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Olgun Guvench, MD., Ph.D. - Publications

Affiliations: 
Pharmacy University of New England, Biddeford, ME, United States 
Area:
Computational chemistry, biophysics, carbohydrates, drug design
Website:
http://www.une.edu/faculty/profiles/oguvench.cfm
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55 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 J N C, Guvench O, MacKerell AD, Yamaguchi T, Mallajosyula SS. Refinement of the Drude Polarizable Force Field for Hexose Monosaccharides: Capturing Ring Conformational Dynamics with Enhanced Accuracy. Journal of Chemical Theory and Computation. PMID 39383338 DOI: 10.1021/acs.jctc.4c00656  0.635
2024 Guvench O. Effect of Lipid Bilayer Anchoring on the Conformational Properties of the Cytochrome P450 2D6 Binding Site. The Journal of Physical Chemistry. B. PMID 39016537 DOI: 10.1021/acs.jpcb.4c03097  0.303
2023 Orr AA, Tao A, Guvench O, MacKerell AD. Site Identification by Ligand Competitive Saturation-Biologics Approach for Structure-Based Protein Charge Prediction. Molecular Pharmaceutics. PMID 37017675 DOI: 10.1021/acs.molpharmaceut.3c00064  0.662
2022 Guvench O. Atomic-Resolution Experimental Structural Biology and Molecular Dynamics Simulations of Hyaluronan and Its Complexes. Molecules (Basel, Switzerland). 27. PMID 36364098 DOI: 10.3390/molecules27217276  0.315
2021 Guvench O, Martin D, Greene M. Pyranose Ring Puckering Thermodynamics for Glycan Monosaccharides Associated with Vertebrate Proteins. International Journal of Molecular Sciences. 23. PMID 35008898 DOI: 10.3390/ijms23010473  0.421
2019 Whitmore EK, Vesenka G, Sihler H, Guvench O. An Algorithm to Construct Biologically Relevant Chondroitin Sulfate Biopolymer Models at Atomic Resolution Biophysical Journal. 116: 295a. DOI: 10.1016/J.Bpj.2018.11.1596  0.301
2018 Whitmore E, Sihler H, Guvench O. Toward an Efficient Computational Method to Construct 3-D Atomic Resolution Glycosaminoglycan Models Biophysical Journal. 114: 675a-676a. DOI: 10.1016/J.Bpj.2017.11.3642  0.309
2017 Ng C, Nandha Premnath P, Guvench O. Rigidity and flexibility in the tetrasaccharide linker of proteoglycans from atomic-resolution molecular simulation. Journal of Computational Chemistry. PMID 28101951 DOI: 10.1002/Jcc.24738  0.47
2017 DeMaria B, Burkham C, Mansberger S, Ganter O, Guvench O. Glycosaminoglycan Sequence Influence on Iduronate Ring Puckering Biophysical Journal. 112. DOI: 10.1016/J.Bpj.2016.11.2413  0.39
2016 Guvench O. Computational functional group mapping for drug discovery. Drug Discovery Today. PMID 27393487 DOI: 10.1016/J.Drudis.2016.06.030  0.328
2015 Guvench O. Revealing the Mechanisms of Protein Disorder and N-Glycosylation in CD44-Hyaluronan Binding Using Molecular Simulation. Frontiers in Immunology. 6: 305. PMID 26136744 DOI: 10.3389/Fimmu.2015.00305  0.38
2015 Faller CE, Guvench O. Sulfation and cation effects on the conformational properties of the glycan backbone of chondroitin sulfate disaccharides. The Journal of Physical Chemistry. B. 119: 6063-73. PMID 25906376 DOI: 10.1021/Jp511431Q  0.388
2015 Faller CE, Raman EP, MacKerell AD, Guvench O. Site Identification by Ligand Competitive Saturation (SILCS) simulations for fragment-based drug design. Methods in Molecular Biology (Clifton, N.J.). 1289: 75-87. PMID 25709034 DOI: 10.1007/978-1-4939-2486-8_7  0.587
