| Year |
Citation |
Score |
| 2023 |
Duarte Ramos Matos G, Pak S, Rizzo RC. Descriptor-Driven de Novo Design Algorithms for DOCK6 Using RDKit. Journal of Chemical Information and Modeling. 63: 5803-5822. PMID 37698425 DOI: 10.1021/acs.jcim.3c01031 |
0.703 |
|
| 2023 |
Coant N, Bickel JD, Rahaim R, Otsuka Y, Choi YM, Xu R, Simoes M, Cariello C, Mao C, Saied EM, Arenz C, Spicer TP, Bannister TD, Tonge PJ, Airola MV, ... ... Rizzo RC, et al. Neutral ceramidase-active site inhibitor chemotypes and binding modes. Bioorganic Chemistry. 139: 106747. PMID 37531819 DOI: 10.1016/j.bioorg.2023.106747 |
0.301 |
|
| 2022 |
Prentis LE, Singleton CD, Bickel JD, Allen WJ, Rizzo RC. A molecular evolution algorithm for ligand design in DOCK. Journal of Computational Chemistry. PMID 36073674 DOI: 10.1002/jcc.26993 |
0.644 |
|
| 2020 |
Telehany S, Humby M, McGee TD, Riley S, Jacobs A, Rizzo RC. Identification of Zika Virus Inhibitors Using Homology Modeling and Similarity-based Screening to Target Glycoprotein E. Biochemistry. PMID 32876433 DOI: 10.1021/Acs.Biochem.0C00458 |
0.383 |
|
| 2019 |
Zhou Y, Elmes MW, Sweeney J, Joseph O, Che J, Hsu HC, Li H, Deutsch DG, Ojima I, Kaczocha M, Rizzo RC. Identification of Fatty Acid Binding Protein 5 Inhibitors Through Similarity-based Screening. Biochemistry. PMID 31539229 DOI: 10.1021/Acs.Biochem.9B00625 |
0.443 |
|
| 2019 |
Kim J, Bogdan DM, Elmes MW, Awwa M, Yan S, Che J, Lee G, Deutsch DG, Rizzo RC, Kaczocha M, Ojima I. Incarvillateine produces antinociceptive and motor suppressive effects via adenosine receptor activation. Plos One. 14: e0218619. PMID 31237895 DOI: 10.1371/Journal.Pone.0218619 |
0.327 |
|
| 2019 |
Elmes MW, Prentis LE, McGoldrick LL, Giuliano CJ, Sweeney JM, Joseph OM, Che J, Carbonetti GS, Studholme K, Deutsch DG, Rizzo RC, Glynn SE, Kaczocha M. FABP1 controls hepatic transport and biotransformation of Δ-THC. Scientific Reports. 9: 7588. PMID 31110286 DOI: 10.1038/S41598-019-44108-3 |
0.621 |
|
| 2019 |
Singleton CD, Humby MS, Yi HA, Rizzo RC, Jacobs A. Identification of Ebola Virus Inhibitors Targeting GP2 using Principles of Molecular Mimicry. Journal of Virology. PMID 31092576 DOI: 10.1128/Jvi.00676-19 |
0.387 |
|
| 2018 |
Guo J, Collins S, Miller WT, Rizzo RC. Identification of a water-coordinating HER2 inhibitor by virtual screening using similarity-based scoring. Biochemistry. PMID 29975516 DOI: 10.1021/Acs.Biochem.8B00524 |
0.421 |
|
| 2018 |
Yan S, Elmes MW, Tong S, Hu K, Awwa M, Teng GYH, Jing Y, Freitag M, Gan Q, Clement T, Wei L, Sweeney JM, Joseph OM, Che J, Carbonetti GS, ... ... Rizzo RC, et al. SAR studies on truxillic acid mono esters as a new class of antinociceptive agents targeting fatty acid binding proteins. European Journal of Medicinal Chemistry. 154: 233-252. PMID 29803996 DOI: 10.1016/J.Ejmech.2018.04.050 |
0.413 |
|
| 2017 |
Allen WJ, Fochtman BC, Balius TE, Rizzo RC. Customizable de novo design strategies for DOCK: Application to HIVgp41 and other therapeutic targets. Journal of Computational Chemistry. PMID 28940386 DOI: 10.1002/Jcc.25052 |
0.505 |
|
| 2017 |
Hsu HC, Tong S, Zhou Y, Elmes MW, Yan S, Kaczocha M, Deutsch DG, Rizzo RC, Ojima I, Li H. The antinociceptive agent SBFI-26 binds to anandamide transporters FABP5 and FABP7 at two different sites. Biochemistry. PMID 28632393 DOI: 10.1021/Acs.Biochem.7B00194 |
0.419 |
|
| 2017 |
