| Year |
Citation |
Score |
| 2024 |
Azzolino VN, Shaqra AM, Ali A, Kurt Yilmaz N, Schiffer CA. Elucidating the Substrate Envelope of Enterovirus 68-3C Protease: Structural Basis of Specificity and Potential Resistance. Viruses. 16. PMID 39339895 DOI: 10.3390/v16091419 |
0.344 |
|
| 2023 |
Flynn JM, Huang QYJ, Zvornicanin SN, Schneider-Nachum G, Shaqra AM, Yilmaz NK, Moquin SA, Dovala D, Schiffer CA, Bolon DNA. Systematic Analyses of the Resistance Potential of Drugs Targeting SARS-CoV-2 Main Protease. Acs Infectious Diseases. PMID 37390404 DOI: 10.1021/acsinfecdis.3c00125 |
0.305 |
|
| 2023 |
Lockbaum GJ, Rusere LN, Henes M, Kosovrasti K, Rao DN, Spielvogel E, Lee SK, Nalivaika EA, Swanstrom R, Yilmaz NK, Schiffer CA, Ali A. HIV-1 protease inhibitors with a P1 phosphonate modification maintain potency against drug-resistant variants by increased interactions with flap residues. European Journal of Medicinal Chemistry. 257: 115501. PMID 37244161 DOI: 10.1016/j.ejmech.2023.115501 |
0.464 |
|
| 2023 |
Spielvogel E, Lee SK, Zhou S, Lockbaum GJ, Henes M, Sondgeroth A, Kosovrasti K, Nalivaika EA, Ali A, Yilmaz NK, Schiffer CA, Swanstrom R. Selection of HIV-1 for resistance to fifth-generation protease inhibitors reveals two independent pathways to high-level resistance. Elife. 12. PMID 36920025 DOI: 10.7554/eLife.80328 |
0.454 |
|
| 2022 |
Shaqra AM, Zvornicanin SN, Huang QYJ, Lockbaum GJ, Knapp M, Tandeske L, Bakan DT, Flynn J, Bolon DNA, Moquin S, Dovala D, Kurt Yilmaz N, Schiffer CA. Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance. Nature Communications. 13: 3556. PMID 35729165 DOI: 10.1038/s41467-022-31210-w |
0.324 |
|
| 2022 |
Zephyr J, Nageswara Rao D, Vo SV, Henes M, Kosovrasti K, Matthew AN, Hedger AK, Timm J, Chan ET, Ali A, Kurt Yilmaz N, Schiffer CA. Deciphering the Molecular Mechanism of HCV Protease Inhibitor Fluorination as a General Approach to Avoid Drug Resistance. Journal of Molecular Biology. 167503. PMID 35183560 DOI: 10.1016/j.jmb.2022.167503 |
0.318 |
|
| 2021 |
Zephyr J, Kurt Yilmaz N, Schiffer CA. Viral proteases: Structure, mechanism and inhibition. The Enzymes. 50: 301-333. PMID 34861941 DOI: 10.1016/bs.enz.2021.09.004 |
0.31 |
|
| 2021 |
Leidner F, Kurt Yilmaz N, Schiffer CA. Deciphering Complex Mechanisms of Resistance and Loss of Potency through Coupled Molecular Dynamics and Machine Learning. Journal of Chemical Theory and Computation. PMID 33783217 DOI: 10.1021/acs.jctc.0c01244 |
0.303 |
|
| 2020 |
Rusere LN, Lockbaum GJ, Henes M, Lee SK, Spielvogel E, Rao DN, Kosovrasti K, Nalivaika EA, Swanstrom R, Kurt Yilmaz N, Schiffer CA, Ali A. Structural Analysis of Potent Hybrid HIV-1 Protease Inhibitors Containing Bis-Tetrahydrofuran in a Pseudo-Symmetric Dipeptide Isostere. Journal of Medicinal Chemistry. PMID 32672965 DOI: 10.1021/Acs.Jmedchem.0C00529 |
0.506 |
|
| 2020 |
Matthew AN, Zephyr J, Nageswara Rao D, Henes M, Kamran W, Kosovrasti K, Hedger AK, Lockbaum GJ, Timm J, Ali A, Kurt Yilmaz N, Schiffer CA. Avoiding Drug Resistance by Substrate Envelope-Guided Design: Toward Potent and Robust HCV NS3/4A Protease Inhibitors. Mbio. 11. PMID 32234812 DOI: 10.1096/Fasebj.2020.34.S1.08779 |
0.478 |
|
| 2020 |
Schiffer C. Constraining evolution → avoiding drug resistance: lessons from viruses The Faseb Journal. 34: 1-1. DOI: 10.1096/Fasebj.2020.34.S1.00171 |
0.43 |
|
| 2020 |
Royer WE, Nichols JC, Schiffer CA. Illuminating the Structural Determinants for Tetrameric Assembly of Oncogenic CtBP to Guide Inhibitor Design Biophysical Journal. 118: 46a. DOI: 10.1016/J.Bpj.2019.11.430 |
0.42 |
|
| 2019 |
Whitfield TW, Ragland DA, Zeldovich KB, Schiffer CA. Characterizing protein-ligand binding using atomistic simulation and machine learning: Application to drug resistance in HIV-1 protease. Journal of Chemical Theory and Computation. PMID 31877249 DOI: 10.1021/Acs.Jctc.9B00781 |
0.511 |
|
| 2019 |
Timm J, Kosovrasti K, Henes M, Leidner F, Hou S, Ali A, Kurt Yilmaz N, Schiffer CA. Molecular and structural mechanism of pan-genotypic HCV NS3/4A protease inhibition by glecaprevir. Acs Chemical Biology. PMID 31868341 DOI: 10.1021/Acschembio.9B00675 |
0.423 |
|
| 2019 |
Solomon WC, Myint W, Hou S, Kanai T, Tripathi R, Kurt Yilmaz N, Schiffer CA, Matsuo H. Mechanism for APOBEC3G catalytic exclusion of RNA and non-substrate DNA. Nucleic Acids Research. 47: 7676-7689. PMID 31424549 DOI: 10.1093/Nar/Gkz550 |
0.433 |
|
| 2019 |
Rusere LN, Lockbaum GJ, Lee SK, Henes M, Kosovrasti K, Spielvogel E, Nalivaika EA, Swanstrom R, Kurt Yilmaz N, Schiffer CA, Ali A. HIV-1 Protease Inhibitors Incorporating Stereochemically Defined P2' Ligands to Optimize Hydrogen Bonding in the Substrate Envelope. Journal of Medicinal Chemistry. PMID 31386368 DOI: 10.1021/Acs.Jmedchem.9B00838 |
0.495 |
|
| 2019 |
Henes M, Kosovrasti K, Lockbaum GJ, Leidner F, Nachum GS, Nalivaika EA, Bolon DNA, Kurt Yilmaz N, Schiffer CA, Whitfield TW. Molecular determinants of epistasis in HIV-1 protease: Elucidating the interdependence of L89V and L90M mutations in resistance. Biochemistry. PMID 31386353 DOI: 10.1021/Acs.Biochem.9B00446 |
0.523 |
|
| 2019 |
Leidner F, Kurt Yilmaz N, Schiffer CA. Target-Specific Prediction of Ligand Affinity with Structure-Based Interaction Fingerprints. Journal of Chemical Information and Modeling. PMID 31381335 DOI: 10.1021/Acs.Jcim.9B00457 |
0.479 |
|
| 2019 |
Henes M, Lockbaum GJ, Kosovrasti K, Leidner F, Nachum GS, Nalivaika EA, Lee SK, Spielvogel E, Zhou S, Swanstrom R, Bolon DNA, Kurt Yilmaz N, Schiffer CA. pM to µM - Elucidating the Role of Distal Mutations in HIV-1 Protease in Conferring Drug Resistance. Acs Chemical Biology. PMID 31361460 DOI: 10.1021/Acschembio.9B00370 |