2015 Lopes PE, Guvench O, MacKerell AD. Current status of protein force fields for molecular dynamics simulations. Methods in Molecular Biology (Clifton, N.J.). 1215: 47-71. PMID 25330958 DOI: 10.1007/978-1-4939-1465-4_3  0.597
2014 Faller CE, Guvench O. Terminal sialic acids on CD44 N-glycans can block hyaluronan binding by forming competing intramolecular contacts with arginine sidechains. Proteins. 82: 3079-89. PMID 25116630 DOI: 10.1002/Prot.24668  0.365
2014 Vanommeslaeghe K, Guvench O, MacKerell AD. Molecular mechanics. Current Pharmaceutical Design. 20: 3281-92. PMID 23947650 DOI: 10.2174/13816128113199990600  0.575
2014 Faller CE, Favreau AJ, Guvench O. Atomic Resolution Mechanism of Cd44-Hyaluronan Protein-Carbohydrate Binding Biophysical Journal. 106: 6-9. DOI: 10.1016/J.Bpj.2013.11.3648  0.408
2013 Favreau AJ, Faller CE, Guvench O. CD44 receptor unfolding enhances binding by freeing basic amino acids to contact carbohydrate ligand. Biophysical Journal. 105: 1217-26. PMID 24010665 DOI: 10.1016/J.Bpj.2013.07.041  0.381
2013 Yu B, Liu W, Yu WM, Loh ML, Alter S, Guvench O, Mackerell AD, Tang LD, Qu CK. Targeting protein tyrosine phosphatase SHP2 for the treatment of PTPN11-associated malignancies. Molecular Cancer Therapeutics. 12: 1738-48. PMID 23825065 DOI: 10.1158/1535-7163.Mct-13-0049-T  0.533
2013 Faller CE, Reilly KA, Hills RD, Guvench O. Peptide backbone sampling convergence with the adaptive biasing force algorithm. The Journal of Physical Chemistry. B. 117: 518-26. PMID 23215032 DOI: 10.1021/Jp309741J  0.397
2013 Yu W, Guvench O, MacKerell AD. Computational approaches for the design of protein-protein interaction inhibitors Understanding and Exploiting Protein-Protein Interactions as Drug Targets. 91-102. DOI: 10.4155/EBO.13.141  0.468
2012 Mallajosyula SS, Guvench O, Hatcher E, Mackerell AD. CHARMM Additive All-Atom Force Field for Phosphate and Sulfate Linked to Carbohydrates. Journal of Chemical Theory and Computation. 8: 759-776. PMID 22685386 DOI: 10.1021/Ct200792V  0.746
2012 Foster TJ, MacKerell AD, Guvench O. Balancing target flexibility and target denaturation in computational fragment-based inhibitor discovery. Journal of Computational Chemistry. 33: 1880-91. PMID 22641475 DOI: 10.1002/Jcc.23026  0.574
2012 Ward AB, Guvench O, Hills RD. Coarse grain lipid-protein molecular interactions and diffusion with MsbA flippase. Proteins. 80: 2178-90. PMID 22552999 DOI: 10.1002/Prot.24108  0.39
2012 Ward A, Guvench O, Hills RD. Coarse Graining Protein-Phospholipid Interactions and Diffusion with MsbA Flippase Biophysical Journal. 102: 661a. DOI: 10.1016/J.Bpj.2011.11.3599  0.383
2011 Guvench O, Mallajosyula SS, Raman EP, Hatcher E, Vanommeslaeghe K, Foster TJ, Jamison FW, Mackerell AD. CHARMM additive all-atom force field for carbohydrate derivatives and its utility in polysaccharide and carbohydrate-protein modeling. Journal of Chemical Theory and Computation. 7: 3162-3180. PMID 22125473 DOI: 10.1021/Ct200328P  0.76
2011 Velvadapu V, Paul T, Wagh B, Klepacki D, Guvench O, Mackerell A, Andrade RB. Desmethyl Macrolide Analogues to Address Antibiotic Resistance: Total Synthesis and Biological Evaluation of 4,8,10-Tridesmethyl Telithromycin. Acs Medicinal Chemistry Letters. 2: 68-72. PMID 21643527 DOI: 10.1021/ml1002184  0.382