McGee TD, Yi HA, Allen WJ, Jacobs A, Rizzo RC. Structure-based identification of inhibitors targeting obstruction of the HIVgp41 N-heptad repeat trimer. Bioorganic & Medicinal Chemistry Letters. PMID 28558972 DOI: 10.1016/J.Bmcl.2017.05.020 |
0.406 |
|
| 2016 |
Zhou Y, McGillick BE, Teng YG, Haranahalli K, Ojima I, Swaminathan S, Rizzo RC. Identification of small molecule inhibitors of botulinum neurotoxin serotype E via footprint similarity. Bioorganic & Medicinal Chemistry. PMID 27543389 DOI: 10.1016/J.Bmc.2016.07.031 |
0.418 |
|
| 2016 |
Yi HA, Fochtman BC, Rizzo RC, Jacobs A. Inhibition of HIV Entry by Targeting the Envelope Transmembrane Subunit gp41. Current Hiv Research. 14: 283-94. PMID 26957202 DOI: 10.2174/1570162X14999160224103908 |
0.363 |
|
| 2015 |
Teng YH, Berger WT, Nesbitt NM, Kumar K, Balius TE, Rizzo RC, Tonge PJ, Ojima I, Swaminathan S. Computer-aided identification, synthesis, and biological evaluation of novel inhibitors for botulinum neurotoxin serotype A. Bioorganic & Medicinal Chemistry. 23: 5489-95. PMID 26275678 DOI: 10.1016/J.Bmc.2015.07.040 |
0.322 |
|
| 2015 |
Airola MV, Allen WJ, Pulkoski-Gross MJ, Obeid LM, Rizzo RC, Hannun YA. Structural Basis for Ceramide Recognition and Hydrolysis by Human Neutral Ceramidase. Structure (London, England : 1993). 23: 1482-91. PMID 26190575 DOI: 10.1016/J.Str.2015.06.013 |
0.384 |
|
| 2015 |
Allen WJ, Yi HA, Gochin M, Jacobs A, Rizzo RC. Small molecule inhibitors of HIVgp41 N-heptad repeat trimer formation. Bioorganic & Medicinal Chemistry Letters. 25: 2853-9. PMID 26013847 DOI: 10.1016/J.Bmcl.2015.04.067 |
0.438 |
|
| 2015 |
Allen WJ, Balius TE, Mukherjee S, Brozell SR, Moustakas DT, Lang PT, Case DA, Kuntz ID, Rizzo RC. DOCK 6: Impact of new features and current docking performance. Journal of Computational Chemistry. 36: 1132-56. PMID 25914306 DOI: 10.1002/Jcc.23905 |
0.449 |
|
| 2015 |
Jiang L, Rizzo RC. Pharmacophore-based similarity scoring for DOCK. The Journal of Physical Chemistry. B. 119: 1083-102. PMID 25229837 DOI: 10.1021/Jp506555W |
0.425 |
|
| 2014 |
Kaczocha M, Rebecchi MJ, Ralph BP, Teng YH, Berger WT, Galbavy W, Elmes MW, Glaser ST, Wang L, Rizzo RC, Deutsch DG, Ojima I. Inhibition of fatty acid binding proteins elevates brain anandamide levels and produces analgesia. Plos One. 9: e94200. PMID 24705380 DOI: 10.1371/Journal.Pone.0094200 |
0.34 |
|
| 2014 |
Allen WJ, Rizzo RC. Implementation of the Hungarian algorithm to account for ligand symmetry and similarity in structure-based design. Journal of Chemical Information and Modeling. 54: 518-29. PMID 24410429 DOI: 10.1021/Ci400534H |
0.43 |
|
| 2014 |
Holden PM, Allen WJ, Gochin M, Rizzo RC. Strategies for lead discovery: application of footprint similarity targeting HIVgp41. Bioorganic & Medicinal Chemistry. 22: 651-61. PMID 24315195 DOI: 10.1016/J.Bmc.2013.10.022 |
0.456 |
|
| 2013 |
Furt F, Allen WJ, Widhalm JR, Madzelan P, Rizzo RC, Basset G, Wilson MA. Functional convergence of structurally distinct thioesterases from cyanobacteria and plants involved in phylloquinone biosynthesis. Acta Crystallographica. Section D, Biological Crystallography. 69: 1876-88. PMID 24100308 DOI: 10.1107/S0907444913015771 |
0.325 |
|
| 2013 |
Balius TE, Allen WJ, Mukherjee S, Rizzo RC. Grid-based molecular footprint comparison method for docking and de novo design: application to HIVgp41. Journal of Computational Chemistry. 34: 1226-40. PMID 23436713 DOI: 10.1002/Jcc.23245 |
0.457 |
|
| 2012 |
