| Year |
Citation |
Score |
| 2020 |
Gossert ST, Parajuli B, Chaiken I, Abrams CF. Roles of Variable Linker Length in Dual Acting Virucidal Entry Inhibitors on HIV-1 Potency via On-the-fly Free Energy Molecular Simulations. Protein Science : a Publication of the Protein Society. PMID 32926485 DOI: 10.1002/Pro.3949 |
0.348 |
|
| 2020 |
Zou S, Zhang S, Gaffney A, Ding H, Lu M, Grover JR, Farrell M, Nguyen HT, Zhao C, Anang S, Zhao M, Mohammadi M, Blanchard SC, Abrams C, Madani N, et al. Long-Acting BMS-378806 Analogues Stabilize the State-1 Conformation of the Human Immunodeficiency Virus (HIV-1) Envelope Glycoproteins. Journal of Virology. PMID 32161177 DOI: 10.1128/Jvi.00148-20 |
0.305 |
|
| 2019 |
Gardner JM, Abrams CF. Energetics of Flap Opening in HIV-1 Protease: String Method Calculations. The Journal of Physical Chemistry. B. PMID 31640343 DOI: 10.1021/Acs.Jpcb.9B08348 |
0.329 |
|
| 2019 |
Shrivastav G, Vanden-Eijnden E, Abrams CF. Mapping saddles and minima on free energy surfaces using multiple climbing strings. The Journal of Chemical Physics. 151: 124112. PMID 31575198 DOI: 10.1063/1.5120372 |
0.316 |
|
| 2019 |
Lu M, Ma X, Castillo-Menendez LR, Gorman J, Alsahafi N, Ermel U, Terry DS, Chambers M, Peng D, Zhang B, Zhou T, Reichard N, Wang K, Grover JR, Carman BP, ... ... Abrams C, et al. Associating HIV-1 envelope glycoprotein structures with states on the virus observed by smFRET. Nature. PMID 30971821 DOI: 10.1038/S41586-019-1101-Y |
0.321 |
|
| 2019 |
Srikanth A, Abrams CF. Effect of molecular packing and hydrogen bonding on the properties of epoxy-amido amine systems Computational Materials Science. 169: 109082. DOI: 10.1016/J.Commatsci.2019.109082 |
0.317 |
|
| 2019 |
Sridhar AS, Abrams CF. Yield and Post-yield Behavior of Fatty-Acid-Functionalized Amidoamine–Epoxy Systems: A Molecular Simulation Study Journal of Dynamic Behavior of Materials. 5: 143-149. DOI: 10.1007/S40870-019-00193-Z |
0.303 |
|
| 2019 |
Huang M, Abrams C. Effects of Reactivity Ratios on Network Topology and Thermomechanical Properties in Vinyl Ester/Styrene Thermosets: Molecular Dynamics Simulations Macromolecular Theory and Simulations. 28: 1900030. DOI: 10.1002/Mats.201900030 |
0.331 |
|
| 2018 |
Gordon R, Stober ST, Abrams CF. Counter-Ion Effects on Aggregate Structure of 12-Hydroxystearate Salts in Hexane: A Quantum Mechanical and Molecular Dynamics Simulation Study. The Journal of Physical Chemistry. B. PMID 30571113 DOI: 10.1021/Acs.Jpcb.8B08477 |
0.318 |
|
| 2018 |
Gossert ST, Parajuli B, Chaiken I, Abrams CF. Roles of Conserved Tryptophans in Trimerization of HIV-1 Membrane-Proximal External Regions: Implications for Virucidal Design via Alchemical Free-Energy Molecular Simulations. Proteins. PMID 29633345 DOI: 10.1002/Prot.25504 |
0.325 |
|
| 2018 |
Paz SA, Maragliano L, Abrams CF. Effect of Intercalated Water on Potassium Ion Transport through Kv1.2 Channels Studied via On-the-Fly Free-Energy Parametrization. Journal of Chemical Theory and Computation. PMID 29570282 DOI: 10.1021/Acs.Jctc.8B00024 |
0.35 |
|
| 2018 |
Parajuli B, Acharya K, Bach HC, Parajuli B, Zhang S, Smith AB, Abrams CF, Chaiken I. Restricted HIV-1 Env Glycan Engagement by Lectin-Reengineered DAVEI Protein Chimera is sufficient for Lytic Inactivation of the Virus. The Biochemical Journal. PMID 29343613 DOI: 10.1042/Bcj20170662 |
0.311 |
|
| 2018 |
