., de Bethune, M.P., Schiffer, C.A. “Structural and thermodynamic basis for the binding of TMC114, a next-generation human immunodeficiency virus type 1 protease inhibitor.” J. Virology. 78(21):12012-12021 (2004). PMID 15479840

Schiffer, C., Hermans, J. “Promise of advances in simulation methods for protein crystallography: implicit solvent models, time-averaging refinement, and quantum mechanical modeling.” Methods in Enzymology. 374: 412-61 (2003). PMID 14696384

Hoffman, N.G., Schiffer, C.A., Swanstrom, R. “Covariation of amino acid positions in HIV-1 Protease.” Virology. 314(2):536-548 (2003). PMID 14554082

Kurt, N., Haliloglu, T., Schiffer, C.A. “Structure-Based Prediction of Potential Binding and Nonbinding Peptides to HIV-1 Protease.” Biophysical Journal.85(2):853-863 (2003). PMID 12885633

Kurt, N., Scott, W.R., Schiffer, C.A., Haliloglu, T. “Cooperative fluctuations of unliganded and substrate-bound HIV-1 protease: a structure-based analysis on a variety of conformations from crystallography and molecular dynamics simulations.” Proteins. 51(3):409-422 (2003). PMID 12696052

Wu, T.D., Schiffer, C.A., Gonzales, M.J., Taylor, J., Kantor, R., Chou, S., Israelski, D., Zolopa, A.R., Fessel, W.J., Shafer, R.W. “Mutation patterns and structural correlates in human immunodeficiency virus type 1 protease following different protease inhibitor treatments.” J Virology. 77(8):4836-4847 (2003). PMID 12663790

Prabu-Jeyabalan, M., Nalivaika, E.A., King, N.M., Schiffer, C.A. “Viability of a drug-resistant human immunodeficiency virus type 1 protease variant: structural insights for better antiviral therapy.” J Virology. 77(2):1306-1315 (2003). PMID 12502847

Schonhoff, C.M., Daou, M.C., Jones, S.N., Schiffer, C.A., Ross, A.H. “Nitric Oxide-Mediated Inhibition of Hdm2-p53 Binding.” Biochemistry. 41(46):13570-13574 (2002). PMID 12427017

Liu, H., Radhakrishnan, P., Magoun, L., Prabu, M., Campellone, K.G., Savage, P., He, F., Schiffer, C.A., Leong, J.M. “Point mutants of EHEC intimin that diminish Tir recognition and actin pedestal formation highlight a putative Tir binding pocket.” Molecular Microbiology. 45(6):1557-1573 (2002). PMID 12354225

Pettit, S.C., Henderson, G.J., Schiffer, C.A., Swanstrom, R. “Replacement of the P1 amino acid of Human Immunodeficiency Virus Type 1 Gag processing sites can inhibit or enhance the rate of cleavage by the viral protease.” J Virology. 76(20):10226-10233 (2002). PMID 12239298

Prabu-Jeyabalan, M., Nalivaika, E., Schiffer, C.A. "Substrate shape determines specificity of recognition for HIV-1 protease: Analysis of crystal structures of six substrate complexes." Structure. 10(3):369-381(2002). PMID 12005435

Schiffer, C., Ultsch, M., Walsh, S., Somers, W., de Vos, A.M., Kossiakoff, A. “Structure of a phage display-derived variant of human growth hormone complexed to two copies of the extracellular domain of its receptor: evidence for strong structural coupling between receptor binding sites” J. Mol. Biol. 316(2):277-289 (2002). PMID 11851338

King, N.M., Melnick, L., Prabu-Jeyabalan, M., Nalivaika, E.A., Yang, S.S., Gao, Y., Nie, X., Zepp, C., Heefner, D.L., Schiffer, C.A. "Lack of Synergy for Inhibitors Targeting a Multi-drug-resistant HIV-1 Protease." Protein Science. 11(2):418-429 (2002). PMID 11790852

Scott, W.R., Schiffer, C.A. “Curling of Flap Tips in HIV-1 Protease as a Mechanism for Substrate Entry and Tolerance of Drug Resistance.” Structure. 8(12):1259-1265 (2000). PMID 11188690

Prabu-Jeyabalan, M., Nalivaika, E., Schiffer, C.A. “How does a symmetric dimer recognize an asymmetric substrate? A substrate complex of HIV-1 protease.” J. Mol. Biol. 301(5):1207-1220 (2000). PMID 10966816

Schiffer, C.A., van Gunsteren, W.F., “Accessibility and order of water sites in and around proteins: a crystallographic time-averaging study.” Proteins 36(4):501-511 (1999). PMID 10450092

Schiffer, C.A. “Time-Averaging Crystallographic Refinement” Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications. Vol. 3, Kluwer Publishers, 265-269 (1997).

