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1

Simulation of multiphase systems utilizing independent force fields to control intraphase and interphase behavior

Pradip K. Biswas, Nadeem A. Vellore, Jeremy A. Yancey, Tugba G. Kucukkal, Galen Collier, Bernard R. Brooks, Steven J. Stuart, Robert A. Latour

Journal:

Journal of Computational Chemistry

Year:

2012

Language:

english

File:

PDF, 1.30 MB

english, 2012

2

A marine analgesic peptide, Contulakin-G, and neurotensin are distinct agonists for neurotensin receptors: uncovering structural determinants of desensitization properties

Lee, Hee-Kyoung, Zhang, Liuyin, Smith, Misty D., Walewska, Aleksandra, Vellore, Nadeem A., Baron, Riccardo, McIntosh, J. Michael, White, H. Steve, Olivera, Baldomero M., Bulaj, Grzegorz

Journal:

Frontiers in Pharmacology

Year:

2015

Language:

english

File:

PDF, 1.29 MB

english, 2015

3

Comparison Between Empirical Protein Force Fields for the Simulation of the Adsorption Behavior of Structured LK Peptides on Functionalized Surfaces

Galen Collier, Nadeem A. Vellore, Jeremy A. Yancey, Steven J. Stuart, Robert A. Latour

Journal:

Year:

2012

Language:

english

File:

PDF, 2.70 MB

english, 2012

4

Molecular Docking of Bisphenol a and its Nitrated and Chlorinated Metabolites Onto Estrogen-Related Receptor-Gamma

Sainath Babu, Nadeem a Vellore, Acuthan C Raghavamenon, Dwayne Jerro, Shizong Yang, Rao M Uppu

Journal:

Free Radical Biology and Medicine

Year:

2011

Language:

english

File:

PDF, 68 KB

english, 2011

5

Molecular docking of bisphenol A and its nitrated and chlorinated metabolites onto human estrogen-related receptor-gamma

Sainath Babu, Nadeem A. Vellore, Agasthya V. Kasibotla, Harlan J. Dwayne, Michael A. Stubblefield, Rao M. Uppu

Journal:

Biochemical and Biophysical Research Communications

Year:

2012

Language:

english

File:

PDF, 569 KB

english, 2012

6

Development of molecular simulation methods to accurately represent protein-surface interactions: The effect of pressure and its determination for a system with constrained atoms

Jeremy A. Yancey, Nadeem A. Vellore, Galen Collier, Steven J. Stuart, Robert A. Latour

Journal:

Year:

2010

Language:

english

File:

PDF, 604 KB

english, 2010

7

Development of molecular simulation methods to accurately represent protein-surface interactions: Method assessment for the calculation of electrostatic effects

Galen Collier, Nadeem A. Vellore, Robert A. Latour, Steven J. Stuart

Journal:

Year:

2009

Language:

english

File:

PDF, 312 KB

english, 2009

8

Protein Recognition by Short Peptide Reversible Inhibitors of the Chromatin-Modifying LSD1/CoREST Lysine Demethylase

Tortorici, Marcello, Borrello, Maria Teresa, Tardugno, Maria, Chiarelli, Laurent R., Pilotto, Simona, Ciossani, Giuseppe, Vellore, Nadeem A., Bailey, Sarah G., Cowan, Jonathan, O’Connell, Maria, Crabb

Journal:

ACS Chemical Biology

Year:

2013

Language:

english

File:

PDF, 1.06 MB

english, 2013

9

Thiuram Disulfides as Pseudo-irreversible Inhibitors of Lymphoid Tyrosine Phosphatase

Kulkarni, Rhushikesh A., Stanford, Stephanie M., Vellore, Nadeem A., Krishnamurthy, Divya, Bliss, Matthew R., Baron, Riccardo, Bottini, Nunzio, Barrios, Amy M.

Journal:

Year:

2013

Language:

english

File:

PDF, 831 KB

english, 2013

10

Substrate Selection Influences Molecular Recognition in a Screen for Lymphoid Tyrosine Phosphatase Inhibitors

Kulkarni, Rhushikesh A., Vellore, Nadeem A., Bliss, Matthew R., Stanford, Stephanie M., Falk, Matthew D., Bottini, Nunzio, Baron, Riccardo, Barrios, Amy M.

Journal:

Year:

2013

Language:

english

File:

PDF, 839 KB

english, 2013

11

Molecular dynamics simulations indicate an induced-fit mechanism for LSD1/CoREST-H3-histone molecular recognition

Vellore, Nadeem A, Baron, Riccardo

Journal:

Year:

2013

Language:

english

File:

PDF, 1.07 MB

english, 2013

12

Epigenetic Molecular Recognition: A Biomolecular Modeling Perspective

Vellore, Nadeem A., Baron, Riccardo

Journal:

Year:

2014

Language:

english

File:

PDF, 2.35 MB

english, 2014

13

LSD1/CoREST - H3-Histone Molecular Recognition: Inter-Domain Motions in an Allosteric Nanoscale Clamp Revealed by Computer Simulations

Vellore, Nadeem Ahmad, Baron, Riccardo

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 40 KB

english, 2014

14

A Complete Configurational Ensemble Approach to Expand Lsd1/Corest Druggability

Robertson, James C., Hurley, Nate C., Kneller, Julie M., Vellore, Nadeem A., Mattevi, Andrea, Baron, Riccardo

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 48 KB

english, 2014

15

LSD1/CoREST Reversible Opening–Closing Dynamics: Discovery of a Nanoscale Clamp for Chromatin and Protein Binding

Baron, Riccardo, Vellore, Nadeem A.

