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Freddie R. Salsbury - Publications

Affiliations: 
Wake Forest University, Winston-Salem, NC, United States 
Area:
Molecular Physics, Molecular Chemistry
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68/83 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
2023 Wu D, Prem A, Xiao J, Salsbury FR. Thrombin - A Molecular Dynamics Perspective. Mini Reviews in Medicinal Chemistry. PMID 37605420 DOI: 10.2174/1389557523666230821102655  0.788
2022 Lu Y, Salsbury FR, Derreumaux P. Impact of A2T and D23N mutations on C99 homodimer conformations. The Journal of Chemical Physics. 157: 085102. PMID 36050011 DOI: 10.1063/5.0101622  0.316
2022 Wu D, Salsbury FR. Simulations suggest double sodium binding induces unexpected conformational changes in thrombin. Journal of Molecular Modeling. 28: 120. PMID 35419655 DOI: 10.1007/s00894-022-05076-0  0.303
2021 Wu D, Xiao J, Salsbury FR. Light Chain Mutation Effects on the Dynamics of Thrombin. Journal of Chemical Information and Modeling. PMID 33450154 DOI: 10.1021/acs.jcim.0c01303  0.772
2019 Lu Y, Shi X, Nguyen PH, Sterpone F, Salsbury FR, Derreumaux P. Amyloid-β(29-42) Dimeric Conformations in Membranes Rich in Omega-3 and Omega-6 Polyunsaturated Fatty Acids. The Journal of Physical Chemistry. B. PMID 30813725 DOI: 10.1021/Acs.Jpcb.9B00431  0.404
2019 Xiao J, Salsbury FR. Na-binding modes involved in thrombin's allosteric response as revealed by molecular dynamics simulations, correlation networks and Markov modeling. Physical Chemistry Chemical Physics : Pccp. PMID 30724273 DOI: 10.1039/c8cp07293k  0.769
2018 Godwin RC, Macnamara LM, Alexander RW, Salsbury FR. Structure and Dynamics of tRNA Containing Core Substitutions. Acs Omega. 3: 10668-10678. PMID 30288458 DOI: 10.1021/acsomega.8b00280  0.771
2018 Melvin RL, Xiao J, Berenhaut KS, Godwin RC, Salsbury FR. Using correlated motions to determine sufficient sampling times for molecular dynamics. Physical Review. E. 98: 023307. PMID 30253618 DOI: 10.1103/Physreve.98.023307  0.749
2018 Xiao J, Melvin RL, Salsbury FR. Probing Light Chain Mutation Effects on Thrombin via Molecular Dynamics Simulations and Machine Learning. Journal of Biomolecular Structure & Dynamics. 1-55. PMID 29471734 DOI: 10.1080/07391102.2018.1445032  0.776
2018 Lu Y, Shi XF, Salsbury FR, Derreumaux P. Influence of electric field on the amyloid-β(29-42) peptides embedded in a membrane bilayer. The Journal of Chemical Physics. 148: 045105. PMID 29390813 DOI: 10.1063/1.5018459  0.38
2017 Melvin RL, Thompson WG, Godwin RC, Gmeiner WH, Salsbury FR. MutS's Multi-Domain Allosteric Response to Three DNA Damage Types Revealed by Machine Learning. Frontiers in Physics. 5. PMID 31938712 DOI: 10.3389/Fphy.2017.00010  0.767
2017 Xiao J, Melvin RL, Salsbury FR. Mechanistic insights into thrombin's switch between "slow" and "fast" forms. Physical Chemistry Chemical Physics : Pccp. PMID 28849814 DOI: 10.1039/C7Cp03671J  0.785
2017 Godwin RC, Gmeiner WH, Salsbury FR. All-atom molecular dynamics comparison of disease-associated zinc fingers. Journal of Biomolecular Structure & Dynamics. 1-14. PMID 28814200 DOI: 10.1080/07391102.2017.1363662  0.801
2017 Melvin RL, Gmeiner WH, Salsbury FR. All-atom MD indicates ion-dependent behavior of therapeutic DNA polymer. Physical Chemistry Chemical Physics : Pccp. PMID 28805211 DOI: 10.1039/C7Cp03479B  0.75
