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One or more keywords matched the following properties of Kurt Yilmaz, Nese

Academic Background

Ph.D., Chemical Engineering, Bogazici University, Istanbul, Turkey, 2002

Postdoc,  Department of Chemistry, University of Wisconsin-Madison, 2005


Research Experience

Associate Professor                                                                                    2017–present

UMASS Medical School, Worcester, MA
Department of Biochemistry and Molecular Pharmacology


Research Assistant Professor                                                                    2011–2017

UMASS Medical School, Worcester, MA
Department of Biochemistry and Molecular Pharmacology

·     Drug resistance in viral proteases: Understanding the molecular basis of drug resistance in viral proteases, including HIV-1 and HCV protease.

·     Substrate recognition and product inhibition in HIV-1 protease.

·     Scientific writing and editing.


Assistant Scientist                                                                                        2005–2011

University of Wisconsin-Madison, Department of Chemistry

·     Protein folding and effect of chaperone interaction on misfolding polypeptides: Investigated protein folding, unfolding and misfolding under various experimental conditions, and the interaction of chaperones with truncated polypeptide chains by biochemical/biophysical methods incuding fluorescence and NMR techniques.


Visiting TUBITAK fellow                                                                              2000 and 2001

UMASS Medical School, Worcester, MA
Department of Biochemistry and Molecular Pharmacology

·     Substrate specificity and simulation of conformational dynamics of HIV-1 protease.


Graduate Researcher at the Polymer Research Center                                   1996–2002                 

Bogazici University, Istanbul, Turkey

·     Coarse-grained simulations and analytical methods to study dynamics of globular proteins in native state.



One or more keywords matched the following items that are connected to Kurt Yilmaz, Nese
Item TypeName
Academic Article Extreme entropy-enthalpy compensation in a drug-resistant variant of HIV-1 protease.
Academic Article Cooperative effects of drug-resistance mutations in the flap region of HIV-1 protease.
Academic Article Structural and thermodynamic basis of amprenavir/darunavir and atazanavir resistance in HIV-1 protease with mutations at residue 50.
Concept Drug Resistance, Viral
Concept RNA, Viral
Concept Antibodies, Viral
Concept Viral Proteins
Concept Viral Nonstructural Proteins
Concept Serine Proteases
Concept Drug Resistance, Multiple, Viral
Concept Peptide Hydrolases
Academic Article Substrate envelope-designed potent HIV-1 protease inhibitors to avoid drug resistance.
Academic Article HIV-1 protease-substrate coevolution in nelfinavir resistance.
Academic Article Drug resistance conferred by mutations outside the active site through alterations in the dynamic and structural ensemble of HIV-1 protease.
Academic Article Structural basis and distal effects of Gag substrate coevolution in drug resistance to HIV-1 protease.
Academic Article Structural and Thermodynamic Effects of Macrocyclization in HCV NS3/4A Inhibitor MK-5172.
Academic Article Improving Viral Protease Inhibitors to Counter Drug Resistance.
Academic Article Molecular and Dynamic Mechanism Underlying Drug Resistance in Genotype 3 Hepatitis C NS3/4A Protease.
Academic Article Dengue Protease Substrate Recognition: Binding of the Prime Side.
Academic Article Molecular Basis for Differential Patterns of Drug Resistance in Influenza N1 and N2 Neuraminidase.
Academic Article Dengue Virus NS2B/NS3 Protease Inhibitors Exploiting the Prime Side.
Academic Article Hepatitis C Virus NS3/4A Protease Inhibitors Incorporating Flexible P2 Quinoxalines Target Drug Resistant Viral Variants.
Academic Article Structural Determination of the Broadly Reactive Anti-IGHV1-69 Anti-idiotypic Antibody G6 and Its Idiotope.
Academic Article Hydration Structure and Dynamics of Inhibitor-Bound HIV-1 Protease.
Academic Article Molecular Mechanism of Resistance in a Clinically Significant Double-Mutant Variant of HCV NS3/4A Protease.
Academic Article Probing Structural Changes among Analogous Inhibitor-Bound Forms of HIV-1 Protease and a Drug-Resistant Mutant in Solution by Nuclear Magnetic Resonance.
Academic Article Mavyret: A Pan-Genotypic Combination Therapy for the Treatment of Hepatitis C InfectionPublished as part of the Biochemistry series "Biochemistry to Bedside".
Academic Article NMR and MD studies combined to elucidate inhibitor and water interactions of HIV-1 protease and their modulations with resistance mutations.
Academic Article Picomolar to Micromolar: Elucidating the Role of Distal Mutations in HIV-1 Protease in Conferring Drug Resistance.
Academic Article Molecular Determinants of Epistasis in HIV-1 Protease: Elucidating the Interdependence of L89V and L90M Mutations in Resistance.
Academic Article Mechanism for APOBEC3G catalytic exclusion of RNA and non-substrate DNA.
Academic Article Molecular and Structural Mechanism of Pan-Genotypic HCV NS3/4A Protease Inhibition by Glecaprevir.
Academic Article Avoiding Drug Resistance by Substrate Envelope-Guided Design: Toward Potent and Robust HCV NS3/4A Protease Inhibitors.
Academic Article Drug Design Strategies to Avoid Resistance in Direct-Acting Antivirals and Beyond.
Academic Article Deciphering Complex Mechanisms of Resistance and Loss of Potency through Coupled Molecular Dynamics and Machine Learning.
Academic Article Crystal Structure of SARS-CoV-2 Main Protease in Complex with the Non-Covalent Inhibitor ML188.
Academic Article Discovery of Quinoxaline-Based P1-P3 Macrocyclic NS3/4A Protease Inhibitors with Potent Activity against Drug-Resistant Hepatitis C Virus Variants.
Academic Article Pan-3C Protease Inhibitor Rupintrivir Binds SARS-CoV-2 Main Protease in a Unique Binding Mode.
Academic Article Viral proteases: Structure, mechanism and inhibition.
Academic Article Deciphering the Molecular Mechanism of HCV Protease Inhibitor Fluorination as a General Approach to Avoid Drug Resistance.
Academic Article Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance.
Academic Article Allosteric quinoxaline-based inhibitors of the flavivirus NS2B/NS3 protease.
Academic Article Crystal Structures of Inhibitor-Bound Main Protease from Delta- and Gamma-Coronaviruses.
Search Criteria
  • Viral
  • Proteases