0.529 |
|
| 2019 |
Ishima R, Kurt Yilmaz N, Schiffer CA. NMR and MD studies combined to elucidate inhibitor and water interactions of HIV-1 protease and their modulations with resistance mutations. Journal of Biomolecular Nmr. PMID 31243634 DOI: 10.1007/S10858-019-00260-6 |
0.541 |
|
| 2019 |
Silvas TV, Schiffer CA. APOBEC3s: DNA-Editing Human Cytidine Deaminases. Protein Science : a Publication of the Protein Society. PMID 31241202 DOI: 10.1002/Pro.3670 |
0.447 |
|
| 2019 |
Lockbaum GJ, Leidner F, Rusere LN, Henes M, Kosovrasti K, Nachum GS, Nalivaika EA, Bolon DNA, Ali A, Kurt Yilmaz N, Schiffer CA. Correction to Structural Adaptation of Darunavir Analogues against Primary Mutations in HIV-1 Protease. Acs Infectious Diseases. PMID 30990653 DOI: 10.1021/Acsinfecdis.9B00098 |
0.488 |
|
| 2019 |
Özen A, Prachanronarong K, Matthew AN, Soumana DI, Schiffer CA. Resistance outside the substrate envelope: hepatitis C NS3/4A protease inhibitors. Critical Reviews in Biochemistry and Molecular Biology. 1-16. PMID 30821513 DOI: 10.1080/10409238.2019.1568962 |
0.54 |
|
| 2019 |
Boucher JI, Whitfield TW, Dauphin A, Nachum G, Hollins C, Zeldovich KB, Swanstrom R, Schiffer CA, Luban J, Bolon DNA. Constrained mutational sampling of amino acids in HIV-1 protease evolution. Molecular Biology and Evolution. PMID 30721995 DOI: 10.1093/Molbev/Msz022 |
0.464 |
|
| 2018 |
Lockbaum GJ, Leidner F, Rusere LN, Henes M, Kosovrasti K, Nachum GS, Nalivaika EA, Ali A, Kurt Yilmaz N, Schiffer CA. Structural Adaptation of Darunavir Analogs Against Primary Mutations in HIV-1 Protease. Acs Infectious Diseases. PMID 30543749 DOI: 10.2210/Pdb6Dh3/Pdb |
0.569 |
|
| 2018 |
Hou S, Silvas T, Leidner F, Nalivaika EA, Matsuo H, Kurt Yilmaz N, Schiffer CA. Structural analysis of the active site and DNA binding of human cytidine deaminase APOBEC3B. Journal of Chemical Theory and Computation. PMID 30457868 DOI: 10.1021/Acs.Jctc.8B00545 |
0.435 |
|
| 2018 |
Potempa M, Lee SK, KurtYilmaz N, Nalivaika EA, Rogers A, Spielvogel E, Carter CW, Schiffer CA, Swanstrom R. HIV-1 Protease Uses Bi-Specific S2/S2' Subsites to Optimize Cleavage of Two Classes of Target Sites. Journal of Molecular Biology. PMID 30414407 DOI: 10.1016/J.Jmb.2018.10.022 |
0.437 |
|
| 2018 |
Prachanronarong KL, Canale AS, Liu P, Somasundaran M, Hou S, Poh YP, Han T, Zhu Q, Renzette N, Zeldovich KB, Kowalik TF, Kurt-Yilmaz N, Jensen JD, Bolon DNA, Marasco WA, ... ... Schiffer CA, et al. Mutations in influenza A virus neuraminidase and hemagglutinin confer resistance against a broadly neutralizing hemagglutinin stem antibody. Journal of Virology. PMID 30381484 DOI: 10.1128/Jvi.01639-18 |
0.417 |
|
| 2018 |
Kaushansky A, Hedstrom L, Goldman A, Singh J, Yang PL, Rathod PK, Cynamon M, Wodarz D, Mahadevan D, Tomaras A, Navia MA, Schiffer CA. A call to arms: Unifying the fight against resistance. Science Signaling. 11. PMID 30352947 DOI: 10.1126/Scisignal.Aav0442 |
0.309 |
|
| 2018 |
Matthew AN, Leidner F, Newton A, Petropoulos CJ, Huang W, Ali A, KurtYilmaz N, Schiffer CA. Molecular Mechanism of Resistance in a Clinically Significant Double-Mutant Variant of HCV NS3/4A Protease. Structure (London, England : 1993). PMID 30146168 DOI: 10.1016/J.Str.2018.07.004 |
0.494 |
|
| 2018 |
Rusere LN, Matthew AN, Lockbaum GJ, Jahangir M, Newton A, Petropoulos CJ, Huang W, Kurt Yilmaz N, Schiffer CA, Ali A. Quinoxaline-Based Linear HCV NS3/4A Protease Inhibitors Exhibit Potent Activity against Drug Resistant Variants. Acs Medicinal Chemistry Letters. 9: 691-696. PMID 30034602 DOI: 10.1021/Acsmedchemlett.8B00150 |
0.509 |
|
| 2018 |
Maiti A, Myint W, Kanai T, Delviks-Frankenberry K, Sierra Rodriguez C, Pathak VK, Schiffer CA, Matsuo H. Crystal structure of the catalytic domain of HIV-1 restriction factor APOBEC3G in complex with ssDNA. Nature Communications. 9: 2460. PMID 29941968 DOI: 10.1038/S41467-018-04872-8 |
0.515 |
|
| 2018 |
Silvas TV, Hou S, Myint W, Nalivaika E, Somasundaran M, Kelch BA, Matsuo H, Kurt Yilmaz N, Schiffer CA. Substrate sequence selectivity of APOBEC3A implicates intra-DNA interactions. Scientific Reports. 8: 7511. PMID 29760455 DOI: 10.1038/S41598-018-25881-Z |
0.443 |
|
| 2018 |
Bellesis AG, Jecrois AM, Hayes JA, Schiffer C, Royer WE. Assembly of human C-terminal Binding Protein (CtBP) into tetramers. The Journal of Biological Chemistry. PMID 29700119 DOI: 10.1074/Jbc.Ra118.002514 |
0.443 |
|
| 2018 |
Leidner F, Kurt Yilmaz N, Paulsen J, Muller YA, Schiffer CA. Hydration Structure and Dynamics of Inhibitor-Bound HIV-1 Protease. Journal of Chemical Theory and Computation. PMID 29570286 DOI: 10.1021/Acs.Jctc.8B00097 |
0.484 |
|
| 2018 |
Canale AS, Venev SV, Whitfield TW, Caffrey DR, Marasco WA, Schiffer CA, Kowalik TF, Jensen JD, Finberg RW, Zeldovich KB, Wang JP, Bolon DNA. Synonymous mutations at the beginning of the influenza A virus hemagglutinin gene impact experimental fitness. Journal of Molecular Biology. PMID 29466705 DOI: 10.1016/J.Jmb.2018.02.009 |
0.422 |
|
| 2018 |
Khan SN, Persons JD, Paulsen JL, Guerrero M, Schiffer CA, Kurt-Yilmaz N, Ishima R. Probing Structural Changes among Analogous Inhibitor-Bound Forms of HIV-1 Protease and a Drug-Resistant Mutant in Solution by Nuclear Magnetic Resonance. Biochemistry. PMID 29457713 DOI: 10.1021/Acs.Biochem.7B01238 |
0.54 |
|
| 2017 |