2017 Melvin RL, Xiao J, Godwin RC, Berenhaut KS, Salsbury FR. Visualizing correlated motion with HDBSCAN clustering. Protein Science : a Publication of the Protein Society. PMID 28799290 DOI: 10.1002/Pro.3268  0.759
2017 Melvin RL, Gmeiner WH, Salsbury FR. All-Atom MD Predicts Magnesium-Induced Hairpin in Chemically Perturbed RNA Analog of F10 Therapeutic. The Journal of Physical Chemistry. B. 121: 7803-7812. PMID 28745046 DOI: 10.1021/Acs.Jpcb.7B04724  0.749
2017 Lu Y, Shi XF, Salsbury FR, Derreumaux P. Small static electric field strength promotes aggregation-prone structures in amyloid-β(29-42). The Journal of Chemical Physics. 146: 145101. PMID 28411614 DOI: 10.1063/1.4979866  0.391
2017 Nelson KJ, Perkins A, Van Swearingen AE, Hartman S, Brereton AE, Parsonage D, Salsbury FR, Karplus PA, Poole LB. Experimentally Dissecting the Origins of Peroxiredoxin Catalysis. Antioxidants & Redox Signaling. PMID 28375740 DOI: 10.1089/Ars.2016.6922  0.323
2017 Godwin RC, Melvin RL, Gmeiner WH, Salsbury FR. Binding Site Configurations Probe the Structure and Dynamics of the Zinc Finger of NEMO (NF-κB Essential Modulator). Biochemistry. 56: 623-633. PMID 28035815 DOI: 10.1021/Acs.Biochem.6B00755  0.794
2016 Melvin RL, Godwin RC, Xiao J, Thompson WG, Berenhaut KS, Salsbury FR. Uncovering large-scale conformational change in molecular dynamics without prior knowledge. Journal of Chemical Theory and Computation. PMID 27802394 DOI: 10.1021/Acs.Jctc.6B00757  0.746
2016 Xiao J, Salsbury FR. Molecular dynamics simulations of aptamer-binding reveal generalized allostery in thrombin. Journal of Biomolecular Structure & Dynamics. 1-59. PMID 27794633 DOI: 10.1080/07391102.2016.1254682  0.796
2016 Melvin RL, Gmeiner WH, Salsbury FR. All-Atom Molecular Dynamics Reveals Mechanism of Zinc Complexation with Therapeutic F10. The Journal of Physical Chemistry. B. 120: 10269-10279. PMID 27606431 DOI: 10.1021/Acs.Jpcb.6B07753  0.751
2016 Melvin RL, Salsbury FR. Visualizing ensembles in structural biology. Journal of Molecular Graphics & Modelling. 67: 44-53. PMID 27179343 DOI: 10.1016/J.Jmgm.2016.05.001  0.76
2016 Melvin RL, Gmeiner WH, Salsbury FR. All-atom molecular dynamics reveals mechanism of zinc complexation with therapeutic F10 Journal of Physical Chemistry B. 120: 10269-10279. DOI: 10.1021/acs.jpcb.6b07753  0.751
2016 Xiao J, Salsbury FR. Generalized Allostery in Thrombin Biophysical Journal. 110: 55a. DOI: 10.1016/J.Bpj.2015.11.364  0.794
2015 Lu Y, Salsbury FR. Recapturing the Correlated Motions of Protein Using Coarse- Grained Models. Protein and Peptide Letters. 22: 654-9. PMID 26100687 DOI: 10.2174/0929866522666150511150332  0.477
2015 Lu Y, Salsbury FR. Autoinhibitory mechanisms of ERG studied by molecular dynamics simulations. Aip Advances. 5: 017130. PMID 25874157 DOI: 10.1063/1.4906572  0.524
2015 Godwin R, Gmeiner W, Salsbury FR. Importance of long-time simulations for rare event sampling in zinc finger proteins. Journal of Biomolecular Structure & Dynamics. 1-10. PMID 25734227 DOI: 10.1080/07391102.2015.1015168  0.782
2015 Godwin R, Gmeiner W, Salsbury F. Influence of Zinc-Binding on Folding and Dynamics of Zinc Finger Proteins: In Silico Biophysical Journal. 108: 519a. DOI: 10.1016/J.Bpj.2014.11.2843  0.809
2015 Melvin RL, Gmeiner W, Salsbury FR. Small Fdu Strand Exhibits Salt-Dependent Stability Biophysical Journal. 108: 237a. DOI: 10.1016/J.Bpj.2014.11.1312  0.744