Moraca F, Rinaldo D, Smith AB, Abrams C. Specific Non-Covalent Interactions Determine Optimal Structure of a Buried Ligand Moiety: QM/MM and Pure QM Modeling of Complexes of the Small-Molecule CD4 Mimetics and HIV1 Gp120. Chemmedchem. PMID 29337418 DOI: 10.1002/Cmdc.201700728 |
0.309 |
|
| 2018 |
Srikanth A, Kinaci E, Vergara J, Palmese G, Abrams CF. The effect of alkyl chain length on mechanical properties of fatty-acid-functionalized amidoamine-epoxy systems Computational Materials Science. 150: 70-76. DOI: 10.1016/J.Commatsci.2018.03.073 |
0.343 |
|
| 2017 |
Herschhorn A, Gu C, Moraca F, Ma X, Farrell M, Smith AB, Pancera M, Kwong PD, Schön A, Freire E, Abrams C, Blanchard SC, Mothes W, Sodroski JG. The β20-β21 of gp120 is a regulatory switch for HIV-1 Env conformational transitions. Nature Communications. 8: 1049. PMID 29051495 DOI: 10.1038/S41467-017-01119-W |
0.305 |
|
| 2017 |
Gordon R, Stober ST, Abrams CF. Effects of Optical Purity and Finite System Size on Self-Assembly of 12-Hydroxystearic Acid in Hexane: Molecular Dynamics Simulations. The Journal of Physical Chemistry. B. PMID 28876930 DOI: 10.1021/Acs.Jpcb.7B05246 |
0.312 |
|
| 2017 |
Paz SA, Vanden-Eijnden E, Abrams CF. Polymorphism at 129 dictates metastable conformations of the human prion protein N-terminal β-sheet. Chemical Science. 8: 1225-1232. PMID 28451263 DOI: 10.1039/C6Sc03275C |
0.312 |
|
| 2017 |
Acharya K, Rashad AA, Moraca F, Klasse PJ, Moore JP, Abrams C, Chaiken I. Recognition of HIV-Inactivating Peptide Triazoles by the Recombinant Soluble Env Trimer, BG505 SOSIP.664. Proteins. PMID 28056499 DOI: 10.1002/Prot.25238 |
0.306 |
|
| 2017 |
Srikanth A, Vergara J, Palmese G, Abrams CF. The effect of alkyl chain length on material properties of fatty-acid-functionalized amidoamine-epoxy systems European Polymer Journal. 89: 1-12. DOI: 10.1016/J.Eurpolymj.2017.01.037 |
0.327 |
|
| 2017 |
Paz SA, Vanden-Eijnden E, Abrams C. Metastabilities in the Human Prion Protein N-Terminal Beta-Sheet are Dictated by the 129 Polymorphism Biophysical Journal. 112. DOI: 10.1016/J.Bpj.2016.11.2661 |
0.3 |
|
| 2016 |
Parajuli B, Acharya K, Yu R, Ngo B, Rashad AA, Abrams CF, Chaiken IM. Lytic Inactivation of HIV-1 by Dual Engagement of gp120 and gp41 Domains in the Virus Env Protein Trimer. Biochemistry. PMID 27731975 DOI: 10.1021/Acs.Biochem.6B00570 |
0.305 |
|
| 2016 |
Yu TQ, Lu J, Abrams CF, Vanden-Eijnden E. Multiscale implementation of infinite-swap replica exchange molecular dynamics. Proceedings of the National Academy of Sciences of the United States of America. PMID 27698148 DOI: 10.1073/Pnas.1605089113 |
0.341 |
|
| 2016 |
Moraca F, Acharya K, Melillo B, Smith Iii AB, Chaiken IM, Abrams CF. Computational evaluation of HIV-1 gp120 conformations of soluble trimeric gp140 structures as targets for de novo docking of first- and second-generation small-molecule CD4 mimics. Journal of Chemical Information and Modeling. PMID 27602436 DOI: 10.1021/Acs.Jcim.6B00393 |
0.318 |
|
| 2016 |
Gordon R, Stober ST, Abrams CF. Aggregation of 12-Hydroxystearic Acid and Its Lithium Salt in Hexane: Molecular Dynamics Simulations. The Journal of Physical Chemistry. B. PMID 27387154 DOI: 10.1021/Acs.Jpcb.6B04193 |
0.324 |
|
| 2016 |
Jang C, Abrams CF. Thermal and mechanical properties of thermosetting polymers using coarse-grained simulation European Physical Journal: Special Topics. 1-9. DOI: 10.1140/Epjst/E2016-60143-0 |
0.351 |
|
| 2016 |