2011 Raman EP, Yu W, Guvench O, Mackerell AD. Reproducing crystal binding modes of ligand functional groups using Site-Identification by Ligand Competitive Saturation (SILCS) simulations. Journal of Chemical Information and Modeling. 51: 877-96. PMID 21456594 DOI: 10.1021/Ci100462T  0.609
2011 Darian E, Guvench O, Yu B, Qu CK, MacKerell AD. Structural mechanism associated with domain opening in gain-of-function mutations in SHP2 phosphatase. Proteins. 79: 1573-88. PMID 21365683 DOI: 10.1002/Prot.22984  0.568
2011 Jamison FW, Foster TJ, Barker JA, Hills RD, Guvench O. Mechanism of binding site conformational switching in the CD44-hyaluronan protein-carbohydrate binding interaction. Journal of Molecular Biology. 406: 631-47. PMID 21216252 DOI: 10.1016/J.Jmb.2010.12.040  0.38
2011 Mallajosyula SS, Guvench O, MacKerell AD. CHARMM Additive All-Atom Force Field for O-Glycan and N-Glycan Linkages in Carbohydrate-Protein Modeling Biophysical Journal. 100: 526a. DOI: 10.1016/J.Bpj.2010.12.3077  0.709
2011 Jamison FW, Foster TJ, Barker JA, Hills RD, Guvench O. Binding Site Flexibility in the CD44:Hyaluronan Protein:Carbohydrate Interaction Biophysical Journal. 100: 3-7. DOI: 10.1016/J.Bpj.2010.12.2248  0.337
2011 He X, Shinoda W, Devane R, Guvench O, Anderson KL, MacKerell AD, Klein ML. Development of a Coarse-Grained Model for the Surfactant Family of Linear Alkylbenzene Sulfonates Biophysical Journal. 100: 147a. DOI: 10.1016/J.Bpj.2010.12.1009  0.375
2010 Raman EP, Guvench O, MacKerell AD. CHARMM additive all-atom force field for glycosidic linkages in carbohydrates involving furanoses. The Journal of Physical Chemistry. B. 114: 12981-94. PMID 20845956 DOI: 10.1021/Jp105758H  0.658
2010 Venable RM, Hatcher E, Guvench O, Mackerell AD, Pastor RW. Comparing simulated and experimental translation and rotation constants: range of validity for viscosity scaling. The Journal of Physical Chemistry. B. 114: 12501-7. PMID 20831149 DOI: 10.1021/Jp105549S  0.523
2010 He X, Guvench O, Mackerell AD, Klein ML. Atomistic simulation study of linear alkylbenzene sulfonates at the water/air interface. The Journal of Physical Chemistry. B. 114: 9787-94. PMID 20614916 DOI: 10.1021/Jp101860V  0.563
2010 Vanommeslaeghe K, Hatcher E, Acharya C, Kundu S, Zhong S, Shim J, Darian E, Guvench O, Lopes P, Vorobyov I, Mackerell AD. CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. Journal of Computational Chemistry. 31: 671-90. PMID 19575467 DOI: 10.1002/Jcc.21367  0.607
2010 Guvench O. Conformational Plasticity in IL-2 Is Captured Via in Silico Fragment-Based Drug Design Using SILCS Fragmaps Biophysical Journal. 98. DOI: 10.1016/J.Bpj.2009.12.210  0.391
2009 Guvench O, Hatcher ER, Venable RM, Pastor RW, Mackerell AD. CHARMM Additive All-Atom Force Field for Glycosidic Linkages between Hexopyranoses. Journal of Chemical Theory and Computation. 5: 2353-2370. PMID 20161005 DOI: 10.1021/Ct900242E  0.664
2009 Hatcher E, Guvench O, Mackerell AD. CHARMM Additive All-Atom Force Field for Acyclic Polyalcohols, Acyclic Carbohydrates and Inositol. Journal of Chemical Theory and Computation. 5: 1315-1327. PMID 20160980 DOI: 10.1021/Ct9000608  0.606
2009 Hatcher E, Guvench O, Mackerell AD. CHARMM additive all-atom force field for aldopentofuranoses, methyl-aldopentofuranosides, and fructofuranose. The Journal of Physical Chemistry. B. 113: 12466-76. PMID 19694450 DOI: 10.1021/Jp905496E  0.634