2014 Negureanu L, Salsbury FR. Non-specificity and synergy at the binding site of the carboplatin-induced DNA adduct via molecular dynamics simulations of the MutSα-DNA recognition complex. Journal of Biomolecular Structure & Dynamics. 32: 969-92. PMID 23799640 DOI: 10.1080/07391102.2013.799437  0.356
2014 Xiao J, Salsbury FR. Computational Studies of the Formation of Peroxiredoxin Dimers Biophysical Journal. 106: 672a-673a. DOI: 10.1016/J.Bpj.2013.11.3725  0.783
2014 Salsbury FR, Negureanu L. Differential Responses of Msh2/6 and Damaged DNA Probed by Molecular Dynamics Biophysical Journal. 106: 658a-659a. DOI: 10.1016/J.Bpj.2013.11.3647  0.367
2014 Lu Y, Salsbury FR. Recapturing the Correlated Motions of Protein by using Coarse Grained Models Biophysical Journal. 106: 6-8. DOI: 10.1016/J.Bpj.2013.11.3587  0.464
2013 Negureanu L, Salsbury FR. Destabilization of the MutSα's protein-protein interface due to binding to the DNA adduct induced by anticancer agent carboplatin via molecular dynamics simulations. Journal of Molecular Modeling. 19: 4969-89. PMID 24061854 DOI: 10.1007/S00894-013-1998-2  0.324
2013 Ghosh S, Salsbury FR, Horita DA, Gmeiner WH. Cooperative stabilization of Zn(2+):DNA complexes through netropsin binding in the minor groove of FdU-substituted DNA. Journal of Biomolecular Structure & Dynamics. 31: 1301-10. PMID 23153072 DOI: 10.1080/07391102.2012.732343  0.321
2013 Negureanu L, Salsbury F. 212 Shifting interfaces: changes in protein–protein and protein–DNA interfaces probed via molecular dynamics Journal of Biomolecular Structure and Dynamics. 31: 138-139. DOI: 10.1080/07391102.2013.790143  0.372
2013 Negureanu L, Salsbury FR. Recognition of Chemotherapeutically Damaged DNA by Mismatch Repair Proteins Biophysical Journal. 104: 68a. DOI: 10.1016/J.Bpj.2012.11.413  0.373
2012 Salsbury FR, Poole LB, Fetrow JS. Electrostatics of cysteine residues in proteins: parameterization and validation of a simple model. Proteins. 80: 2583-91. PMID 22777874 DOI: 10.1002/Prot.24142  0.32
2012 Negureanu L, Salsbury FR. The molecular origin of the MMR-dependent apoptosis pathway from dynamics analysis of MutSα-DNA complexes. Journal of Biomolecular Structure & Dynamics. 30: 347-61. PMID 22712459 DOI: 10.1080/07391102.2012.680034  0.352
2012 Salsbury FR, Yuan Y, Knaggs MH, Poole LB, Fetrow JS. Structural and electrostatic asymmetry at the active site in typical and atypical peroxiredoxin dimers. The Journal of Physical Chemistry. B. 116: 6832-43. PMID 22401569 DOI: 10.1021/Jp212606K  0.546
2012 Negureanu L, Salsbury FR. Insights into protein - DNA interactions, stability and allosteric communications: a computational study of mutSα-DNA recognition complexes. Journal of Biomolecular Structure & Dynamics. 29: 757-76. PMID 22208277 DOI: 10.1080/07391102.2012.10507412  0.361
2012 Nelson KJ, Parsonage D, Van Swearingen AE, Yuan Y, Salsbury FR, Hall A, Andrew Karplus P, Poole LB. Specific Residues in Peroxiredoxins Promote Peroxide Reactivity Through Effects on Cysteine pKa, Transition State Stabilization and Oligomerization Free Radical Biology and Medicine. 53: S151. DOI: 10.1016/J.Freeradbiomed.2012.10.411  0.423
2011 Gmeiner WH, Salsbury F, Olsen CM, Marky LA. The stability of a model substrate for topoisomerase 1-mediated DNA religation depends on the presence of mismatched base pairs. Journal of Nucleic Acids. 2011: 631372. PMID 21904666 DOI: 10.4061/2011/631372  0.314
2011 Gassman NR, Clodfelter JE, McCauley AK, Bonin K, Salsbury FR, Scarpinato KD. Cooperative nuclear localization sequences lend a novel role to the N-terminal region of MSH6. Plos One. 6: e17907. PMID 21437237 DOI: 10.1371/Journal.Pone.0017907  0.305