Jang C, Sharifi M, Palmese GR, Abrams CF. Toughness enhancement of thermosetting polymers using a novel partially reacted substructure curing protocol: A combined molecular simulation and experimental study Polymer (United Kingdom). 90: 249-255. DOI: 10.1016/J.Polymer.2016.03.023 |
0.315 |
|
| 2016 |
Yang JH, Srikanth A, Jang C, Abrams CF. Relationships between molecular structure and thermomechanical properties of bio-based thermosetting polymers Journal of Polymer Science Part B: Polymer Physics. 55: 285-292. DOI: 10.1002/Polb.24270 |
0.349 |
|
| 2015 |
Paz SA, Abrams CF. Free Energy and Hidden Barriers of the β-Sheet Structure of Prion Protein. Journal of Chemical Theory and Computation. 11: 5024-34. PMID 26574287 DOI: 10.1021/Acs.Jctc.5B00576 |
0.331 |
|
| 2015 |
Yu TQ, Lapelosa M, Vanden-Eijnden E, Abrams CF. Full kinetics of CO entry, internal diffusion, and exit in myoglobin from transition-path theory simulations. Journal of the American Chemical Society. 137: 3041-50. PMID 25664858 DOI: 10.1021/Ja512484Q |
0.379 |
|
| 2015 |
Yu T, Bucci A, Vanden-Eijnden E, Abrams C. Markovian Milestoning for Computing Entry, Exit, and Internal Diffusion Rates of Ligands in Proteins Biophysical Journal. 108. DOI: 10.1016/J.Bpj.2014.11.1192 |
0.342 |
|
| 2015 |
Jang C, Sirk TW, Andzelm JW, Abrams CF. Comparison of crosslinking algorithms in molecular dynamics simulation of thermosetting polymers Macromolecular Theory and Simulations. 24: 260-270. DOI: 10.1002/Mats.201400094 |
0.331 |
|
| 2014 |
Baker MK, Abrams CF. Dynamics of lipids, cholesterol, and transmembrane α-helices from microsecond molecular dynamics simulations. The Journal of Physical Chemistry. B. 118: 13590-600. PMID 25380392 DOI: 10.1021/Jp507027T |
0.324 |
|
| 2014 |
Sharifi M, Jang CW, Abrams CF, Palmese GR. Toughened epoxy polymers via rearrangement of network topology Journal of Materials Chemistry A. 2: 16071-16082. DOI: 10.1039/C4Ta03051F |
0.326 |
|
| 2014 |
Jang C, Sharifi M, Palmese GR, Abrams CF. Crosslink network rearrangement via reactive encapsulation of solvent in epoxy curing: A combined molecular simulation and experimental study Polymer (United Kingdom). 55: 3859-3868. DOI: 10.1016/J.Polymer.2014.06.022 |
0.349 |
|
| 2013 |
Emileh A, Tuzer F, Yeh H, Umashankara M, Moreira DR, Lalonde JM, Bewley CA, Abrams CF, Chaiken IM. A model of peptide triazole entry inhibitor binding to HIV-1 gp120 and the mechanism of bridging sheet disruption. Biochemistry. 52: 2245-61. PMID 23470147 DOI: 10.1021/Bi400166B |
0.308 |
|
| 2013 |
Baker M, Gangupomu V, Abrams C. Effects of the Midspan Arginine on the Interactions between a Solvated Lipid Bilayer and the HIV-1 Gp41 Membrane Spanning Domain Biophysical Journal. 104. DOI: 10.1016/J.Bpj.2012.11.3665 |
0.306 |
|
| 2012 |
Abrams CF, Vanden-Eijnden E. On-the-fly free energy parameterization via temperature accelerated molecular dynamics. Chemical Physics Letters. 547: 114-119. PMID 23226688 DOI: 10.1016/J.Cplett.2012.07.064 |
0.353 |
|
| 2012 |
Stober ST, Abrams CF. Energetics and mechanism of the normal-to-amyloidogenic isomerization of β2-microglobulin: on-the-fly string method calculations. The Journal of Physical Chemistry. B. 116: 9371-5. PMID 22793795 DOI: 10.1021/Jp304805V |
0.311 |
|
| 2012 |
Vashisth H, Maragliano L, Abrams CF. "DFG-flip" in the insulin receptor kinase is facilitated by a helical intermediate state of the activation loop. Biophysical Journal. 102: 1979-87. PMID 22768955 DOI: 10.1016/J.Bpj.2012.03.031 |
