Senior Scientist II, Computational Chemistry, Repare Therapeutics
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Virtual screening with AutoDock: theory and practice
S Cosconati, S Forli, AL Perryman, R Harris, DS Goodsell, AJ Olson
Expert opinion on drug discovery 5 (6), 597-607, 2010
Computational drug design accommodating receptor flexibility: the relaxed complex scheme
JH Lin, AL Perryman, JR Schames, JA McCammon
Journal of the American Chemical Society 124 (20), 5632-5633, 2002
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
AL Perryman, JH Lin, JA McCammon
Protein Science 13 (4), 1108-1123, 2004
The relaxed complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme
JH Lin, AL Perryman, JR Schames, JA McCammon
Biopolymers: Original Research on Biomolecules 68 (1), 47-62, 2003
Non-classical transpeptidases yield insight into new antibacterials
P Kumar, A Kaushik, EP Lloyd, SG Li, R Mattoo, NC Ammerman, DT Bell, ...
Nature chemical biology 13 (1), 54-61, 2017
Fragment‐based screen against HIV protease
AL Perryman, Q Zhang, HH Soutter, R Rosenfeld, DE McRee, AJ Olson, ...
Chemical biology & drug design 75 (3), 257-268, 2010
A dynamic model of HIV integrase inhibition and drug resistance
AL Perryman, S Forli, GM Morris, C Burt, Y Cheng, MJ Palmer, K Whitby, ...
Journal of molecular biology 397 (2), 600-615, 2010
Comparing and Validating Machine Learning Models for Mycobacterium tuberculosis Drug Discovery
T Lane, DP Russo, KM Zorn, AM Clark, A Korotcov, V Tkachenko, ...
Molecular pharmaceutics 15 (10), 4346-4360, 2018
Restrained molecular dynamics simulations of HIV‐1 protease: The first step in validating a new target for drug design
AL Perryman, JH Lin, JA McCammon
Biopolymers: Original Research on Biomolecules 82 (3), 272-284, 2006
Robust scoring functions for protein–ligand interactions with quantum chemical charge models
JC Wang, JH Lin, CM Chen, AL Perryman, AJ Olson
Journal of chemical information and modeling 51 (10), 2528-2537, 2011
Virtual screening of integrase inhibitors by large scale binding free energy calculations: the SAMPL4 challenge
E Gallicchio, N Deng, P He, L Wickstrom, AL Perryman, DN Santiago, ...
Journal of computer-aided molecular design 28 (4), 475-490, 2014
Blind prediction of HIV integrase binding from the SAMPL4 challenge
DL Mobley, S Liu, NM Lim, KL Wymer, AL Perryman, S Forli, N Deng, J Su, ...
Journal of computer-aided molecular design 28 (4), 327-345, 2014
A Novel Small-Molecule Inhibitor of the Mycobacterium tuberculosis Demethylmenaquinone Methyltransferase MenG Is Bactericidal to Both Growing and …
P Sukheja, P Kumar, N Mittal, SG Li, E Singleton, R Russo, AL Perryman, ...
MBio 8 (1), e02022-16, 2017
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 …
AL Perryman, DN Santiago, S Forli, D Santos-Martins, AJ Olson
Journal of computer-aided molecular design 28 (4), 429-441, 2014
Distinguishing binders from false positives by free energy calculations: fragment screening against the flap site of HIV protease
N Deng, S Forli, P He, A Perryman, L Wickstrom, RSK Vijayan, ...
The Journal of Physical Chemistry B 119 (3), 976-988, 2014
Predicting mouse liver microsomal stability with “pruned” machine learning models and public data
AL Perryman, TP Stratton, S Ekins, JS Freundlich
Pharmaceutical research 33 (2), 433-449, 2016
AutoDocking dinucleotides to the HIV-1 integrase core domain: exploring possible binding sites for viral and genomic DNA
AL Perryman, JA McCammon
Journal of medicinal chemistry 45 (26), 5624-5627, 2002
The A–Z of Zika drug discovery
M Mottin, JVVB Borba, RC Braga, PHM Torres, MC Martini, ...
Drug discovery today 23 (11), 1833-1847, 2018
Small molecule regulation of protein conformation by binding in the flap of HIV protease
T Tiefenbrunn, S Forli, MM Baksh, MW Chang, M Happer, YC Lin, ...
ACS chemical biology 8 (6), 1223-1231, 2013
A Virtual Screen Discovers Novel, Fragment-Sized Inhibitors of Mycobacterium tuberculosis InhA
AL Perryman, W Yu, X Wang, S Ekins, S Forli, SG Li, JS Freundlich, ...
Journal of chemical information and modeling 55 (3), 645-659, 2015
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