| Year |
Citation |
Score |
| 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 |
0.395 |
|
| 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 |
0.302 |
|
| 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 |
0.452 |
|
| 2015 |
Small MC, Lakkaraju SK, Raman EP, Andrade RB, MacKerell, AD. Molecular Understanding of the Binding of Macrolide Antibiotics to the Ribosome using Site-Identification via Ligand Competitive Saturation Biophysical Journal. 108: 469a. DOI: 10.1016/j.bpj.2014.11.2566 |
0.373 |
|
| 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 |
0.342 |
|
| 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 |
0.336 |
|
| 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 |
0.323 |
|
| 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 |
0.747 |
|
| 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 |
0.615 |
|
| 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 |
0.639 |
|
| 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 |
0.757 |
|
| 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 |
0.701 |
|
| 2007 |
Raman EP, Barsegov V, Klimov DK. Folding of tandem-linked domains. Proteins. 67: 795-810. PMID 17380511 DOI: 10.1002/Prot.21339 |
0.464 |
|
| Low-probability matches (unlikely to be authored by this person) |
| 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 |
0.284 |
|
| 2019 |
Raman EP. A Template Based Method for Conformation Generation and Scoring for Congeneric Series of Ligands. Journal of Chemical Information and Modeling. PMID 31045363 DOI: 10.1021/acs.jcim.9b00032 |
0.281 |
|
| 2016 |
Raman EP, Lakkaraju SK, Denny RA, MacKerell AD. Estimation of relative free energies of binding using pre-computed ensembles based on the single-step free energy perturbation and the site-identification by Ligand competitive saturation approaches. Journal of Computational Chemistry. PMID 27782307 DOI: 10.1002/jcc.24522 |
0.28 |
|
| 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 |
0.254 |
|
| 2011 |
Raman EP, Yu W, MacKerell AD. Protein Affinity Pattern Calculations using Protein-Fragment Site Identification by Ligand Competitive Saturation (SILCS) Biophysical Journal. 100: 526a. DOI: 10.1016/j.bpj.2010.12.3076 |
0.24 |
|
| 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 |
0.231 |
|
| 2016 |
Cavalier MC, Melville Z, Aligholizadeh E, Raman EP, Yu W, Fang L, Alasady M, Pierce AD, Wilder PT, MacKerell AD, Weber DJ. Novel protein-inhibitor interactions in site 3 of Ca(2+)-bound S100B as discovered by X-ray crystallography. Acta Crystallographica. Section D, Structural Biology. 72: 753-760. PMID 27303795 DOI: 10.1107/S2059798316005532 |
0.193 |
|
| 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 |
0.175 |
|
| 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 |
0.174 |
|
| 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 |
0.162 |
|
| 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 |
0.153 |
|
| 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 |
0.136 |
|
| 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 |
0.11 |
|
| 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 |
0.104 |
|
| 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 |
0.086 |
|
| 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 |
0.078 |
|
| Hide low-probability matches. |