Ma L, Boucher JI, Paulsen J, Matuszewski S, Eide CA, Ou J, Eickelberg G, Press RD, Zhu LJ, Druker BJ, Branford S, Wolfe SA, Jensen JD, Schiffer CA, Green MR, et al. CRISPR-Cas9-mediated saturated mutagenesis screen predicts clinical drug resistance with improved accuracy. Proceedings of the National Academy of Sciences of the United States of America. PMID 29078326 DOI: 10.1073/Pnas.1708268114 |
0.449 |
|
| 2017 |
Ragland DA, Whitfield TW, Lee SK, Swanstrom R, Zeldovich KB, Kurt Yilmaz N, Schiffer CA. Elucidating the Interdependence of Drug Resistance from Combinations of Mutations. Journal of Chemical Theory and Computation. PMID 28915040 DOI: 10.1021/Acs.Jctc.7B00601 |
0.543 |
|
| 2017 |
Matthew AN, Zephyr J, Hill CJ, Jahangir M, Newton A, Petropoulos CJ, Huang W, Kurt Yilmaz N, Schiffer CA, Ali A. Hepatitis C Virus NS3/4A Protease Inhibitors Incorporating Flexible P2 Quinoxalines Target Drug Resistant Viral Variants. Journal of Medicinal Chemistry. PMID 28594175 DOI: 10.1021/Acs.Jmedchem.7B00426 |
0.525 |
|
| 2017 |
Kouno T, Silvas TV, Hilbert BJ, Shandilya SMD, Bohn MF, Kelch BA, Royer WE, Somasundaran M, Kurt Yilmaz N, Matsuo H, Schiffer CA. Crystal structure of APOBEC3A bound to single-stranded DNA reveals structural basis for cytidine deamination and specificity. Nature Communications. 8: 15024. PMID 28452355 DOI: 10.1038/Ncomms15024 |
0.48 |
|
| 2017 |
Paulsen JL, Leidner F, Ragland DA, Kurt Yilmaz N, Schiffer CA. Interdependence of Inhibitor Recognition in HIV-1 Protease. Journal of Chemical Theory and Computation. PMID 28358514 DOI: 10.1021/Acs.Jctc.6B01262 |
0.542 |
|
| 2017 |
Lin KH, Ali A, Rusere L, Soumana DI, Yilmaz NK, Schiffer CA. Dengue Virus NS2B/NS3 Protease Inhibitors Exploiting the Prime Side. Journal of Virology. PMID 28298600 DOI: 10.1128/Jvi.00045-17 |
0.482 |
|
| 2016 |
Prachanronarong KL, Özen A, Thayer KM, Yilmaz LS, Zeldovich KB, Bolon DN, Kowalik TF, Jensen JD, Finberg RW, Wang JP, Kurt-Yilmaz N, Schiffer CA. Molecular Basis for Differential Patterns of Drug Resistance in Influenza N1 and N2 Neuraminidase. Journal of Chemical Theory and Computation. 12: 6098-6108. PMID 27951676 DOI: 10.1021/Acs.Jctc.6B00703 |
0.752 |
|
| 2016 |
Lin KH, Nalivaika EA, Prachanronarong KL, Yilmaz NK, Schiffer CA. Dengue Protease Substrate Recognition: Binding of the Prime Side. Acs Infectious Diseases. PMID 27657335 DOI: 10.1021/Acsinfecdis.6B00131 |
0.489 |
|
| 2016 |
Soumana DI, Kurt Yilmaz N, Ali A, Prachanronarong KL, Schiffer CA. Molecular and Dynamic Mechanism Underlying Drug Resistance in Genotype 3 Hepatitis C NS3/4A Protease. Journal of the American Chemical Society. PMID 27512818 DOI: 10.1021/Jacs.6B06454 |
0.486 |
|
| 2016 |
Kurt Yilmaz N, Swanstrom R, Schiffer CA. Improving Viral Protease Inhibitors to Counter Drug Resistance. Trends in Microbiology. PMID 27090931 DOI: 10.1016/J.Tim.2016.03.010 |
0.516 |
|
| 2015 |
Soumana DI, Kurt Yilmaz N, Prachanronarong KL, Aydin C, Ali A, Schiffer CA. Structural and Thermodynamic Effects of Macrocyclization in HCV NS3/4A Inhibitor MK-5172. Acs Chemical Biology. PMID 26682473 DOI: 10.1021/Acschembio.5B00647 |
0.491 |
|
| 2015 |
Jiang L, Liu P, Bank C, Renzette N, Prachanronarong K, Yilmaz LS, Caffrey DR, Zeldovich KB, Schiffer CA, Kowalik TF, Jensen JD, Finberg RW, Wang JP, Bolon DN. A balance between inhibitor binding and substrate processing confers influenza drug resistance. Journal of Molecular Biology. PMID 26656922 DOI: 10.1016/J.Jmb.2015.11.027 |
0.502 |
|
| 2015 |
Prabhu P, Shandilya SM, Britan-Rosich E, Nagler A, Schiffer CA, Kotler M. Inhibition of APOBEC3G activity impedes double-stranded DNA repair. The Febs Journal. PMID 26460502 DOI: 10.1111/Febs.13556 |
0.31 |
|
| 2015 |
Boopathy S, Silvas TV, Tischbein M, Jansen S, Shandilya SM, Zitzewitz JA, Landers JE, Goode BL, Schiffer CA, Bosco DA. Structural basis for mutation-induced destabilization of profilin 1 in ALS. Proceedings of the National Academy of Sciences of the United States of America. PMID 26056300 DOI: 10.1073/Pnas.1424108112 |
0.413 |
|
| 2015 |
Potempa M, Nalivaika E, Ragland D, Lee SK, Schiffer CA, Swanstrom R. A Direct Interaction with RNA Dramatically Enhances the Catalytic Activity of the HIV-1 Protease In Vitro. Journal of Molecular Biology. 427: 2360-78. PMID 25986307 DOI: 10.1016/J.Jmb.2015.05.007 |
0.451 |
|
| 2015 |
Kouno T, Luengas EM, Shigematsu M, Shandilya SM, Zhang J, Chen L, Hara M, Schiffer CA, Harris RS, Matsuo H. Structure of the Vif-binding domain of the antiviral enzyme APOBEC3G. Nature Structural & Molecular Biology. 22: 485-91. PMID 25984970 DOI: 10.1038/Nsmb.3033 |
0.43 |
|
| 2015 |
Ndjomou J, Corby MJ, Sweeney NL, Hanson AM, Aydin C, Ali A, Schiffer CA, Li K, Frankowski KJ, Schoenen FJ, Frick DN. Simultaneously Targeting the NS3 Protease and Helicase Activities for More Effective Hepatitis C Virus Therapy. Acs Chemical Biology. PMID 25961497 DOI: 10.1021/Acschembio.5B00101 |
0.455 |
|
| 2015 |
Bohn MF, Shandilya SM, Silvas TV, Nalivaika EA, Kouno T, Kelch BA, Ryder SP, Kurt-Yilmaz N, Somasundaran M, Schiffer CA. The ssDNA Mutator APOBEC3A Is Regulated by Cooperative Dimerization. Structure (London, England : 1993). 23: 903-11. PMID 25914058 DOI: 10.1016/J.Str.2015.03.016 |
0.463 |
|
| 2015 |
Özer N, Özen A, Schiffer CA, Halilo?lu T. Drug-resistant HIV-1 protease regains functional dynamics through cleavage site coevolution. Evolutionary Applications. 8: 185-98. PMID 25685193 DOI: 10.1111/Eva.12241 |
0.508 |
|
| 2015 |