Kossiakoff, A.A., Schiffer, C.A., De Vos, A.M. “The Role of Molecular Recognition in Activation and Regulation in the Growth Hormone-Prolactin Family of Hormones and Receptors.” Hanford Symposium, Biomacromolecules: From 3-D Structure to Applications, Battelle Press, 123-131 (1997).

Peng, J.W., Schiffer, C.A., Xu, P., van Gunsteren, W.F., Ernst, R.R. "Investigations of peptide hydration using NMR and molecular dynamics simulations: A study of effects of water on the conformation and dynamics of antamanide." J. Biol. NMR. 8(4):453-476 (1996). PMID 20859779

Schiffer, C.A., van Gunsteren, W.F., "Structural Stability of Disulfide Mutants of Basic Pancreatic Trypsin Inhibitor: A Molecular Dynamics Study." Proteins.26(1):66-71 (1996).PMID 8880930

Schiffer, C.A., Dötsch, V., “The Role of Protein - Solvent Interactions in Protein Unfolding.” Curr. Opin. in Biotechnology. 7(4):428-432 (1996). PMID 8768902

Schiffer, C.A., Clifton, I.J., Davisson, V.J., Santi, D.V., Stroud, R.M. "Crystal Structure of Human Thymidylate Synthase: A Structural Mechanism for Guiding Substrates into the Active Site." Biochemistry. 34(50):16279-16287 (1995). PMID 8845352

Schiffer, C.A., Dötsch, V., Wüthrich, K., van Gunsteren, W.F. "Exploring the Role of the Solvent in the Denaturation of a Protein: A Molecular Dynamics Study of the DNA Binding Domain of the 434 Repressor.” Biochemistry. 34(46):15057-15067 (1995). PMID 7578118

Bisang, C., Weber, C., Inglis, J., Schiffer, C.A., van Gunsteren, W.F., Jelesarov, I., Bosshard, H.R., Robinson, J.A., "Stabilization of Type-I .beta.-Turn Conformations in Peptides Containing the NPNA-Repeat Motif of the Plasmodium falciparum Circumsporozoite Protein by Substituting Proline for (S)-.alpha.-Methylproline." J. Amer. Chem. Soc. 117(30):7904-7915 (1995).

Van Gunsteren, W.F., Hünenberger, P.H., Kovacs, H., Mark, A.E., Schiffer, C.A., "Investigation of Protein Unfolding and Stability by Computer Simulation." Phil. Trans. Royal Society, Biol. Sci. 348(1323):49-59 (1995). PMID 7770486

Schiffer, C.A., Gros, P., van Gunsteren, W.F. "Time-averaging Crystallographic Refinement: Possibilities and Limitations Using alpha-cyclodextrin as a test system." Acta Cryst. D. 51(Pt.1):85-92 (1995). PMID 15299339

Schiffer, C.A., Huber, R., Wüthrich, K., van Gunsteren, W.F., “Simultaneous Refinement of the Structure of BPTI against NMR data measured in solution and X-ray diffraction data measured in single crystals." J. Mol. Biol. 241(4):588-599 (1994). PMID 7520085

van Gunsteren, W.F., Brunne, R.M., Gros, P., van Schaik, R.C., Schiffer, C.A., Torda, A.E. "Accounting for Molecular Mobility in Structure Determination Based on Nuclear Magnetic Resonance Spectroscopic and X-ray Diffraction Data." Methods in Enzymology. 239:619-54 (1994). PMID 7530320

Greene, P.J., Yu, P.L., Zhao, J., Schiffer, C.A., Santi, D. "Expression, Purification, and Characterization of Thymidylate Synthase from Lactococcus lactis."Protein Science. 3(7):1114-1116 (1994). PMID 7920258

Schiffer, C.A., Caldwell, J.W., Kollman, P.A., Stroud, R.M. "Protein Structure Prediction with a Combined Solvation Free Energy-Molecular Mechanics Force Field." Molecular Simulation. 10(2):121-149 (1993).

Schiffer, C.A., Caldwell, J.W., Stroud, R.M., Kollman, P.A. "Inclusion of Solvation Free Energy with Molecular Mechanics Energy: Alanyl Dipeptide as a Test Case.“ Protein Science. 1(3):396-400 (1992). PMID 1304346

Schiffer, C.A., Davisson, V.J., Santi, D.V., Stroud, R.M. "Crystallization of Human Thymidylate Synthase." J. Mol. Biol. 219(2):161-63 (1991). PMID 2038053

Schiffer, C.A., Caldwell, J.W., Kollman, P.A., Stroud, R.M. "Prediction of Homologous Protein Structures Based on Conformational Searches and Energetics.“Proteins. 8(1):30-43 (1990). PMID 2217162