Journal:

Year:

2012

Language:

english

File:

PDF, 1.44 MB

english, 2012

16

Assessment of the Transferability of a Protein Force Field for the Simulation of Peptide-Surface Interactions

Vellore, Nadeem A., Yancey, Jeremy A., Collier, Galen, Latour, Robert A., Stuart, Steven J.

Journal:

Year:

2010

Language:

english

File:

PDF, 4.78 MB

english, 2010

17

BCR-ABL1 Compound Mutations Combining Key Kinase Domain Positions Confer Clinical Resistance to Ponatinib in Ph Chromosome-Positive Leukemia

Zabriskie, Matthew S., Eide, Christopher A., Tantravahi, Srinivas K., Vellore, Nadeem A., Estrada, Johanna, Nicolini, Franck E., Khoury, Hanna J., Larson, Richard A., Konopleva, Marina, Cortes, Jorge

Journal:

Year:

2014

Language:

english

File:

PDF, 2.49 MB

english, 2014

18

Expanding the Druggable Space of the LSD1/CoREST Epigenetic Target: New Potential Binding Regions for Drug-Like Molecules, Peptides, Protein Partners, and Chromatin

Robertson, James C., Hurley, Nate C., Tortorici, Marcello, Ciossani, Giuseppe, Borrello, Maria Teresa, Vellore, Nadeem A., Ganesan, A., Mattevi, Andrea, Baron, Riccardo, Briggs, James M.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 8.49 MB

english, 2013

19

An improved replica-exchange sampling method: Temperature intervals with global energy reassignment

Li, Xianfeng, O’Brien, Christopher P., Collier, Galen, Vellore, Nadeem A., Wang, Feng, Latour, Robert A., Bruce, David A., Stuart, Steven J.

Journal:

The Journal of Chemical Physics

Year:

2007

Language:

english

File:

PDF, 573 KB

english, 2007

20

Structural insight into selectivity and resistance profiles of ROS1 tyrosine kinase inhibitors

Davare, Monika A., Vellore, Nadeem A., Wagner, Jacob P., Eide, Christopher A., Goodman, James R., Drilon, Alexander, Deininger, Michael W., O’Hare, Thomas, Druker, Brian J.

Journal:

Proceedings of the National Academy of Sciences

Year:

2015

Language:

english

File:

PDF, 1.43 MB

english, 2015

21

Disarming an Electrophilic Warhead: Retaining Potency in Tyrosine Kinase Inhibitor (TKI)-Resistant CML Lines While Circumventing Pharmacokinetic Liabilities

Ali, Ahmed M., Gómez-Biagi, Rodolfo F., Rosa, David A., Lai, Ping-Shan, Heaton, William L., Park, Ji Sung, Eiring, Anna M., Vellore, Nadeem A., de Araujo, Elvin D., Ball, Dan P., Shouksmith, Andrew E.

Journal:

Year:

2016

Language:

english

File:

PDF, 1.40 MB

english, 2016

22

Inside Cover: Disarming an Electrophilic Warhead: Retaining Potency in Tyrosine Kinase Inhibitor (TKI)-Resistant CML Lines While Circumventing Pharmacokinetic Liabilities (ChemMedChem 8/2016)

Ali, Ahmed M., Gómez-Biagi, Rodolfo F., Rosa, David A., Lai, Ping-Shan, Heaton, William L., Park, Ji Sung, Eiring, Anna M., Vellore, Nadeem A., de Araujo, Elvin D., Ball, Dan P., Shouksmith, Andrew E.

Journal:

Year:

2016

File:

PDF, 1.06 MB

2016

23

Combining the Allosteric Inhibitor Asciminib with Ponatinib Suppresses Emergence of and Restores Efficacy against Highly Resistant BCR-ABL1 Mutants

Eide, Christopher A., Zabriskie, Matthew S., Savage Stevens, Samantha L., Antelope, Orlando, Vellore, Nadeem A., Than, Hein, Schultz, Anna Reister, Clair, Phillip, Bowler, Amber D., Pomicter, Anthony

Journal:

Year:

2019

Language:

english

File:

PDF, 3.57 MB

english, 2019

24

Combining the Allosteric Inhibitor Asciminib with Ponatinib Suppresses Emergence of and Restores Efficacy against Highly Resistant BCR-ABL1 Mutants

Eide, Christopher A., Zabriskie, Matthew S., Savage Stevens, Samantha L., Antelope, Orlando, Vellore, Nadeem A., Than, Hein, Schultz, Anna Reister, Clair, Phillip, Bowler, Amber D., Pomicter, Anthony

Journal:

Year:

2019

File:

PDF, 3.57 MB

2019

25

Identification of novel thioureaâstilbeneâtriazine conjugates as persuasive lymphoid tyrosine phosphatase inhibitors

Batool, Iram, Jabeen, Farukh, Vellore, Nadeem Ahmed, Shabir, Ghulam, Saeed, Aamer

Journal:

Journal of Heterocyclic Chemistry

Year:

2020

File:

PDF, 2.74 MB

2020