Hilbert BJ, Morris BL, Ellis KC, Paulsen JL, Schiffer CA, Grossman SR, Royer WE. Structure-guided design of a high affinity inhibitor to human CtBP. Acs Chemical Biology. 10: 1118-27. PMID 25636004 DOI: 10.1021/Cb500820B |
0.479 |
|
| 2014 |
Zhou H, Li S, Badger J, Nalivaika E, Cai Y, Foulkes-Murzycki J, Schiffer C, Makowski L. Modulation of HIV protease flexibility by the T80N mutation. Proteins. PMID 25488402 DOI: 10.1002/Prot.24737 |
0.498 |
|
| 2014 |
Shandilya SM, Bohn MF, Schiffer CA. A computational analysis of the structural determinants of APOBEC3's catalytic activity and vulnerability to HIV-1 Vif. Virology. 471: 105-16. PMID 25461536 DOI: 10.1016/J.Virol.2014.09.023 |
0.444 |
|
| 2014 |
Özen A, Lin KH, Kurt Yilmaz N, Schiffer CA. Structural basis and distal effects of Gag substrate coevolution in drug resistance to HIV-1 protease. Proceedings of the National Academy of Sciences of the United States of America. 111: 15993-8. PMID 25355911 DOI: 10.1073/Pnas.1414063111 |
0.564 |
|
| 2014 |
Soumana DI, Ali A, Schiffer CA. Structural analysis of asunaprevir resistance in HCV NS3/4A protease. Acs Chemical Biology. 9: 2485-90. PMID 25243902 DOI: 10.1021/Cb5006118 |
0.53 |
|
| 2014 |
Cai Y, Myint W, Paulsen JL, Schiffer CA, Ishima R, Kurt Yilmaz N. Drug Resistance Mutations Alter Dynamics of Inhibitor-Bound HIV-1 Protease. Journal of Chemical Theory and Computation. 10: 3438-3448. PMID 25136270 DOI: 10.1021/Ct4010454 |
0.543 |
|
| 2014 |
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. Journal of the American Chemical Society. 136: 11956-63. PMID 25091085 DOI: 10.1021/Ja504096M |
0.565 |
|
| 2014 |
Kolli M, Ozen A, Kurt-Yilmaz N, Schiffer CA. HIV-1 protease-substrate coevolution in nelfinavir resistance. Journal of Virology. 88: 7145-54. PMID 24719428 DOI: 10.1128/Jvi.00266-14 |
0.566 |
|
| 2014 |
Hilbert BJ, Grossman SR, Schiffer CA, Royer WE. Crystal structures of human CtBP in complex with substrate MTOB reveal active site features useful for inhibitor design. Febs Letters. 588: 1743-8. PMID 24657618 DOI: 10.1016/J.Febslet.2014.03.026 |
0.467 |
|
| 2014 |
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, et al. Influenza virus drug resistance: a time-sampled population genetics perspective. Plos Genetics. 10: e1004185. PMID 24586206 DOI: 10.1371/Journal.Pgen.1004185 |
0.44 |
|
| 2014 |
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. Journal of Virology. 88: 272-81. PMID 24155392 DOI: 10.1128/Jvi.01067-13 |
0.449 |
|
| 2014 |
Schiffer C. Combatting Drug Resistance: Lessons from the viral proteases of HIV and HCV Acta Crystallographica Section a Foundations and Advances. 70: C116-C116. DOI: 10.1107/S2053273314098830 |
0.442 |
|
| 2013 |
Ozen A, Sherman W, Schiffer CA. Improving the Resistance Profile of Hepatitis C NS3/4A Inhibitors: Dynamic Substrate Envelope Guided Design. Journal of Chemical Theory and Computation. 9: 5693-5705. PMID 24587770 DOI: 10.1021/Ct400603P |
0.522 |
|
| 2013 |
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. Journal of Laboratory Automation. 19: 297-303. PMID 24305957 DOI: 10.1177/2211068213513453 |
0.491 |
|
| 2013 |
Silver NW, King BM, Nalam MN, Cao H, Ali A, Kiran Kumar Reddy GS, Rana TM, Schiffer CA, Tidor B. Efficient Computation of Small-Molecule Configurational Binding Entropy and Free Energy Changes by Ensemble Enumeration. Journal of Chemical Theory and Computation. 9: 5098-5115. PMID 24250277 DOI: 10.1021/Ct400383V |
0.62 |
|
| 2013 |
Aydin C, Mukherjee S, Hanson AM, Frick DN, Schiffer CA. The interdomain interface in bifunctional enzyme protein 3/4A (NS3/4A) regulates protease and helicase activities. Protein Science : a Publication of the Protein Society. 22: 1786-98. PMID 24123290 DOI: 10.1002/Pro.2378 |
0.303 |
|
| 2013 |
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. Chemistry & Biology. 20: 1116-24. PMID 24012370 DOI: 10.1016/J.Chembiol.2013.07.014 |
0.696 |
|
| 2013 |
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 Chemical Biology. 8: 2433-41. PMID 23952265 DOI: 10.1021/Cb400468C |
0.673 |
|
| 2013 |
Schiffer C. Interview with celia schiffer Future Medicinal Chemistry. 5: 1193-1197. PMID 23859201 DOI: 10.4155/Fmc.13.106 |
0.464 |
|
| 2013 |
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. Antimicrobial Agents and Chemotherapy. PMID 23796938 DOI: 10.1128/Aac.00614-13 |
0.475 |
|
| 2013 |
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. 52: 4929-40. PMID 23763575 DOI: 10.1021/Bi4005232 |
0.472 |
|
| 2013 |
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, et al. Crystal structure of the DNA cytosine deaminase APOBEC3F: the catalytically active and HIV-1 Vif-binding domain. Structure (London, England : 1993). 21: 1042-50. PMID 23685212 DOI: 10.1016/J.Str.2013.04.010 |
0.497 |
|
| 2013 |
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 Chemical Biology. 8: 1469-78. PMID 23594083 DOI: 10.1021/Cb400100G |
0.494 |
|
| 2013 |
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. Journal of Virology. 87: 4176-84. PMID 23365446 DOI: 10.1128/Jvi.03486-12 |
0.553 |
|
| 2013 |
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 Chemical Biology. 8: 513-8. PMID 23252515 DOI: 10.1021/Cb3006193 |
0.549 |
|
| 2013 |
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 Journal of Antimicrobial Chemotherapy. 68: 414-418. PMID 23085775 DOI: 10.1093/Jac/Dks409 |
0.494 |
|
| 2012 |
Ozen A, Halilo?lu T, Schiffer CA. HIV-1 Protease and Substrate Coevolution Validates the Substrate Envelope As the Substrate Recognition Pattern. Journal of Chemical Theory and Computation. 8. PMID 24348205 DOI: 10.1021/Ct200668A |
0.557 |
|
| 2012 |
