Olgun Guvench

发表

Efficient approximate all‐atom solvent accessible surface area method parameterized for folded and denatured protein conformations

Charles L. Brooks, Olgun Guvench, Olgun Guvench, 2004, J. Comput. Chem..

CHARMM Additive All-Atom Force Field for Glycosidic Linkages between Hexopyranoses.

Alexander D. MacKerell, Olgun Guvench, Alexander D Mackerell, 2009, Journal of chemical theory and computation.

CHARMM additive all-atom force field for carbohydrate derivatives and its utility in polysaccharide and carbohydrate-protein modeling.

Alexander D. MacKerell, Kenno Vanommeslaeghe, Olgun Guvench, 2011, Journal of chemical theory and computation.

CHARMM Additive All-Atom Force Field for Acyclic Carbohydrates and Inositol.

Alexander D. MacKerell, Ganesh Kamath, Olgun Guvench, 2008, Journal of chemical theory and computation.

CHARMM additive all-atom force field for glycosidic linkages in carbohydrates involving furanoses.

Alexander D. MacKerell, Olgun Guvench, Alexander D MacKerell, 2010, The journal of physical chemistry. B.

Molecular mechanics.

Alexander D. MacKerell, Olgun Guvench, K. Vanommeslaeghe, 2014, Current pharmaceutical design.

Current status of protein force fields for molecular dynamics simulations.

Alexander D. MacKerell, Pedro E. M. Lopes, Olgun Guvench, 2015, Methods in molecular biology.

Computational functional group mapping for drug discovery.

Olgun Guvench, 2016, Drug discovery today.

Receptor rigidity and ligand mobility in trypsin–ligand complexes

Olgun Guvench, Charles L Brooks, D. J. Price, 2005, Proteins.

Site Identification by Ligand Competitive Saturation (SILCS) simulations for fragment-based drug design.

Alexander D. MacKerell, Olgun Guvench, E. P. Raman, 2015, Methods in molecular biology.

Targeting Protein Tyrosine Phosphatase SHP2 for the Treatment of PTPN11-Associated Malignancies

Alexander D. MacKerell, M. Loh, Olgun Guvench, 2013, Molecular Cancer Therapeutics.

Small Molecule Therapeutics Targeting Protein Tyrosine Phosphatase SHP 2 for the Treatment of PTPN 11-Associated Malignancies

Alexander D. MacKerell, M. Loh, Olgun Guvench, 2013 .

Constructing 3-Dimensional Atomic-Resolution Models of Nonsulfated Glycosaminoglycans with Arbitrary Lengths Using Conformations from Molecular Dynamics

Olgun Guvench, Elizabeth K Whitmore, Devon Martin, 2020, International journal of molecular sciences.

CHARMM Additive All-Atom Force Field for Phosphate and Sulfate Linked to Carbohydrates.

Alexander D. MacKerell, Olgun Guvench, Sairam S. Mallajosyula, 2012, Journal of chemical theory and computation.

Efficient Construction of Atomic-Resolution Models of Non-Sulfated Chondroitin Glycosaminoglycan Using Molecular Dynamics Data

Olgun Guvench, Elizabeth K Whitmore, Gabriel Vesenka, 2020, Biomolecules.

Sulfation and cation effects on the conformational properties of the glycan backbone of chondroitin sulfate disaccharides.

Olgun Guvench, Christina E. Faller, 2015, The journal of physical chemistry. B.

Revealing the Mechanisms of Protein Disorder and N-Glycosylation in CD44-Hyaluronan Binding Using Molecular Simulation

Olgun Guvench, 2015, Front. Immunol..

Atomic-Resolution Experimental Structural Biology and Molecular Dynamics Simulations of Hyaluronan and Its Complexes

Olgun Guvench, 2022, Molecules.

Coarse grain lipid–protein molecular interactions and diffusion with MsbA flippase

Ronald D. Hills, Olgun Guvench, A. Ward, 2012, Proteins.

CHARMM general force field: A force field for drug‐like molecules compatible with the CHARMM all‐atom additive biological force fields

Alexander D. MacKerell, Sibsankar Kundu, Chayan Acharya, 2009, J. Comput. Chem..

Automated conformational energy fitting for force-field development

Alexander D. MacKerell, Olgun Guvench, 2008, Journal of molecular modeling.

Additive empirical force field for hexopyranose monosaccharides

Alexander D. MacKerell, Ganesh Kamath, Olgun Guvench, 2008, J. Comput. Chem..

CHARMM additive all-atom force field for aldopentofuranoses, methyl-aldopentofuranosides, and fructofuranose.

Alexander D. MacKerell, Olgun Guvench, Alexander D Mackerell, 2009, The journal of physical chemistry. B.

Desmethyl Macrolide Analogues to Address Antibiotic Resistance: Total Synthesis and Biological Evaluation of 4,8,10-Tridesmethyl Telithromycin.

Alexander D. MacKerell, D. Klepacki, Olgun Guvench, 2011, ACS medicinal chemistry letters.

Supramolecular Assemblies of a Conjugate of Nucleobase, Amino Acids, and Saccharide Act as Agonists for Proliferation of Embryonic Stem Cells and Development of Zygotes

Olgun Guvench, Bing Xu, Xuewen Du, 2014, Bioconjugate chemistry.

Structural mechanism associated with domain opening in gain‐of‐function mutations in SHP2 phosphatase

Alexander D. MacKerell, Olgun Guvench, Alexander D MacKerell, 2011, Proteins.

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.

Alexander D. MacKerell, Olgun Guvench, Alexander D Mackerell, 2008, Journal of medicinal chemistry.

