R. Rizzo

发表

DOCK 6: combining techniques to model RNA-small molecule complexes.

I. Kuntz, D. Case, E. Meng, 2009, RNA.

Structural Basis for Ceramide Recognition and Hydrolysis by Human Neutral Ceramidase.

W. J. Allen, Y. Hannun, L. Obeid, 2015, Structure.

Estimation of Absolute Free Energies of Hydration Using Continuum Methods: Accuracy of Partial Charge Models and Optimization of Nonpolar Contributions

Irwin D Kuntz, Tiba Aynechi, David A Case, 2022 .

Strategies for lead discovery: application of footprint similarity targeting HIVgp41.

W. J. Allen, M. Gochin, R. Rizzo, 2014, Bioorganic & medicinal chemistry.

Small molecule inhibitors of HIVgp41 N-heptad repeat trimer formation.

W. J. Allen, M. Gochin, R. Rizzo, 2015, Bioorganic & medicinal chemistry letters.

Computer-Aided Approaches for Targeting HIVgp41

W. J. Allen, R. Rizzo, 2012, Biology.

Origins of resistance to the HIVgp41 viral entry inhibitor T20.

Trent E Balius, T. E. Balius, Sudipto Mukherjee, 2010, Biochemistry.

Binding of antifusion peptides with HIVgp41 from molecular dynamics simulations: Quantitative correlation with experiment

Bentley Strockbine, B. Strockbine, R. Rizzo, 2007, Proteins.

A molecular basis for the selectivity of thiadiazole urea inhibitors with stromelysin-1 and gelatinase-A from generalized born molecular dynamics simulations.

Irwin D Kuntz, Samuel Toba, I. Kuntz, 2004, Journal of medicinal chemistry.

Origins of Resistance Conferred by the R292K Neuraminidase Mutation via Molecular Dynamics and Free Energy Calculations.

Ricky Chachra, Ricky Chachra, R. Rizzo, 2008, Journal of chemical theory and computation.

HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations.

Viktor Hornak, Carlos Simmerling, Asim Okur, 2006, Proceedings of the National Academy of Sciences of the United States of America.

Functional convergence of structurally distinct thioesterases from cyanobacteria and plants involved in phylloquinone biosynthesis.

W. J. Allen, R. Rizzo, Joshua R. Widhalm, 2013, Acta crystallographica. Section D, Biological crystallography.

Computer-aided identification, synthesis, and biological evaluation of novel inhibitors for botulinum neurotoxin serotype A.

S. Swaminathan, P. Tonge, T. E. Balius, 2015, Bioorganic & Medicinal Chemistry.

Free Energy Landscapes for RBD Opening in SARS-CoV-2 Spike Glycoprotein Simulations Suggest Key Interactions and a Potentially Druggable Allosteric Pocket

C. Simmerling, L. Fallon, L. Raguette, 2020 .

Identification of a Water-Coordinating HER2 Inhibitor by Virtual Screening Using Similarity-Based Scoring

W. Miller, R. Rizzo, Jiaye Guo, 2018, Biochemistry.

Structure and inhibition of Cryptococcus neoformans sterylglucosidase to develop antifungal agents

M. Del Poeta, J. Burke, R. Rizzo, 2021, Nature Communications.

Identification of small molecule inhibitors of botulinum neurotoxin serotype E via footprint similarity.

S. Swaminathan, R. Rizzo, I. Ojima, 2016, Bioorganic & medicinal chemistry.

Structure-based identification of inhibitors targeting obstruction of the HIVgp41 N-heptad repeat trimer.

W. J. Allen, R. Rizzo, T. D. McGee, 2017, Bioorganic & medicinal chemistry letters.

Footprint-based identification of viral entry inhibitors targeting HIVgp41.