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. Journal of Chemical Theory and Computation. 8: 3452-3462. PMID 23144597 DOI: 10.1021/Ct300076Y |
0.543 |
|
| 2012 |
Romano KP, Ali A, Aydin C, Soumana D, Ozen A, Deveau LM, Silver C, Cao H, Newton A, Petropoulos CJ, Huang W, Schiffer CA. The molecular basis of drug resistance against hepatitis C virus NS3/4A protease inhibitors. Plos Pathogens. 8: e1002832. PMID 22910833 DOI: 10.1371/Journal.Ppat.1002832 |
0.521 |
|
| 2012 |
King NM, Prabu-Jeyabalan M, Bandaranayake RM, Nalam MN, Nalivaika EA, Özen A, Halilo?lu T, Yilmaz NK, Schiffer CA. Extreme entropy-enthalpy compensation in a drug-resistant variant of HIV-1 protease. Acs Chemical Biology. 7: 1536-46. PMID 22712830 DOI: 10.1021/Cb300191K |
0.57 |
|
| 2012 |
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. Journal of Medicinal Chemistry. 55: 6328-41. PMID 22708897 DOI: 10.1021/Jm300238H |
0.694 |
|
| 2012 |
Alvizo O, Mittal S, Mayo SL, Schiffer CA. Structural, kinetic, and thermodynamic studies of specificity designed HIV-1 protease. Protein Science : a Publication of the Protein Society. 21: 1029-41. PMID 22549928 DOI: 10.1002/Pro.2086 |
0.556 |
|
| 2012 |
Lee SK, Potempa M, Kolli M, Özen A, Schiffer CA, Swanstrom R. Context surrounding processing sites is crucial in determining cleavage rate of a subset of processing sites in HIV-1 Gag and Gag-Pro-Pol polyprotein precursors by viral protease. The Journal of Biological Chemistry. 287: 13279-90. PMID 22334652 DOI: 10.1074/Jbc.M112.339374 |
0.472 |
|
| 2012 |
Mittal S, Cai Y, Nalam MN, Bolon DN, Schiffer CA. Hydrophobic core flexibility modulates enzyme activity in HIV-1 protease. Journal of the American Chemical Society. 134: 4163-8. PMID 22295904 DOI: 10.1021/Ja2095766 |
0.544 |
|
| 2012 |
Cai Y, Schiffer C. Decomposing the energetic impact of drug-resistant mutations: The example of HIV-1 protease-DRV binding Methods in Molecular Biology. 819: 551-560. PMID 22183557 DOI: 10.1007/978-1-61779-465-0_32 |
0.546 |
|
| 2012 |
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, et al. First-in-class small molecule inhibitors of the single-strand DNA cytosine deaminase APOBEC3G. Acs Chemical Biology. 7: 506-17. PMID 22181350 DOI: 10.1021/Cb200440Y |
0.487 |
|
| 2011 |
Dierynck I, Van Marck H, Van Ginderen M, Jonckers TH, Nalam MN, Schiffer CA, 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. 55: 5723-31. PMID 21896904 DOI: 10.1128/Aac.00748-11 |
0.523 |
|
| 2011 |
Anderson AC, Pollastri MP, Schiffer CA, Peet NP. The challenge of developing robust drugs to overcome resistance. Drug Discovery Today. 16: 755-61. PMID 21784168 DOI: 10.1016/J.Drudis.2011.07.001 |
0.615 |
|
| 2011 |
Ozen A, Halilo?lu T, Schiffer CA. Dynamics of preferential substrate recognition in HIV-1 protease: redefining the substrate envelope. Journal of Molecular Biology. 410: 726-44. PMID 21762811 DOI: 10.1016/J.Jmb.2011.03.053 |
0.551 |
|
| 2011 |
Romano KP, Laine JM, Deveau LM, Cao H, Massi F, Schiffer CA. Molecular mechanisms of viral and host cell substrate recognition by hepatitis C virus NS3/4A protease. Journal of Virology. 85: 6106-16. PMID 21507982 DOI: 10.1128/Jvi.00377-11 |
0.441 |
|
| 2011 |
Parry CM, Kolli M, Myers RE, Cane PA, Schiffer C, Pillay D. Three residues in HIV-1 matrix contribute to protease inhibitor susceptibility and replication capacity Antimicrobial Agents and Chemotherapy. 55: 1106-1113. PMID 21149628 DOI: 10.1128/Aac.01228-10 |
0.494 |
|
| 2011 |
Straza MW, Kovi RC, Paliwal S, Rajeshkumar B, Hilbert B, Doughty T, Parker D, Royer W, Whalen GF, Lyle S, Schiffer CA, Grossman SR. Abstract 1633: C-terminal binding proteins are novel drug targets Cancer Research. 71: 1633-1633. DOI: 10.1158/1538-7445.Am2011-1633 |
0.306 |
|
| 2010 |
Ali A, Bandaranayake RM, Cai Y, King NM, Kolli M, Mittal S, Murzycki JF, Nalam MN, Nalivaika EA, Ozen A, Prabu-Jeyabalan MM, Thayer K, Schiffer CA. Molecular Basis for Drug Resistance in HIV-1 Protease. Viruses. 2: 2509-35. PMID 21994628 DOI: 10.3390/V2112509 |
0.773 |
|
| 2010 |
Romano KP, Ali A, Royer WE, Schiffer CA. Drug resistance against HCV NS3/4A inhibitors is defined by the balance of substrate recognition versus inhibitor binding. Proceedings of the National Academy of Sciences of the United States of America. 107: 20986-91. PMID 21084633 DOI: 10.1073/Pnas.1006370107 |
0.541 |
|
| 2010 |
Ali A, Reddy GS, Nalam MN, Anjum SG, Cao H, Schiffer CA, Rana TM. Structure-based design, synthesis, and structure-activity relationship studies of HIV-1 protease inhibitors incorporating phenyloxazolidinones. Journal of Medicinal Chemistry. 53: 7699-708. PMID 20958050 DOI: 10.1021/Jm1008743 |
0.54 |
|
| 2010 |
Ozer N, Schiffer CA, Haliloglu T. Rationale for more diverse inhibitors in competition with substrates in HIV-1 protease. Biophysical Journal. 99: 1650-9. PMID 20816079 DOI: 10.1016/J.Bpj.2010.06.064 |
0.524 |
|
| 2010 |
Bandaranayake RM, Kolli M, King NM, Nalivaika EA, Heroux A, Kakizawa J, Sugiura W, Schiffer CA. The effect of clade-specific sequence polymorphisms on HIV-1 protease activity and inhibitor resistance pathways. Journal of Virology. 84: 9995-10003. PMID 20660190 DOI: 10.1128/Jvi.00505-10 |
0.539 |
|
| 2010 |
Cai Y, Schiffer CA. Decomposing the energetic impact of drug resistant mutations in HIV-1 protease on binding DRV. Journal of Chemical Theory and Computation. 6: 1358-1368. PMID 20543885 DOI: 10.1021/Ct9004678 |
0.539 |
|
| 2010 |
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. Journal of Virology. 84: 5368-78. PMID 20237088 DOI: 10.1128/Jvi.02531-09 |