0.334 |
|
| 2012 |
Stober ST, Abrams CF. Enhanced meta-analysis of acetylcholine binding protein structures reveals conformational signatures of agonism in nicotinic receptors. Protein Science : a Publication of the Protein Society. 21: 307-17. PMID 22170867 DOI: 10.1002/Pro.2016 |
0.322 |
|
| 2012 |
Emileh A, Tuzer F, Moreira DR, LaLonde JM, Bewley CA, Chaiken IM, Abrams CF. A Molecular Dynamics Simulation of Peptide-Triazole HIV Entry Inhibitor Binding to gp120 Hydrophobic Core Biophysical Journal. 102: 621a. DOI: 10.1016/J.Bpj.2011.11.3383 |
0.314 |
|
| 2010 |
Gangupomu VK, Abrams CF. All-atom models of the membrane-spanning domain of HIV-1 gp41 from metadynamics. Biophysical Journal. 99: 3438-44. PMID 21081093 DOI: 10.1016/J.Bpj.2010.09.054 |
0.318 |
|
| 2010 |
Abrams CF, Vanden-Eijnden E. Large-scale conformational sampling of proteins using temperature-accelerated molecular dynamics. Proceedings of the National Academy of Sciences of the United States of America. 107: 4961-6. PMID 20194785 DOI: 10.1016/J.Bpj.2009.12.154 |
0.383 |
|
| 2010 |
Vashisth H, Abrams CF. Docking of insulin to a structurally equilibrated insulin receptor ectodomain. Proteins. 78: 1531-43. PMID 20112420 DOI: 10.1002/Prot.22670 |
0.308 |
|
| 2010 |
Karayiannis NC, Foteinopoulou K, Abrams CF, Laso M. Modeling of crystal nucleation and growth in athermal polymers: Self-assembly of layered nano-morphologies Soft Matter. 6: 2160-2173. DOI: 10.1039/B923369E |
0.313 |
|
| 2009 |
Mukherji D, Abrams CF. Anomalous ductility in thermoset/thermoplastic polymer alloys. Physical Chemistry Chemical Physics : Pccp. 11: 2113-5. PMID 19280022 DOI: 10.1039/B818039C |
0.32 |
|
| 2009 |
Vashisth H, Abrams CF. A Thermodynamic Study Of Ligand Access/escape From Protein Cavities Biophysical Journal. 96. DOI: 10.1016/J.Bpj.2008.12.3119 |
0.336 |
|
| 2008 |
Vashisth H, Abrams CF. Ligand escape pathways and (un)binding free energy calculations for the hexameric insulin-phenol complex. Biophysical Journal. 95: 4193-204. PMID 18676643 DOI: 10.1529/Biophysj.108.139675 |
0.356 |
|
| 2007 |
Sliozberg Y, Abrams CF. Spontaneous conformational changes in the E. coli GroEL subunit from all-atom molecular dynamics simulations. Biophysical Journal. 93: 1906-16. PMID 17513353 DOI: 10.1529/Biophysj.107.108043 |
0.327 |
|
| 2006 |
Abrams CF, Lee NK, Johner A. Diffusion/reaction in confined polymer chains Macromolecules. 39: 3655-3663. DOI: 10.1021/Ma060044D |
0.301 |
|
| 2005 |
Abrams CF. Concurrent dual-resolution Monte Carlo simulation of liquid methane. The Journal of Chemical Physics. 123: 234101. PMID 16392908 DOI: 10.1063/1.2136884 |
0.316 |
|
| 2005 |
Sliozberg Y, Abrams CF. Effects of confinement on the thermodynamics of a collapsing heteropolymer: An off-lattice Wang-Landau Monte Carlo simulation study Macromolecules. 38: 5321-5329. DOI: 10.1021/Ma050443T |
0.322 |
|
| 2005 |
Sliozberg Y, Abrams CF. Structural correlations in comb heteropolymers in good and backbone-selective solvents Journal of Polymer Science, Part B: Polymer Physics. 43: 983-993. DOI: 10.1002/Polb.20388 |
0.335 |
|
| 2004 |
Lee NK, Abrams CF. Kinetics of a polysoap collapse. The Journal of Chemical Physics. 121: 7484-93. PMID 15473823 DOI: 10.1063/1.1793151 |
0.347 |
|
| 2004 |
Sliozberg Y, Abrams CF. Polysoaps in backbone-selective solvents: Effects of side-chain length on collapse dynamics Soft Materials. 2: 11-25. DOI: 10.1081/Smts-120030472 |