Tyr66 acts as a conformational switch in the closed-to-open transition of the SHP-2 N-SH2-domain phosphotyrosine-peptide binding cleft

Alexander D. MacKerell, Olgun Guvench, C. Qu, 2007, BMC Structural Biology.

Computational Fragment-Based Binding Site Identification by Ligand Competitive Saturation

Alexander D. MacKerell, Olgun Guvench, Olgun Guvench, 2009, PLoS Comput. Biol..

Comparison of protein force fields for molecular dynamics simulations.

Alexander D. MacKerell, Olgun Guvench, 2008, Methods in molecular biology.

Reproducing Crystal Binding Modes of Ligand Functional Groups Using Site-Identification by Ligand Competitive Saturation (SILCS) Simulations

Alexander D. MacKerell, Wenbo Yu, E. Prabhu Raman, 2011, J. Chem. Inf. Model..

Peptide backbone sampling convergence with the adaptive biasing force algorithm.

Olgun Guvench, Ronald D. Hills, Olgun Guvench, 2013, The journal of physical chemistry. B.

Pyranose Ring Puckering Thermodynamics for Glycan Monosaccharides Associated with Vertebrate Proteins

Olgun Guvench, Devon Martin, Megan Greene, 2021, International journal of molecular sciences.

Balancing target flexibility and target denaturation in computational fragment‐based inhibitor discovery

Alexander D. MacKerell, Olgun Guvench, Theresa J. Foster, 2012, J. Comput. Chem..

Terminal sialic acids on CD44 N‐glycans can block hyaluronan binding by forming competing intramolecular contacts with arginine sidechains

Olgun Guvench, Christina E. Faller, 2014, Proteins.

Folding of Fibroblast Growth Factor 1 Is Critical for Its Nonclassical Release.

Olgun Guvench, R. Soldi, I. Prudovsky, 2016, Biochemistry.

CHARMM Additive All-Atom Force Field for Acyclic Polyalcohols, Acyclic Carbohydrates and Inositol.

Alexander D. MacKerell, Olgun Guvench, Alexander D Mackerell, 2009, Journal of chemical theory and computation.

Sulfation and Calcium Favor Compact Conformations of Chondroitin in Aqueous Solutions

Olgun Guvench, Elizabeth K Whitmore, 2021, ACS omega.

Computational evaluation of protein-small molecule binding.

Alexander D. MacKerell, Olgun Guvench, Alexander D MacKerell, 2009, Current opinion in structural biology.

CD44 receptor unfolding enhances binding by freeing basic amino acids to contact carbohydrate ligand.

Olgun Guvench, Amanda J. Favreau, Christina E. Faller, 2013, Biophysical journal.

Mechanism of binding site conformational switching in the CD44-hyaluronan protein-carbohydrate binding interaction.

Ronald D. Hills, Olgun Guvench, T. J. Foster, 2011, Journal of molecular biology.

Site Identification by Ligand Competitive Saturation-Biologics Approach for Structure-Based Protein Charge Prediction.

Alexander D. MacKerell, Asuka A. Orr, Olgun Guvench, 2023, Molecular pharmaceutics.

Tryptophan side chain electrostatic interactions determine edge-to-face vs parallel-displaced tryptophan side chain geometries in the designed beta-hairpin "trpzip2".

Olgun Guvench, Charles L Brooks, Olgun Guvench, 2005, Journal of the American Chemical Society.

Rigidity and flexibility in the tetrasaccharide linker of proteoglycans from atomic‐resolution molecular simulation

Olgun Guvench, Cathy Ng, Padmavathy Nandha Premnath, 2017, J. Comput. Chem..

Application of the frozen atom approximation to the GB/SA continuum model for solvation free energy

Jörg Weiser, Peter S. Shenkin, W. Clark Still, 2002, J. Comput. Chem..

Computational approaches for the design of protein–protein interaction inhibitors

Alexander D. MacKerell, Olgun Guvench, Wenbo Yu, 2013 .

Atomistic simulation study of linear alkylbenzene sulfonates at the water/air interface.

Alexander D. MacKerell, Olgun Guvench, Michael L Klein, 2010, The journal of physical chemistry. B.

Tyr66 acts as a conformational switch in the closed-to-open transition of the SHP-2 N-SH2-domain phosphotyrosine-peptide binding cleft

Alexander D. MacKerell, Olgun Guvench, C. Qu, 2007 .

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.

Alexander D. MacKerell, Olgun Guvench, C. Qu, 2008, Journal of Medicinal Chemistry.

CHARMM additive all-atom force field for glycosidic linkages in carbohydrates involving furanoses.

Alexander D. MacKerell, Olgun Guvench, E. P. Raman, 2010, The journal of physical chemistry. B.

CHARMM additive all-atom force field for aldopentofuranoses, methyl-aldopentofuranosides, and fructofuranose.

Alexander D. MacKerell, Olgun Guvench, Elizabeth Hatcher, 2009, The journal of physical chemistry. B.

CHARMM Additive All-Atom Force Field for Acyclic Polyalcohols, Acyclic Carbohydrates and Inositol.

Alexander D. MacKerell, Olgun Guvench, Elizabeth Hatcher, 2009, Journal of chemical theory and computation.

Water Exchange from the Buried Binding Sites of Cytochrome P450 Enzymes 1A2, 2D6, and 3A4 Correlates with Conformational Fluctuations

Olgun Guvench, 2024, Molecules.

Balancing target flexibility and target denaturation in computational fragment‐based inhibitor discovery

Alexander D. MacKerell, Olgun Guvench, T. J. Foster, 2012, J. Comput. Chem..