0.711 |
|
| 2010 |
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 (London, England : 1993). 18: 28-38. PMID 20152150 DOI: 10.1016/J.Str.2009.10.016 |
0.466 |
|
| 2009 |
Kolli M, Stawiski E, Chappey C, Schiffer CA. Human immunodeficiency virus type 1 protease-correlated cleavage site mutations enhance inhibitor resistance. Journal of Virology. 83: 11027-42. PMID 19706699 DOI: 10.1128/Jvi.00628-09 |
0.505 |
|
| 2009 |
Kairys V, Gilson MK, Lather V, Schiffer CA, Fernandes MX. Toward the design of mutation-resistant enzyme inhibitors: further evaluation of the substrate envelope hypothesis. Chemical Biology & Drug Design. 74: 234-45. PMID 19703025 DOI: 10.1111/J.1747-0285.2009.00851.X |
0.492 |
|
| 2009 |
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. Journal of Medicinal Chemistry. 52: 737-54. PMID 19193159 DOI: 10.1021/Jm8009525 |
0.657 |
|
| 2009 |
Anderson J, Schiffer C, Lee SK, Swanstrom R. Viral protease inhibitors. Handbook of Experimental Pharmacology. 85-110. PMID 19048198 DOI: 10.1007/978-3-540-79086-0_4 |
0.5 |
|
| 2009 |
Ozen A, Haliloglu T, Schiffer CA. Using Molecular Dynamics to Investigate Substrate Recognition and Co-evolution in HIV-1 Protease Biophysical Journal. 96: 598a. DOI: 10.1016/J.Bpj.2008.12.3129 |
0.527 |
|
| 2009 |
Royer WE, Chen W, Lam SS, Srinath H, Jiang Z, Correia JJ, Schiffer CA, Fitzgerald KA, Lin K. Activation Of Interferon Regulatory Factors Revealed By The Crystal Structure Of Dimeric IRF-5 Biophysical Journal. 96: 586a-587a. DOI: 10.1016/J.Bpj.2008.12.3070 |
0.447 |
|
| 2009 |
Bandaranayake RM, Kolli M, Prabu-Jeyabalan M, Nalam M, Ng C, Kakizawa J, Heroux A, King NM, Sugiura W, Schiffer CA. Structural Explanations to Altered Drug Resistance Pathways in HIV-1 Non-Clade B Proteases Biophysical Journal. 96: 447a. DOI: 10.1016/J.Bpj.2008.12.2298 |
0.524 |
|
| 2009 |
Mittal S, Schiffer CA. Protein Engineering as a tool For Probing Potential Protein Dynamics in HIV-1 Protease Biophysical Journal. 96: 321a. DOI: 10.1016/J.Bpj.2008.12.1609 |
0.541 |
|
| 2008 |
Nalam MN, Schiffer CA. 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: 642-6. PMID 19373036 DOI: 10.1097/Coh.0B013E3283136Cee |
0.555 |
|
| 2008 |
Chen W, Lam SS, Srinath H, Jiang Z, Correia JJ, Schiffer CA, Fitzgerald KA, Lin K, Royer WE. Insights into interferon regulatory factor activation from the crystal structure of dimeric IRF5. Nature Structural & Molecular Biology. 15: 1213-20. PMID 18836453 DOI: 10.1038/Nsmb.1496 |
0.428 |
|
| 2008 |
Lefebvre E, Schiffer CA. Resilience to resistance of HIV-1 protease inhibitors: profile of darunavir. Aids Reviews. 10: 131-42. PMID 18820715 |
0.497 |
|
| 2008 |
Chen W, Srinath H, Lam SS, Schiffer CA, Royer WE, Lin K. Contribution of Ser386 and Ser396 to activation of interferon regulatory factor 3. Journal of Molecular Biology. 379: 251-60. PMID 18440553 DOI: 10.1016/J.Jmb.2008.03.050 |
0.426 |
|
| 2008 |
Bandaranayake RM, Prabu-Jeyabalan M, Kakizawa J, Sugiura W, Schiffer CA. Structural analysis of human immunodeficiency virus type 1 CRF01_AE protease in complex with the substrate p1-p6. Journal of Virology. 82: 6762-6. PMID 18434392 DOI: 10.1128/Jvi.00018-08 |
0.523 |
|
| 2008 |
Altman MD, Ali A, Reddy GS, Nalam MN, Anjum SG, Cao H, Chellappan S, Kairys V, Fernandes MX, Gilson MK, Schiffer CA, Rana TM, Tidor B. HIV-1 protease inhibitors from inverse design in the substrate envelope exhibit subnanomolar binding to drug-resistant variants. Journal of the American Chemical Society. 130: 6099-113. PMID 18412349 DOI: 10.1021/Ja076558P |
0.702 |
|
| 2008 |
Altman MD, Nalivaika EA, Prabu-Jeyabalan M, Schiffer CA, Tidor B. Computational design and experimental study of tighter binding peptides to an inactivated mutant of HIV-1 protease. Proteins. 70: 678-94. PMID 17729291 DOI: 10.1002/Prot.21514 |
0.66 |
|
| 2007 |
Reddy GS, Ali A, Nalam MN, Anjum SG, Cao H, Nathans RS, Schiffer CA, Rana TM. Design and synthesis of HIV-1 protease inhibitors incorporating oxazolidinones as P2/P2' ligands in pseudosymmetric dipeptide isosteres. Journal of Medicinal Chemistry. 50: 4316-28. PMID 17696512 DOI: 10.1021/Jm070284Z |
0.538 |
|
| 2007 |
Auclair JR, Green KM, Shandilya S, Evans JE, Somasundaran M, Schiffer CA. Mass spectrometry analysis of HIV-1 Vif reveals an increase in ordered structure upon oligomerization in regions necessary for viral infectivity. Proteins. 69: 270-84. PMID 17598142 DOI: 10.1002/Prot.21471 |
0.471 |
|
| 2007 |
Nalam MN, Peeters A, Jonckers TH, Dierynck I, Schiffer CA. Crystal structure of lysine sulfonamide inhibitor reveals the displacement of the conserved flap water molecule in human immunodeficiency virus type 1 protease. Journal of Virology. 81: 9512-8. PMID 17596316 DOI: 10.1128/Jvi.00799-07 |
0.538 |
|
| 2007 |
Chellappan S, Kiran Kumar Reddy GS, Ali A, Nalam MN, Anjum SG, Cao H, Kairys V, Fernandes MX, Altman MD, Tidor B, Rana TM, Schiffer CA, Gilson MK. Design of mutation-resistant HIV protease inhibitors with the substrate envelope hypothesis. Chemical Biology & Drug Design. 69: 298-313. PMID 17539822 DOI: 10.1111/J.1747-0285.2007.00514.X |
0.693 |
|
| 2007 |
Chellappan S, Kairys V, Fernandes MX, Schiffer C, Gilson MK. Evaluation of the substrate envelope hypothesis for inhibitors of HIV-1 protease. Proteins. 68: 561-7. PMID 17474129 DOI: 10.1002/Prot.21431 |
0.549 |
|
| 2007 |
Foulkes-Murzycki JE, Scott WR, Schiffer CA. Hydrophobic sliding: a possible mechanism for drug resistance in human immunodeficiency virus type 1 protease. Structure (London, England : 1993). 15: 225-33. PMID 17292840 DOI: 10.1016/J.Str.2007.01.006 |
