☰

Alexander Luke Perryman - Publications

Affiliations: 
2005 University of California, San Diego, La Jolla, CA 
Tree Info Similar researchers PubMed Report error

32 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Mottin M, de Paula Sousa BK, de Moraes Roso Mesquita NC, de Oliveira KIZ, Noske GD, Sartori GR, de Oliveira Albuquerque A, Urbina F, Puhl AC, Moreira-Filho JT, Souza GE, Guido RVC, Muratov E, Neves BJ, Martins da Silva JH, ... ... Perryman AL, et al. Discovery of New Zika Protease and Polymerase Inhibitors through the Open Science Collaboration Project OpenZika. Journal of Chemical Information and Modeling. PMID 36239304 DOI: 10.1021/acs.jcim.2c00596  0.321
2020 Pereira JC, Daher SS, Zorn KM, Sherwood M, Russo R, Perryman AL, Wang X, Freundlich MJ, Ekins S, Freundlich JS. Machine Learning Platform to Discover Novel Growth Inhibitors of Neisseria gonorrhoeae. Pharmaceutical Research. 37: 141. PMID 32661900 DOI: 10.1007/S11095-020-02876-Y  0.303
2019 Silva S, Shimizu JF, Oliveira DM, Assis LR, Bittar C, Mottin M, Sousa BKP, Mesquita NCMR, Regasini LO, Rahal P, Oliva G, Perryman AL, Ekins S, Andrade CH, Goulart LR, et al. A diarylamine derived from anthranilic acid inhibits ZIKV replication. Scientific Reports. 9: 17703. PMID 31776405 DOI: 10.1038/S41598-019-54169-Z  0.342
2019 Wang X, Perryman A, Li SG, Paget S, Stratton T, Lemenze A, Olson AJ, Ekins S, Kumar P, Freundlich JS. Intrabacterial Metabolism Obscures the Successful Prediction of an InhA Inhibitor of Mycobacterium tuberculosis. Acs Infectious Diseases. PMID 31625383 DOI: 10.1021/Acsinfecdis.9B00295  0.372
2018 Kumar P, Capodagli GC, Awasthi D, Shrestha R, Maharaja K, Sukheja P, Li SG, Inoyama D, Zimmerman M, Ho Liang HP, Sarathy J, Mina M, Rasic G, Russo R, Perryman AL, et al. Synergistic Lethality of a Binary Inhibitor of Mycobacterium tuberculosis KasA. Mbio. 9. PMID 30563908 DOI: 10.1128/Mbio.02101-17  0.42
2018 Perryman AL, Patel JS, Russo R, Singleton E, Connell N, Ekins S, Freundlich JS. Naïve Bayesian Models for Vero Cell Cytotoxicity. Pharmaceutical Research. 35: 170. PMID 29959603 DOI: 10.1007/S11095-018-2439-9  0.309
2018 Mottin M, Borba JVVB, Braga RC, Torres PHM, Martini MC, Proenca-Modena JL, Judice CC, Costa FTM, Ekins S, Perryman AL, Andrade CH. The A-Z of Zika drug discovery. Drug Discovery Today. PMID 29935345 DOI: 10.1016/J.Drudis.2018.06.014  0.376
2018 Lane T, Russo DP, Zorn KM, Clark AM, Korotcov A, Tkachenko V, Reynolds RC, Perryman AL, Freundlich JS, Ekins S. Comparing and Validating Machine Learning Models for Mycobacterium tuberculosis Drug Discovery. Molecular Pharmaceutics. PMID 29672063 DOI: 10.1021/Acs.Molpharmaceut.8B00083  0.353
2018 Inoyama D, Paget SD, Russo R, Kandasamy S, Kumar P, Singleton E, Occi J, Tuckman M, Zimmerman MD, Ho HP, Perryman AL, Dartois V, Connell N, Freundlich JS. Novel Pyrimidines as Antitubercular Agents. Antimicrobial Agents and Chemotherapy. PMID 29311070 DOI: 10.1128/Aac.02063-17  0.369
2017 Stratton TP, Perryman AL, Vilchèze C, Russo R, Li SG, Patel JS, Singleton E, Ekins S, Connell N, Jacobs WR, Freundlich JS. Addressing the Metabolic Stability of Antituberculars through Machine Learning. Acs Medicinal Chemistry Letters. 8: 1099-1104. PMID 29057058 DOI: 10.1021/Acsmedchemlett.7B00299  0.33