2011 Ghosh S, Salsbury FR, Horita DA, Gmeiner WH. Zn2+ selectively stabilizes FdU-substituted DNA through a unique major groove binding motif. Nucleic Acids Research. 39: 4490-8. PMID 21296761 DOI: 10.1093/Nar/Gkr029  0.319
2010 Salsbury FR. Molecular dynamics simulations of protein dynamics and their relevance to drug discovery. Current Opinion in Pharmacology. 10: 738-44. PMID 20971684 DOI: 10.1016/J.Coph.2010.09.016  0.394
2010 Vasilyeva A, Clodfelter JE, Gorczynski MJ, Gerardi AR, King SB, Salsbury F, Scarpinato KD. Parameters of Reserpine Analogs That Induce MSH2/MSH6-Dependent Cytotoxic Response. Journal of Nucleic Acids. 2010. PMID 20936178 DOI: 10.4061/2010/162018  0.359
2010 Yuan Y, Knaggs M, Poole L, Fetrow J, Salsbury F. Conformational and oligomeric effects on the cysteine pK(a) of tryparedoxin peroxidase. Journal of Biomolecular Structure & Dynamics. 28: 51-70. PMID 20476795 DOI: 10.1080/07391102.2010.10507343  0.472
2010 Salsbury FR. Effects of Cisplatin binding to DNA on the dynamics of the E. Coli MutS dimer. Protein and Peptide Letters. 17: 744-50. PMID 19995335 DOI: 10.2174/092986610791190318  0.365
2009 Salsbury FR, Crowder MW, Kingsmore SF, Huntley JJ. Molecular dynamic simulations of the metallo-beta-lactamase from Bacteroides fragilis in the presence and absence of a tight-binding inhibitor. Journal of Molecular Modeling. 15: 133-45. PMID 19039608 DOI: 10.1007/S00894-008-0410-0  0.401
2009 Vasilyeva A, Clodfelter JE, Rector B, Hollis T, Scarpinato KD, Salsbury FR. Small molecule induction of MSH2-dependent cell death suggests a vital role of mismatch repair proteins in cell death. Dna Repair. 8: 103-13. PMID 18955167 DOI: 10.1016/J.Dnarep.2008.09.008  0.376
2008 Salsbury FR, Knutson ST, Poole LB, Fetrow JS. Functional site profiling and electrostatic analysis of cysteines modifiable to cysteine sulfenic acid. Protein Science : a Publication of the Protein Society. 17: 299-312. PMID 18227433 DOI: 10.1110/Ps.073096508  0.34
2007 Knaggs MH, Salsbury FR, Edgell MH, Fetrow JS. Insights into correlated motions and long-range interactions in CheY derived from molecular dynamics simulations. Biophysical Journal. 92: 2062-79. PMID 17172298 DOI: 10.1529/Biophysj.106.081950  0.456
2006 Salsbury FR, Clodfelter JE, Gentry MB, Hollis T, Scarpinato KD. The molecular mechanism of DNA damage recognition by MutS homologs and its consequences for cell death response. Nucleic Acids Research. 34: 2173-85. PMID 16648361 DOI: 10.1093/Nar/Gkl238  0.373
2004 Lee MS, Salsbury FR, Olson MA. An efficient hybrid explicit/implicit solvent method for biomolecular simulations. Journal of Computational Chemistry. 25: 1967-78. PMID 15470756 DOI: 10.1002/Jcc.20119  0.373
2004 Lee MS, Salsbury FR, Brooks CL. Constant-pH molecular dynamics using continuous titration coordinates. Proteins. 56: 738-52. PMID 15281127 DOI: 10.1002/Prot.20128  0.533
2004 Drotschmann K, Topping RP, Clodfelter JE, Salsbury FR. Mutations in the nucleotide-binding domain of MutS homologs uncouple cell death from cell survival. Dna Repair. 3: 729-42. PMID 15177182 DOI: 10.1016/J.Dnarep.2004.02.011  0.337
2003 Salsbury FR, Han WG, Noodleman L, Brooks CL. Temperature-dependent behavior of protein-chromophore interactions: a theoretical study of a blue fluorescent antibody. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. 4: 848-55. PMID 12961983 DOI: 10.1002/Cphc.200300694  0.501