0.578 |
|
| 2006 |
Mitsuya Y, Winters MA, Fessel WJ, Rhee SY, Hurley L, Horberg M, Schiffer CA, Zolopa AR, Shafer RW. 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: 1300-5. PMID 17209774 DOI: 10.1089/Aid.2006.22.1300 |
0.499 |
|
| 2006 |
Ali A, Reddy GS, Cao H, Anjum SG, Nalam MN, Schiffer CA, Rana TM. Discovery of HIV-1 protease inhibitors with picomolar affinities incorporating N-aryl-oxazolidinone-5-carboxamides as novel P2 ligands. Journal of Medicinal Chemistry. 49: 7342-56. PMID 17149864 DOI: 10.1021/Jm060666P |
0.51 |
|
| 2006 |
Foulkes JE, Prabu-Jeyabalan M, Cooper D, Henderson GJ, Harris J, Swanstrom R, Schiffer CA. Role of invariant Thr80 in human immunodeficiency virus type 1 protease structure, function, and viral infectivity. Journal of Virology. 80: 6906-16. PMID 16809296 DOI: 10.1128/Jvi.01900-05 |
0.528 |
|
| 2006 |
Ozer N, Haliloglu T, Schiffer CA. Substrate specificity in HIV-1 protease by a biased sequence search method. Proteins. 64: 444-56. PMID 16741993 DOI: 10.1002/Prot.21023 |
0.462 |
|
| 2006 |
Prabu-Jeyabalan M, King NM, Nalivaika EA, Heilek-Snyder G, Cammack N, Schiffer CA. 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: 1518-21. PMID 16569872 DOI: 10.1128/Aac.50.4.1518-1521.2006 |
0.546 |
|
| 2006 |
Prabu-Jeyabalan M, Nalivaika EA, Romano K, Schiffer CA. Mechanism of substrate recognition by drug-resistant human immunodeficiency virus type 1 protease variants revealed by a novel structural intermediate. Journal of Virology. 80: 3607-16. PMID 16537628 DOI: 10.1128/Jvi.80.7.3607-3616.2006 |
0.549 |
|
| 2006 |
Kolli M, Lastere S, Schiffer CA. Co-evolution of nelfinavir-resistant HIV-1 protease and the p1-p6 substrate. Virology. 347: 405-9. PMID 16430939 DOI: 10.1016/J.Virol.2005.11.049 |
0.522 |
|
| 2005 |
Surleraux DL, de Kock HA, Verschueren WG, Pille GM, Maes LJ, Peeters A, Vendeville S, De Meyer S, Azijn H, Pauwels R, de Bethune MP, King NM, Prabu-Jeyabalan M, Schiffer CA, Wigerinck PB. Design of HIV-1 protease inhibitors active on multidrug-resistant virus. Journal of Medicinal Chemistry. 48: 1965-73. PMID 15771440 DOI: 10.1021/Jm049454N |
0.523 |
|
| 2005 |
Surleraux DL, Tahri A, Verschueren WG, Pille GM, de Kock HA, Jonckers TH, Peeters A, De Meyer S, Azijn H, Pauwels R, de Bethune MP, King NM, Prabu-Jeyabalan M, Schiffer CA, Wigerinck PB. Discovery and selection of TMC114, a next generation HIV-1 protease inhibitor. Journal of Medicinal Chemistry. 48: 1813-22. PMID 15771427 DOI: 10.1021/Jm049560P |
0.54 |
|
| 2005 |
Prabu-Jeyabalan M, Nalivaika EA, Schiffer CA. A representation of a possible intermediate step during substrate recognition of HIV-1 protease: crystal structures of substrate bound enzyme exhibiting a novel flap conformation Acta Crystallographica Section a Foundations of Crystallography. 61: c196-c196. DOI: 10.1107/S0108767305091634 |
0.49 |
|
| 2005 |
Hoffman NG, Schiffer CA, Swanstrom R. Erratum to “Covariation of amino acid positions in HIV-1 protease” [Virology 314 (2003) 536–548] Virology. 331: 206-207. DOI: 10.1016/J.Virol.2004.10.029 |
0.318 |
|
| 2004 |
Johnston E, Winters MA, Rhee SY, Merigan TC, Schiffer CA, Shafer RW. 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: 4864-8. PMID 15561868 DOI: 10.1128/Aac.48.12.4864-4868.2004 |
0.5 |
|
| 2004 |
Prabu-Jeyabalan M, Nalivaika EA, King NM, Schiffer CA. Structural basis for coevolution of a human immunodeficiency virus type 1 nucleocapsid-p1 cleavage site with a V82A drug-resistant mutation in viral protease. Journal of Virology. 78: 12446-54. PMID 15507631 DOI: 10.1128/Jvi.78.22.12446-12454.2004 |
0.536 |
|
| 2004 |
King NM, Prabu-Jeyabalan M, Nalivaika EA, Schiffer CA. Combating susceptibility to drug resistance: lessons from HIV-1 protease. Chemistry & Biology. 11: 1333-8. PMID 15489160 DOI: 10.1016/S1074-5521(04)00243-1 |
0.541 |
|
| 2004 |
King NM, Prabu-Jeyabalan M, Nalivaika EA, Wigerinck P, de Béthune MP, Schiffer CA. Structural and thermodynamic basis for the binding of TMC114, a next-generation human immunodeficiency virus type 1 protease inhibitor. Journal of Virology. 78: 12012-21. PMID 15479840 DOI: 10.1128/Jvi.78.21.12012-12021.2004 |
0.539 |
|
| 2003 |
Hoffman NG, Schiffer CA, Swanstrom R. Covariation of amino acid positions in HIV-1 protease. Virology. 314: 536-48. PMID 14554082 DOI: 10.1016/S0042-6822(03)00484-7 |
0.445 |
|
| 2003 |
Kurt N, Haliloglu T, Schiffer CA. Structure-based prediction of potential binding and nonbinding peptides to HIV-1 protease. Biophysical Journal. 85: 853-63. PMID 12885633 DOI: 10.1016/S0006-3495(03)74525-1 |
0.507 |
|
| 2003 |
Kurt N, Scott WR, Schiffer CA, 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: 409-22. PMID 12696052 DOI: 10.1002/Prot.10350 |
0.495 |
|
| 2003 |
Wu TD, Schiffer CA, Gonzales MJ, Taylor J, Kantor R, Chou S, Israelski D, Zolopa AR, Fessel WJ, Shafer RW. Mutation patterns and structural correlates in human immunodeficiency virus type 1 protease following different protease inhibitor treatments. Journal of Virology. 77: 4836-47. PMID 12663790 DOI: 10.1128/Jvi.77.8.4836-4847.2003 |
0.529 |
|
| 2003 |
Prabu-Jeyabalan M, Nalivaika EA, King NM, Schiffer CA. Viability of a drug-resistant human immunodeficiency virus type 1 protease variant: structural insights for better antiviral therapy. Journal of Virology. 77: 1306-15. PMID 12502847 DOI: 10.1128/Jvi.77.2.1306-1315.2003 |
0.56 |
|
| 2002 |