0.343 |
|
| 2004 |
Lee NK, Abrams CF, Johner A, Obukhov S. Swelling dynamics of collapsed polymers Macromolecules. 37: 651-661. DOI: 10.1021/Ma034808Q |
0.332 |
|
| 2003 |
Abrams CF, Delle Site L, Kremer K. Dual-resolution coarse-grained simulation of the bisphenol-A-polycarbonate/nickel interface. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 67: 021807. PMID 12636708 DOI: 10.1103/Physreve.67.021807 |
0.329 |
|
| 2003 |
Abrams CF, Kremer K. Combined coarse-grained and atomistic simulation of liquid bisphenol A-polycarbonate: Liquid packing and intramolecular structure Macromolecules. 36: 260-267. DOI: 10.1021/Ma0213495 |
0.332 |
|
| 2002 |
Delle Site L, Abrams CF, Alavi A, Kremer K. Polymers near metal surfaces: selective adsorption and global conformations. Physical Review Letters. 89: 156103. PMID 12366003 DOI: 10.1103/Physrevlett.89.156103 |
0.335 |
|
| 2002 |
Abrams CF, Lee NK, Obukhov SP. Collapse dynamics of a polymer chain: Theory and simulation Europhysics Letters. 59: 391-397. DOI: 10.1209/Epl/I2002-00207-5 |
0.327 |
|
| 2001 |
Abrams CF. Atomistic simulation of fluorocarbon deposition on Si by continuous bombardment with energetic CF+ and CF2 + Journal of Vacuum Science and Technology a: Vacuum, Surfaces and Films. 19: 175-181. DOI: 10.1116/1.1322652 |
0.308 |
|
| 2001 |
Graves DB, Abrams CF. Molecular dynamics simulations of ion-surface interactions with applications to plasma processing Advances in Chemical Engineering. 28: 149-201. DOI: 10.1016/S0065-2377(01)28006-5 |
0.531 |
|
| 2000 |
Tanaka J, Abrams CF, Graves DB. New C-F interatomic potential for molecular dynamics simulation of fluorocarbon film formation Journal of Vacuum Science and Technology a: Vacuum, Surfaces and Films. 18: 938-945. DOI: 10.1116/1.582279 |
0.548 |
|
| 2000 |
Abrams CF, Graves DB. On the active surface layer in CF3 + etching of Si: atomistic simulation and a simple mass balance model Journal of Vacuum Science and Technology a: Vacuum, Surfaces and Films. 18: 411-416. DOI: 10.1116/1.582202 |
0.518 |
|
| 2000 |
Abrams CF, Graves DB. Molecular dynamics simulations of Si etching with energetic F+: Sensitivity of results to the interatomic potential Journal of Applied Physics. 88: 3734-3738. DOI: 10.1063/1.1288701 |
0.531 |
|
| 2000 |
Abrams CF, Graves DB. Atomistic simulation of silicon bombardment by energetic CF3 +: Product distributions and energies Thin Solid Films. 374: 150-156. DOI: 10.1016/S0040-6090(00)01145-7 |
0.53 |
|
| 1999 |
Abrams CF, Graves DB. Three-dimensional spatiokinetic distributions of sputtered and scattered products of Ar+ and Cu+ impacts onto the Cu surface: Molecular dynamics simulations Ieee Transactions On Plasma Science. 27: 1426-1432. DOI: 10.1109/27.799821 |
0.443 |
|
| 1999 |
Abrams CF, Graves DB. Molecular dynamics simulations of Si etching by energetic CF+ 3 Journal of Applied Physics. 86: 5938-5948. DOI: 10.1063/1.371637 |
0.531 |
|
| 1999 |
Abrams CF, Graves DB. Cu sputtering and deposition by off-normal, near-threshold Cu+ bombardment: Molecular dynamics simulations Journal of Applied Physics. 86: 2263-2267. DOI: 10.1063/1.371040 |
0.524 |
|
| 1998 |
Abrams CF, Graves DB. Energetic ion bombardment of SiO2 surfaces: Molecular dynamics simulations Journal of Vacuum Science and Technology a: Vacuum, Surfaces and Films. 16: 3006-3019. DOI: 10.1116/1.581452 |
0.528 |
|
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