M. Gochin, R. Rizzo, H. Kaur, 2012, Bioorganic & medicinal chemistry letters.

Identification of Ebola Virus Inhibitors Targeting GP2 Using Principles of Molecular Mimicry

R. Rizzo, A. Jacobs, H. Yi, 2019, Journal of Virology.

Identification of Zika Virus Inhibitors Using Homology Modeling and Similarity-Based Screening to Target Glycoprotein E

R. Rizzo, T. D. McGee, A. Jacobs, 2020, Biochemistry.

The Antinociceptive Agent SBFI-26 Binds to Anandamide Transporters FABP5 and FABP7 at Two Different Sites.

D. Deutsch, Huilin Li, R. Rizzo, 2017, Biochemistry.

Targeting Fatty Acid Binding Protein (FABP) Anandamide Transporters – A Novel Strategy for Development of Anti-Inflammatory and Anti-Nociceptive Drugs

S. Haj-Dahmane, D. Deutsch, T. E. Balius, 2012, PloS one.

Inhibition of mutationally activated HER2

W. Miller, R. Rizzo, Jiaye Guo, 2022, Chemical biology & drug design.

Estimation of binding affinities for HEPT and nevirapine analogues with HIV-1 reverse transcriptase via Monte Carlo simulations.

J Tirado-Rives, W L Jorgensen, W. L. Jorgensen, 2001, Journal of medicinal chemistry.

DOCK 6: Impact of new features and current docking performance

William J. Allen, Irwin D. Kuntz, Sudipto Mukherjee, 2015, J. Comput. Chem..

Prediction of activity for nonnucleoside inhibitors with HIV-1 reverse transcriptase based on Monte Carlo simulations.

Julian Tirado-Rives, William L Jorgensen, W. L. Jorgensen, 2002, Journal of medicinal chemistry.

Ab Initio/IGLO/NMR Investigation of nido-C(4)B(7)H(11) Configurations: Structural Assignment of the Three Known Isomers and Reconfirmation of Empirical Carbon Placement Patterns.

L. Sneddon, R. Rizzo, R. Williams, 1996, Inorganic chemistry.

Computational Advances in Structure Based Drug Design with Applications to HIV-1 Reverse Transcriptase

Robert Christopher Rizzo, R. Rizzo, 2001 .

Free Energy Landscapes from SARS-CoV-2 Spike Glycoprotein Simulations Suggest that RBD Opening Can Be Modulated via Interactions in an Allosteric Pocket

C. Simmerling, L. Fallon, L. Raguette, 2021, Journal of the American Chemical Society.

Development and validation of a modular, extensible docking program: DOCK 5

Irwin D. Kuntz, Scott C.-H. Pegg, Demetri Moustakas, 2006, J. Comput. Aided Mol. Des..

FABP1 controls hepatic transport and biotransformation of Δ9-THC

S. Glynn, D. Deutsch, R. Rizzo, 2019, Scientific Reports.

Quantitative prediction of fold resistance for inhibitors of EGFR.

Trent E Balius, T. E. Balius, R. Rizzo, 2009, Biochemistry.

Implementation of the Hungarian Algorithm to Account for Ligand Symmetry and Similarity in Structure-Based Design

William J. Allen, Robert C. Rizzo, W. J. Allen, 2014, J. Chem. Inf. Model..

A water-based mechanism of specificity and resistance for lapatinib with ErbB family kinases.

R. Rizzo, Yulin Huang, 2012, Biochemistry.

Docking Validation Resources: Protein Family and Ligand Flexibility Experiments

Sudipto Mukherjee, Trent E. Balius, Robert C. Rizzo, 2010, J. Chem. Inf. Model..

Identification of Fatty Acid Binding Protein 5 Inhibitors Through Similarity-Based Screening

D. Deutsch, Huilin Li, R. Rizzo, 2019, Biochemistry.

Inhibition of Fatty Acid Binding Proteins Elevates Brain Anandamide Levels and Produces Analgesia

D. Deutsch, M. Rebecchi, R. Rizzo, 2014, PloS one.

Inhibition of HIV Entry by Targeting the Envelope Transmembrane Subunit gp41.

Brian C. Fochtman, R. Rizzo, A. Jacobs, 2016, Current HIV research.

Customizable de novo design strategies for DOCK: Application to HIVgp41 and other therapeutic targets

William J. Allen, Trent E. Balius, Robert C. Rizzo, 2017, J. Comput. Chem..