2017 Mottin M, Braga RC, da Silva RA, Martins da Silva JH, Perryman AL, Ekins S, Andrade CH. Molecular dynamics simulations of Zika virus NS3 helicase: Insights into RNA binding site activity. Biochemical and Biophysical Research Communications. PMID 28341122 DOI: 10.1016/J.Bbrc.2017.03.070  0.372
2017 Sukheja P, Kumar P, Mittal N, Li SG, Singleton E, Russo R, Perryman AL, Shrestha R, Awasthi D, Husain S, Soteropoulos P, Brukh R, Connell N, Freundlich JS, Alland D. A Novel Small-Molecule Inhibitor of the Mycobacterium tuberculosis Demethylmenaquinone Methyltransferase MenG Is Bactericidal to Both Growing and Nutritionally Deprived Persister Cells. Mbio. 8. PMID 28196957 DOI: 10.1128/Mbio.02022-16  0.37
2016 Ekins S, Perryman AL, Horta Andrade C. OpenZika: An IBM World Community Grid Project to Accelerate Zika Virus Drug Discovery. Plos Neglected Tropical Diseases. 10: e0005023. PMID 27764115 DOI: 10.1371/Journal.Pntd.0005023  0.36
2016 Ekins S, Perryman AL, Clark AM, Reynolds RC, Freundlich JS. Machine Learning Model Analysis and Data Visualization with Small Molecules Tested in a Mouse Model of Mycobacterium tuberculosis Infection (2014-2015). Journal of Chemical Information and Modeling. PMID 27335215 DOI: 10.1021/Acs.Jcim.6B00004  0.357
2015 Perryman AL, Yu W, Wang X, Ekins S, Forli S, Li SG, Freundlich JS, Tonge PJ, Olson AJ. A virtual screen discovers novel, fragment-sized inhibitors of Mycobacterium tuberculosis InhA. Journal of Chemical Information and Modeling. 55: 645-59. PMID 25636146 DOI: 10.1021/Ci500672V  0.403
2015 Deng N, Forli S, He P, Perryman A, Wickstrom L, Vijayan RS, Tiefenbrunn T, Stout D, Gallicchio E, Olson AJ, Levy RM. Distinguishing binders from false positives by free energy calculations: fragment screening against the flap site of HIV protease. The Journal of Physical Chemistry. B. 119: 976-88. PMID 25189630 DOI: 10.1021/Jp506376Z  0.427
2014 Al Olaby RR, Cocquerel L, Zemla A, Saas L, Dubuisson J, Vielmetter J, Marcotrigiano J, Khan AG, Vences Catalan F, Perryman AL, Freundlich JS, Forli S, Levy S, Balhorn R, Azzazy HM. Identification of a novel drug lead that inhibits HCV infection and cell-to-cell transmission by targeting the HCV E2 glycoprotein. Plos One. 9: e111333. PMID 25357246 DOI: 10.1371/Journal.Pone.0111333  0.31
2014 Stec J, Vilchèze C, Lun S, Perryman AL, Wang X, Freundlich JS, Bishai W, Jacobs WR, Kozikowski AP. Biological evaluation of potent triclosan-derived inhibitors of the enoyl-acyl carrier protein reductase InhA in drug-sensitive and drug-resistant strains of Mycobacterium tuberculosis. Chemmedchem. 9: 2528-37. PMID 25165007 DOI: 10.1002/Cmdc.201402255  0.379
2014 Mobley DL, Liu S, Lim NM, Wymer KL, Perryman AL, Forli S, Deng N, Su J, Branson K, Olson AJ. Blind prediction of HIV integrase binding from the SAMPL4 challenge. Journal of Computer-Aided Molecular Design. 28: 327-45. PMID 24595873 DOI: 10.1007/S10822-014-9723-5  0.415
2014 Gallicchio E, Deng N, He P, Wickstrom L, Perryman AL, Santiago DN, Forli S, Olson AJ, Levy RM. Virtual screening of integrase inhibitors by large scale binding free energy calculations: the SAMPL4 challenge. Journal of Computer-Aided Molecular Design. 28: 475-90. PMID 24504704 DOI: 10.1007/S10822-014-9711-9  0.391