Liu H, Radhakrishnan P, Magoun L, Prabu M, Campellone KG, Savage P, He F, Schiffer CA, Leong JM. Point mutants of EHEC intimin that diminish Tir recognition and actin pedestal formation highlight a putative Tir binding pocket. Molecular Microbiology. 45: 1557-73. PMID 12354225 DOI: 10.1046/J.1365-2958.2002.03137.X |
0.42 |
|
| 2002 |
Pettit SC, Henderson GJ, Schiffer CA, 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. Journal of Virology. 76: 10226-33. PMID 12239298 DOI: 10.1128/Jvi.76.20.10226-10233.2002 |
0.428 |
|
| 2002 |
Prabu-Jeyabalan M, Nalivaika E, Schiffer CA. Substrate shape determines specificity of recognition for HIV-1 protease: analysis of crystal structures of six substrate complexes. Structure (London, England : 1993). 10: 369-81. PMID 12005435 DOI: 10.1016/S0969-2126(02)00720-7 |
0.512 |
|
| 2002 |
Schiffer C, Ultsch M, Walsh S, Somers W, De Vos AM, 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 Journal of Molecular Biology. 316: 277-289. PMID 11851338 DOI: 10.1006/Jmbi.2001.5348 |
0.697 |
|
| 2002 |
King NM, Melnick L, Prabu-Jeyabalan M, Nalivaika EA, Yang SS, Gao Y, Nie X, Zepp C, Heefner DL, Schiffer CA. Lack of synergy for inhibitors targeting a multi-drug-resistant HIV-1 protease. Protein Science : a Publication of the Protein Society. 11: 418-29. PMID 11790852 DOI: 10.1110/Ps.25502 |
0.567 |
|
| 2000 |
Scott WR, Schiffer CA. Curling of flap tips in HIV-1 protease as a mechanism for substrate entry and tolerance of drug resistance. Structure (London, England : 1993). 8: 1259-65. PMID 11188690 DOI: 10.1016/S0969-2126(00)00537-2 |
0.546 |
|
| 2000 |
Prabu-Jeyabalan M, Nalivaika E, Schiffer CA. How does a symmetric dimer recognize an asymmetric substrate? A substrate complex of HIV-1 protease. Journal of Molecular Biology. 301: 1207-20. PMID 10966816 DOI: 10.1006/Jmbi.2000.4018 |
0.483 |
|
| 1999 |
Schiffer CA, van Gunsteren WF. Accessibility and order of water sites in and around proteins: A crystallographic time-averaging study. Proteins. 36: 501-11. PMID 10450092 DOI: 10.1002/(Sici)1097-0134(19990901)36:4<501::Aid-Prot14>3.0.Co;2-1 |
0.525 |
|
| 1996 |
Peng JW, Schiffer CA, Xu P, van Gunsteren WF, Ernst RR. Investigations of peptide hydration using NMR and molecular dynamics simulations: A study of effects of water on the conformation and dynamics of antamanide. Journal of Biomolecular Nmr. 8: 453-76. PMID 20859779 DOI: 10.1007/Bf00228147 |
0.521 |
|
| 1996 |
Schiffer CA, van Gunsteren WF. Structural stability of disulfide mutants of basic pancreatic trypsin inhibitor: a molecular dynamics study. Proteins. 26: 66-71. PMID 8880930 DOI: 10.1002/(Sici)1097-0134(199609)26:1<66::Aid-Prot6>3.0.Co;2-E |
0.572 |
|
| 1995 |
Schiffer CA, Gros P, van Gunsteren WF. Time-averaging crystallographic refinement: possibilities and limitations using alpha-cyclodextrin as a test system. Acta Crystallographica. Section D, Biological Crystallography. 51: 85-92. PMID 15299339 DOI: 10.1107/S0907444994007158 |
0.497 |
|
| 1995 |
Schiffer CA, Clifton IJ, Davisson VJ, Santi DV, Stroud RM. Crystal structure of human thymidylate synthase: a structural mechanism for guiding substrates into the active site. Biochemistry. 34: 16279-87. PMID 8845352 DOI: 10.1021/Bi00050A007 |
0.68 |
|
| 1995 |
Van Gunsteren WF, Hünenberger PH, Kovacs H, Mark AE, Schiffer CA. Investigation of protein unfolding and stability by computer simulation. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 348: 49-59. PMID 7770486 DOI: 10.1098/Rstb.1995.0045 |
0.541 |
|
| 1995 |
Schiffer CA, Dötsch V, Wüthrich K, van Gunsteren WF. 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: 15057-67. PMID 7578118 DOI: 10.1021/Bi00046A011 |
0.533 |
|
| 1995 |
Bisang C, Weber C, Inglis J, Schiffer CA, van Gunsteren WF, Jelesarov I, Bosshard HR, Robinson JA. 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 Journal of the American Chemical Society. 117: 7904-7915. DOI: 10.1021/Ja00135A008 |
0.505 |
|
| 1994 |
van Gunsteren WF, Brunne RM, Gros P, van Schaik RC, Schiffer CA, Torda AE. Accounting for molecular mobility in structure determination based on nuclear magnetic resonance spectroscopic and X-ray diffraction data. Methods in Enzymology. 239: 619-54. PMID 7530320 DOI: 10.1016/S0076-6879(94)39024-X |
0.518 |
|
| 1994 |
Schiffer CA, Huber R, Wüthrich K, van Gunsteren WF. Simultaneous refinement of the structure of BPTI against NMR data measured in solution and X-ray diffraction data measured in single crystals. Journal of Molecular Biology. 241: 588-99. PMID 7520085 DOI: 10.1006/Jmbi.1994.1533 |
0.521 |
|
| 1993 |
Schiffer CA, Caldwell JW, Kollman PA, Stroud RM. Protein Structure Prediction with a Combined Solvation Free Energy-Molecular Mechanics Force Field Molecular Simulation. 10: 121-149. DOI: 10.1080/08927029308022162 |
0.623 |
|
| 1992 |
Schiffer CA, Caldwell JW, Stroud RM, Kollman PA. Inclusion of solvation free energy with molecular mechanics energy: alanyl dipeptide as a test case. Protein Science : a Publication of the Protein Society. 1: 396-400. PMID 1304346 DOI: 10.1002/Pro.5560010311 |
0.596 |
|
| 1991 |
Schiffer CA, Davisson VJ, Santi DV, Stroud RM. Crystallization of human thymidylate synthase. Journal of Molecular Biology. 219: 161-3. PMID 2038053 DOI: 10.1016/0022-2836(91)90558-N |
0.598 |
|
| 1990 |
Schiffer CA, Caldwell JW, Kollman PA, Stroud RM. Prediction of homologous protein structures based on conformational searches and energetics. Proteins. 8: 30-43. PMID 2217162 DOI: 10.1002/Prot.340080107 |
0.635 |
|
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