2009 Guvench O, MacKerell AD. Computational fragment-based binding site identification by ligand competitive saturation. Plos Computational Biology. 5: e1000435. PMID 19593374 DOI: 10.1371/Journal.Pcbi.1000435  0.6
2009 Guvench O, MacKerell AD. Computational evaluation of protein-small molecule binding. Current Opinion in Structural Biology. 19: 56-61. PMID 19162472 DOI: 10.1016/J.Sbi.2008.11.009  0.558
2008 Kamath G, Guvench O, MacKerell AD. CHARMM Additive All-Atom Force Field for Acyclic Carbohydrates and Inositol. Journal of Chemical Theory and Computation. 4: 765-78. PMID 26621091 DOI: 10.1021/Ct800019U  0.581
2008 Kamath G, Guvench O, MacKerell AD. CHARMM Additive All-Atom Force Field for Acyclic Carbohydrates and Inositol. Journal of Chemical Theory and Computation. 4: 1990. PMID 26620340 DOI: 10.1021/ct800423m  0.536
2008 Yu WM, Guvench O, Mackerell AD, Qu CK. Identification of small molecular weight inhibitors of Src homology 2 domain-containing tyrosine phosphatase 2 (SHP-2) via in silico database screening combined with experimental assay. Journal of Medicinal Chemistry. 51: 7396-404. PMID 19007293 DOI: 10.1021/Jm800229D  0.541
2008 Guvench O, Greene SN, Kamath G, Brady JW, Venable RM, Pastor RW, Mackerell AD. Additive empirical force field for hexopyranose monosaccharides. Journal of Computational Chemistry. 29: 2543-64. PMID 18470966 DOI: 10.1002/Jcc.21004  0.647
2008 Guvench O, MacKerell AD. Automated conformational energy fitting for force-field development. Journal of Molecular Modeling. 14: 667-79. PMID 18458967 DOI: 10.1007/S00894-008-0305-0  0.586
2008 Guvench O, MacKerell AD. Comparison of protein force fields for molecular dynamics simulations. Methods in Molecular Biology (Clifton, N.J.). 443: 63-88. PMID 18446282 DOI: 10.1007/978-1-59745-177-2_4  0.635
2007 Guvench O, Qu CK, MacKerell AD. Tyr66 acts as a conformational switch in the closed-to-open transition of the SHP-2 N-SH2-domain phosphotyrosine-peptide binding cleft. Bmc Structural Biology. 7: 14. PMID 17378938 DOI: 10.1186/1472-6807-7-14  0.55
2006 Guvench O, Mackerell AD. Quantum mechanical analysis of 1,2-ethanediol conformational energetics and hydrogen bonding. The Journal of Physical Chemistry. A. 110: 9934-9. PMID 16898697 DOI: 10.1021/Jp0623241  0.561
2005 Guvench O, Brooks CL. Tryptophan side chain electrostatic interactions determine edge-to-face vs parallel-displaced tryptophan side chain geometries in the designed beta-hairpin "trpzip2". Journal of the American Chemical Society. 127: 4668-74. PMID 15796532 DOI: 10.1021/Ja043492E  0.515
2005 Guvench O, Price DJ, Brooks CL. Receptor rigidity and ligand mobility in trypsin-ligand complexes. Proteins. 58: 407-17. PMID 15578663 DOI: 10.1002/Prot.20326  0.555
2004 Guvench O, Brooks CL. Efficient approximate all-atom solvent accessible surface area method parameterized for folded and denatured protein conformations. Journal of Computational Chemistry. 25: 1005-14. PMID 15067676 DOI: 10.1002/Jcc.20026  0.58
2002 Guvench O, Weiser J, Shenkin P, Kolossváry I, Still WC. Application of the frozen atom approximation to the GB/SA continuum model for solvation free energy. Journal of Computational Chemistry. 23: 214-21. PMID 11924735 DOI: 10.1002/Jcc.1167  0.43
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