Small-molecule anticancer compounds selectively target the hemopexin domain of matrix metalloproteinase-9.

Jian Li, Jizu Zhi, Nadia Jaber, 2011, Cancer research.

Small Molecule Anti-Cancer Compounds Selectively Target the Hemopexin Domain of Matrix Metalloproteinase-9 ( MMP-9 )

A. Dufour, Cem Kuscu, S. Zucker, 2011 .

Grid‐based molecular footprint comparison method for docking and de novo design: Application to HIVgp41

William J. Allen, Sudipto Mukherjee, Trent E. Balius, 2013, J. Comput. Chem..

Fatty-acid-binding protein inhibition produces analgesic effects through peripheral and central mechanisms

D. Deutsch, Huilin Li, M. Rebecchi, 2017, Molecular pain.

Pharmacophore-Based Similarity Scoring for DOCK

Lingling Jiang, Robert C. Rizzo, R. Rizzo, 2014, The journal of physical chemistry. B.

Antiviral drug design: computational analyses of the effects of the L100I mutation for HIV-RT on the binding of NNRTIs.

J Tirado-Rives, W L Jorgensen, W. L. Jorgensen, 2001, Bioorganic & medicinal chemistry letters.

A molecular evolution algorithm for ligand design in DOCK

W. J. Allen, R. Rizzo, John Bickel, 2022, J. Comput. Chem..

New Linear Interaction Method for Binding Affinity Calculations Using a Continuum Solvent Model

Ruhong Zhou, Richard A. Friesner, Ronald M. Levy, 2001 .

Molecular modeling calculations of HIV-1 reverse transcriptase nonnucleoside inhibitors: correlation of binding energy with biological activity for novel 2-aryl-substituted benzimidazole analogues.

Stephen H Hughes, Julian Tirado-Rives, William L Jorgensen, 2003, Journal of medicinal chemistry.

Evaluation of DOCK 6 as a pose generation and database enrichment tool

Sudipto Mukherjee, David A. Case, Daniel R. Roe, 2012, Journal of Computer-Aided Molecular Design.

Incarvillateine produces antinociceptive and motor suppressive effects via adenosine receptor activation

D. Deutsch, R. Rizzo, M. Kaczocha, 2019, PloS one.

SAR studies on truxillic acid mono esters as a new class of antinociceptive agents targeting fatty acid binding proteins.

D. Deutsch, Huilin Li, Su Yan, 2018, European journal of medicinal chemistry.

Validation of a Model for the Complex of HIV-1 Reverse Transcriptase with Sustiva through Computation of Resistance Profiles

William L. Jorgensen, Robert C. Rizzo, W. L. Jorgensen, 2000 .

Neutral ceramidase-active site inhibitor chemotypes and binding modes

Y. Hannun, T. Spicer, P. Tonge, 2023, Bioorganic Chemistry.

FABP1 controls hepatic transport and biotransformation of Δ9-THC

S. Glynn, D. Deutsch, R. Rizzo, 2019, Scientific Reports.

HIV-1 protease flaps spontaneously close to the correct structure in simulations following manual placement of an inhibitor into the open state.

Viktor Hornak, Carlos Simmerling, Robert C. Rizzo, 2006, Journal of the American Chemical Society.

Quantitative prediction of fold resistance for inhibitors of EGFR.

T. E. Balius, R. Rizzo, 2009, Biochemistry.

Implementation and evaluation of a docking‐rescoring method using molecular footprint comparisons

Sudipto Mukherjee, Trent E. Balius, Robert C. Rizzo, 2011, J. Comput. Chem..

Calculation of binding free energies for non-zinc chelating pyrimidine dicarboxamide inhibitors with MMP-13.

R. Rizzo, Noel Carrascal, 2009, Bioorganic & medicinal chemistry letters.

Identification of Ebola Virus Inhibitors Targeting GP2 Using Principles of Molecular Mimicry

R. Rizzo, A. Jacobs, H. Yi, 2019, Journal of Virology.