Allen WJ, Rizzo RC. Computer-Aided Approaches for Targeting HIVgp41. Biology. 1: 311-38. PMID 23730525 DOI: 10.3390/Biology1020311 |
0.378 |
|
| 2012 |
Berger WT, Ralph BP, Kaczocha M, Sun J, Balius TE, Rizzo RC, Haj-Dahmane S, Ojima I, Deutsch DG. Targeting fatty acid binding protein (FABP) anandamide transporters - a novel strategy for development of anti-inflammatory and anti-nociceptive drugs. Plos One. 7: e50968. PMID 23236415 DOI: 10.1371/Journal.Pone.0050968 |
0.419 |
|
| 2012 |
Brozell SR, Mukherjee S, Balius TE, Roe DR, Case DA, Rizzo RC. Evaluation of DOCK 6 as a pose generation and database enrichment tool. Journal of Computer-Aided Molecular Design. 26: 749-73. PMID 22569593 DOI: 10.1007/S10822-012-9565-Y |
0.383 |
|
| 2012 |
Holden PM, Kaur H, Goyal R, Gochin M, Rizzo RC. Footprint-based identification of viral entry inhibitors targeting HIVgp41. Bioorganic & Medicinal Chemistry Letters. 22: 3011-6. PMID 22425565 DOI: 10.1016/J.Bmcl.2012.02.017 |
0.421 |
|
| 2012 |
Huang Y, Rizzo RC. A water-based mechanism of specificity and resistance for lapatinib with ErbB family kinases. Biochemistry. 51: 2390-406. PMID 22352796 DOI: 10.1021/Bi2016553 |
0.353 |
|
| 2011 |
Dufour A, Sampson NS, Li J, Kuscu C, Rizzo RC, Deleon JL, Zhi J, Jaber N, Liu E, Zucker S, Cao J. Small-molecule anticancer compounds selectively target the hemopexin domain of matrix metalloproteinase-9. Cancer Research. 71: 4977-88. PMID 21646471 DOI: 10.1158/0008-5472.Can-10-4552 |
0.302 |
|
| 2011 |
Balius TE, Mukherjee S, Rizzo RC. Implementation and evaluation of a docking-rescoring method using molecular footprint comparisons. Journal of Computational Chemistry. 32: 2273-89. PMID 21541962 DOI: 10.1002/Jcc.21814 |
0.491 |
|
| 2010 |
Mukherjee S, Balius TE, Rizzo RC. Docking validation resources: protein family and ligand flexibility experiments. Journal of Chemical Information and Modeling. 50: 1986-2000. PMID 21033739 DOI: 10.1021/Ci1001982 |
0.407 |
|
| 2010 |
McGillick BE, Balius TE, Mukherjee S, Rizzo RC. Origins of resistance to the HIVgp41 viral entry inhibitor T20. Biochemistry. 49: 3575-92. PMID 20230061 DOI: 10.1021/Bi901915G |
0.357 |
|
| 2009 |
Balius TE, Rizzo RC. Quantitative prediction of fold resistance for inhibitors of EGFR. Biochemistry. 48: 8435-48. PMID 19627157 DOI: 10.1021/Bi900729A |
0.403 |
|
| 2009 |
Lang PT, Brozell SR, Mukherjee S, Pettersen EF, Meng EC, Thomas V, Rizzo RC, Case DA, James TL, Kuntz ID. DOCK 6: combining techniques to model RNA-small molecule complexes. Rna (New York, N.Y.). 15: 1219-30. PMID 19369428 DOI: 10.1261/Rna.1563609 |
0.396 |
|
| 2009 |
Carrascal N, Rizzo RC. Calculation of binding free energies for non-zinc chelating pyrimidine dicarboxamide inhibitors with MMP-13. Bioorganic & Medicinal Chemistry Letters. 19: 47-50. PMID 19042129 DOI: 10.1016/J.Bmcl.2008.11.038 |
0.387 |
|
| 2008 |
Chachra R, Rizzo RC. Origins of Resistance Conferred by the R292K Neuraminidase Mutation via Molecular Dynamics and Free Energy Calculations. Journal of Chemical Theory and Computation. 4: 1526-40. PMID 26621436 DOI: 10.1021/Ct800068V |
0.393 |
|
| 2007 |
Strockbine B, Rizzo RC. Binding of antifusion peptides with HIVgp41 from molecular dynamics simulations: quantitative correlation with experiment. Proteins. 67: 630-42. PMID 17335007 DOI: 10.1002/Prot.21301 |
0.403 |
|
| 2006 |