2014 Perryman AL, Santiago DN, Forli S, Santos-Martins D, Olson AJ. Virtual screening with AutoDock Vina and the common pharmacophore engine of a low diversity library of fragments and hits against the three allosteric sites of HIV integrase: participation in the SAMPL4 protein-ligand binding challenge. Journal of Computer-Aided Molecular Design. 28: 429-41. PMID 24493410 DOI: 10.1007/S10822-014-9709-3  0.495
2013 Tiefenbrunn T, Forli S, Baksh MM, Chang MW, Happer M, Lin YC, Perryman AL, Rhee JK, Torbett BE, Olson AJ, Elder JH, Finn MG, Stout CD. Small molecule regulation of protein conformation by binding in the Flap of HIV protease. Acs Chemical Biology. 8: 1223-31. PMID 23540839 DOI: 10.1021/Cb300611P  0.369
2011 Lin YC, Perryman AL, Olson AJ, Torbett BE, Elder JH, Stout CD. Structural basis for drug and substrate specificity exhibited by FIV encoding a chimeric FIV/HIV protease. Acta Crystallographica. Section D, Biological Crystallography. 67: 540-8. PMID 21636894 DOI: 10.1107/S0907444911011681  0.404
2010 Cosconati S, Forli S, Perryman AL, Harris R, Goodsell DS, Olson AJ. Virtual Screening with AutoDock: Theory and Practice. Expert Opinion On Drug Discovery. 5: 597-607. PMID 21532931 DOI: 10.1517/17460441.2010.484460  0.345
2010 Perryman AL, Zhang Q, Soutter HH, Rosenfeld R, McRee DE, Olson AJ, Elder JE, Stout CD. Fragment-based screen against HIV protease. Chemical Biology & Drug Design. 75: 257-68. PMID 20659109 DOI: 10.1111/J.1747-0285.2009.00943.X  0.423
2010 Perryman AL, Forli S, Morris GM, Burt C, Cheng Y, Palmer MJ, Whitby K, McCammon JA, Phillips C, Olson AJ. A dynamic model of HIV integrase inhibition and drug resistance. Journal of Molecular Biology. 397: 600-15. PMID 20096702 DOI: 10.1016/J.Jmb.2010.01.033  0.619
2006 Perryman AL, Lin JH, Andrew McCammon J. Optimization and computational evaluation of a series of potential active site inhibitors of the V82F/I84V drug-resistant mutant of HIV-1 protease: an application of the relaxed complex method of structure-based drug design. Chemical Biology & Drug Design. 67: 336-45. PMID 16784458 DOI: 10.1111/J.1747-0285.2006.00382.X  0.503
2006 Perryman AL, Lin JH, McCammon JA. Restrained molecular dynamics simulations of HIV-1 protease: the first step in validating a new target for drug design. Biopolymers. 82: 272-84. PMID 16508951 DOI: 10.1002/Bip.20497  0.518
2004 Perryman AL, Lin JH, McCammon JA. HIV-1 protease molecular dynamics of a wild-type and of the V82F/I84V mutant: possible contributions to drug resistance and a potential new target site for drugs. Protein Science : a Publication of the Protein Society. 13: 1108-23. PMID 15044738 DOI: 10.1110/Ps.03468904  0.55
2003 Lin JH, Perryman AL, Schames JR, McCammon JA. The relaxed complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme. Biopolymers. 68: 47-62. PMID 12579579 DOI: 10.1002/Bip.10218  0.481
2002 Perryman AL, McCammon JA. AutoDocking dinucleotides to the HIV-1 integrase core domain: exploring possible binding sites for viral and genomic DNA. Journal of Medicinal Chemistry. 45: 5624-7. PMID 12477345 DOI: 10.1021/Jm025554M  0.426
2002 Lin JH, Perryman AL, Schames JR, McCammon JA. Computational drug design accommodating receptor flexibility: the relaxed complex scheme. Journal of the American Chemical Society. 124: 5632-3. PMID 12010024 DOI: 10.1021/Ja0260162  0.498
Show low-probability matches.