Eshwar P. Raman, Ph.D. - Publications

Affiliations: 
2008 George Mason University, Washington, DC 
Area:
General Biophysics, Bioinformatics Biology

24 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
2016 Cavalier MC, Ansari MI, Pierce AD, Wilder PT, McKnight LE, Raman EP, Neau DB, Bezawada P, Alasady MJ, Charpentier TH, Varney K, Toth EA, MacKerell AD, Coop A, Weber DJ. Small Molecule Inhibitors of Ca(2+)-S100B Reveal Two Protein Conformations. Journal of Medicinal Chemistry. PMID 26727270 DOI: 10.1021/acs.jmedchem.5b01369  1
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  1
2015 Samadani R, Zhang J, Brophy A, Oashi T, Priyakumar UD, Raman EP, St John FJ, Jung KY, Fletcher S, Pozharski E, MacKerell AD, Shapiro P. Small-molecule inhibitors of ERK-mediated immediate early gene expression and proliferation of melanoma cells expressing mutated BRaf. The Biochemical Journal. 467: 425-38. PMID 25695333 DOI: 10.1042/BJ20131571  1
2015 Lakkaraju SK, Yu W, Raman EP, Hershfeld AV, Fang L, Deshpande DA, MacKerell AD. Mapping functional group free energy patterns at protein occluded sites: nuclear receptors and G-protein coupled receptors. Journal of Chemical Information and Modeling. 55: 700-8. PMID 25692383 DOI: 10.1021/ci500729k  1
2015 Raman EP, MacKerell AD. Spatial analysis and quantification of the thermodynamic driving forces in protein-ligand binding: binding site variability. Journal of the American Chemical Society. 137: 2608-21. PMID 25625202 DOI: 10.1021/ja512054f  1
2015 Yu W, Lakkaraju SK, Raman EP, Fang L, MacKerell AD. Pharmacophore modeling using site-identification by ligand competitive saturation (SILCS) with multiple probe molecules. Journal of Chemical Information and Modeling. 55: 407-20. PMID 25622696 DOI: 10.1021/ci500691p  1
2014 Lakkaraju SK, Raman EP, Yu W, MacKerell AD. Sampling of Organic Solutes in Aqueous and Heterogeneous Environments Using Oscillating Excess Chemical Potentials in Grand Canonical-like Monte Carlo-Molecular Dynamics Simulations. Journal of Chemical Theory and Computation. 10: 2281-2290. PMID 24932136 DOI: 10.1021/ct500201y  1
2014 Yu W, Lakkaraju SK, Raman EP, MacKerell AD. Site-Identification by Ligand Competitive Saturation (SILCS) assisted pharmacophore modeling. Journal of Computer-Aided Molecular Design. 28: 491-507. PMID 24610239 DOI: 10.1007/s10822-014-9728-0  1
2013 Raman EP, Yu W, Lakkaraju SK, MacKerell AD. Inclusion of multiple fragment types in the site identification by ligand competitive saturation (SILCS) approach. Journal of Chemical Information and Modeling. 53: 3384-98. PMID 24245913 DOI: 10.1021/ci4005628  1
2013 Raman EP, MacKerell AD. Rapid estimation of hydration thermodynamics of macromolecular regions. The Journal of Chemical Physics. 139: 055105. PMID 23927290 DOI: 10.1063/1.4817344  1
2012 McKnight LE, Raman EP, Bezawada P, Kudrimoti S, Wilder PT, Hartman KG, Godoy-Ruiz R, Toth EA, Coop A, Mackerell AD, Weber DJ. Structure-Based Discovery of a Novel Pentamidine-Related Inhibitor of the Calcium-Binding Protein S100B. Acs Medicinal Chemistry Letters. 3: 975-979. PMID 23264854 DOI: 10.1021/ml300166s  1
2012 Vanommeslaeghe K, Raman EP, MacKerell AD. Automation of the CHARMM General Force Field (CGenFF) II: assignment of bonded parameters and partial atomic charges. Journal of Chemical Information and Modeling. 52: 3155-68. PMID 23145473 DOI: 10.1021/ci3003649  1
2012 Raman EP, Vanommeslaeghe K, Mackerell AD. Site-Specific Fragment Identification Guided by Single-Step Free Energy Perturbation Calculations. Journal of Chemical Theory and Computation. 8: 3513-3525. PMID 23144598 DOI: 10.1021/ct300088r  1
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  1
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  1
2011 Abel S, Dupradeau FY, Raman EP, MacKerell AD, Marchi M. Molecular simulations of dodecyl-β-maltoside micelles in water: influence of the headgroup conformation and force field parameters. The Journal of Physical Chemistry. B. 115: 487-99. PMID 21192681 DOI: 10.1021/jp109545v  1
2011 Oashi T, Ringer AL, Raman EP, Mackerell AD. Automated selection of compounds with physicochemical properties to maximize bioavailability and druglikeness. Journal of Chemical Information and Modeling. 51: 148-58. PMID 21142079 DOI: 10.1021/ci100359a  1
2010 Takeda T, Kumar R, Raman EP, Klimov DK. Nonsteroidal anti-inflammatory drug naproxen destabilizes Aβ amyloid fibrils: a molecular dynamics investigation. The Journal of Physical Chemistry. B. 114: 15394-402. PMID 20979356 DOI: 10.1021/jp107955v  1
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  1
2010 Takeda T, Chang WE, Raman EP, Klimov DK. Binding of nonsteroidal anti-inflammatory drugs to Abeta fibril. Proteins. 78: 2849-60. PMID 20635343 DOI: 10.1002/prot.22804  1
2010 Chang WE, Takeda T, Raman EP, Klimov DK. Molecular dynamics simulations of anti-aggregation effect of ibuprofen. Biophysical Journal. 98: 2662-70. PMID 20513411 DOI: 10.1016/j.bpj.2010.02.031  1
2009 Raman EP, Takeda T, Klimov DK. Molecular dynamics simulations of Ibuprofen binding to Abeta peptides. Biophysical Journal. 97: 2070-9. PMID 19804739 DOI: 10.1016/j.bpj.2009.07.032  1
2007 Raman EP, Takeda T, Barsegov V, Klimov DK. Mechanical unbinding of abeta peptides from amyloid fibrils. Journal of Molecular Biology. 373: 785-800. PMID 17868685 DOI: 10.1016/j.jmb.2007.08.034  1
2007 Raman EP, Barsegov V, Klimov DK. Folding of tandem-linked domains. Proteins. 67: 795-810. PMID 17380511 DOI: 10.1002/prot.21339  1
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