Rizzo RC, Aynechi T, Case DA, Kuntz ID. Estimation of Absolute Free Energies of Hydration Using Continuum Methods: Accuracy of Partial Charge Models and Optimization of Nonpolar Contributions. Journal of Chemical Theory and Computation. 2: 128-39. PMID 26626387 DOI: 10.1021/Ct050097L |
0.363 |
|
| 2006 |
Moustakas DT, Lang PT, Pegg S, Pettersen E, Kuntz ID, Brooijmans N, Rizzo RC. Development and validation of a modular, extensible docking program: DOCK 5. Journal of Computer-Aided Molecular Design. 20: 601-19. PMID 17149653 DOI: 10.1007/S10822-006-9060-4 |
0.41 |
|
| 2006 |
Hornak V, Okur A, Rizzo RC, Simmerling C. HIV-1 protease flaps spontaneously close to the correct structure in simulations following manual placement of an inhibitor into the open state. Journal of the American Chemical Society. 128: 2812-3. PMID 16506755 DOI: 10.1021/Ja058211X |
0.357 |
|
| 2006 |
Hornak V, Okur A, Rizzo RC, Simmerling C. HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations. Proceedings of the National Academy of Sciences of the United States of America. 103: 915-20. PMID 16418268 DOI: 10.1073/Pnas.0508452103 |
0.331 |
|
| 2004 |
Rizzo RC, Toba S, Kuntz ID. A molecular basis for the selectivity of thiadiazole urea inhibitors with stromelysin-1 and gelatinase-A from generalized born molecular dynamics simulations. Journal of Medicinal Chemistry. 47: 3065-74. PMID 15163188 DOI: 10.1021/Jm030570K |
0.408 |
|
| 2003 |
Kroeger Smith MB, Hose BM, Hawkins A, Lipchock J, Farnsworth DW, Rizzo RC, Tirado-Rives J, Arnold E, Zhang W, Hughes SH, Jorgensen WL, Michejda CJ, Smith RH. Molecular modeling calculations of HIV-1 reverse transcriptase nonnucleoside inhibitors: correlation of binding energy with biological activity for novel 2-aryl-substituted benzimidazole analogues. Journal of Medicinal Chemistry. 46: 1940-7. PMID 12723956 DOI: 10.1021/Jm020271F |
0.554 |
|
| 2002 |
Rizzo RC, Udier-Blagović M, Wang DP, Watkins EK, Kroeger Smith MB, Smith RH, Tirado-Rives J, Jorgensen WL. Prediction of activity for nonnucleoside inhibitors with HIV-1 reverse transcriptase based on Monte Carlo simulations. Journal of Medicinal Chemistry. 45: 2970-87. PMID 12086483 DOI: 10.1021/Jm010580Q |
0.546 |
|
| 2001 |
Wang DP, Rizzo RC, Tirado-Rives J, Jorgensen WL. Antiviral drug design: computational analyses of the effects of the L100I mutation for HIV-RT on the binding of NNRTIs. Bioorganic & Medicinal Chemistry Letters. 11: 2799-802. PMID 11597403 DOI: 10.1016/S0960-894X(01)00510-8 |
0.542 |
|
| 2001 |
Rizzo RC, Tirado-Rives J, Jorgensen WL. Estimation of binding affinities for HEPT and nevirapine analogues with HIV-1 reverse transcriptase via Monte Carlo simulations. Journal of Medicinal Chemistry. 44: 145-54. PMID 11170624 DOI: 10.1021/Jm000255N |
0.566 |
|
| 2001 |
Zhou R, Friesner RA, Ghosh A, Rizzo RC, Jorgensen WL, Levy RM. New linear interaction method for binding affinity calculations using a continuum solvent model Journal of Physical Chemistry B. 105: 10388-10397. DOI: 10.1021/Jp011480Z |
0.592 |
|
| 2000 |
Rizzo RC, Wang DP, Tirado-Rives J, Jorgensen WL. Validation of a model for the complex of HIV-1 reverse transcriptase with sustiva through computation of resistance profiles [18] Journal of the American Chemical Society. 122: 12898-12900. DOI: 10.1021/Ja003113R |
0.437 |
|
| 1999 |
Rizzo RC, Jorgensen WL. OPLS all-atom model for amines: Resolution of the amine hydration problem Journal of the American Chemical Society. 121: 4827-4836. DOI: 10.1021/Ja984106U |
0.365 |
|
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