2003 Lee MS, Feig M, Salsbury FR, Brooks CL. New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations. Journal of Computational Chemistry. 24: 1348-56. PMID 12827676 DOI: 10.1002/Jcc.10272  0.645
2003 Lee MS, Feig M, Salsbury FR, Brooks CL. Erratum: New Analytic Approximation to the Standard Molecular Volume Definition and Its Application to Generalized Born Calculations (Journal of Computational Chemistry (2003) 24:11 (1348-1356)) Journal of Computational Chemistry. 24. DOI: 10.1002/Jcc.10367  0.603
2002 Lee MS, Salsbury FR, Brooks CL. Novel generalized Born methods Journal of Chemical Physics. 116: 10606-10614. DOI: 10.1063/1.1480013  0.5
2001 Salsbury FR, Crowley MF, Brooks CL. Modeling of the metallo-beta-lactamase from B. fragilis: structural and dynamic effects of inhibitor binding. Proteins. 44: 448-59. PMID 11484222 DOI: 10.1002/Prot.1110  0.573
1998 Salsbury FR, Harris RA. Estimation of the Fermi contact contribution to the xenon-hydrogen and xenon-xenon spin-spin coupling constants Molecular Physics. 94: 307-312. DOI: 10.1080/002689798168187  0.418
1998 Salsbury FR, Harris RA. The origin of the magnetic-field-dependent quadrupolar splitting Journal of Chemical Physics. 109: 8338-8341. DOI: 10.1063/1.477627  0.399
1998 Harris RA, Salsbury FR. The exchange energy functional in a weak magnetic field Journal of Chemical Physics. 109: 2609-2613. DOI: 10.1063/1.476874  0.424
1998 Salsbury FR, Harris RA. A nonlocal current density functional for magnetic responses Journal of Chemical Physics. 108: 6102-6108. DOI: 10.1063/1.476319  0.398
1997 Salsbury FR, Harris RA. The current in magnetic field density functional theory and its application to the chemical shielding and magnetic susceptibility Journal of Chemical Physics. 107: 7350-7359. DOI: 10.1063/1.475165  0.42
Low-probability matches (unlikely to be authored by this person)
2011 Salsbury FR, Scarpinato K, Vasilyeva A. Conformational Selectivity:Targeting the “death” Conformation of Mutsalpha Biophysical Journal. 100: 379a. DOI: 10.1016/J.Bpj.2010.12.2255  0.293
2006 Salsbury FR. Analysis of errors in Still's equation for macromolecular electrostatic solvation energies Molecular Physics. 104: 1299-1309. DOI: 10.1080/00268970500525879  0.259
2020 Guinto FC, Alexander RW, Salsbury FR. Dissecting Contributions to Efficient Catalysis in the tRNA Modifying Enzyme TilS Biophysical Journal. 118: 194a. DOI: 10.1016/J.Bpj.2019.11.1172  0.221
2012 Baiz D, Pinder TA, Hassan S, Karpova Y, Salsbury F, Welker ME, Kulik G. Synthesis and characterization of a novel prostate cancer-targeted phosphatidylinositol-3-kinase inhibitor prodrug. Journal of Medicinal Chemistry. 55: 8038-46. PMID 22924393 DOI: 10.1021/Jm300881A  0.213
2023 Wu D, Salsbury FR. Unraveling the Role of Hydrogen Bonds in Thrombin via Two Machine Learning Methods. Journal of Chemical Information and Modeling. 63: 3705-3718. PMID 37285464 DOI: 10.1021/acs.jcim.3c00153  0.185
2013 AbdelHafez EM, Diamanduros A, Negureanu L, Luy Y, Bean JH, Zielke K, Crowe B, Vasilyeva A, Clodfelter JE, Aly OM, Abuo-Rahma GE, Scarpinato KD, Salsbury FR, King SB. Computational and synthetic studies towards improving rescinnamine as an inducer of MSH2-dependent apoptosis in cancer treatment. Molecular Cancer Biology. 1. PMID 25485184  0.153
2015 Lu Y, Salsbury FR. Recapturing the correlated motions of protein using coarse-grained models Protein and Peptide Letters. 22: 654-659.  0.148
2014 Stuart CH, Horita DA, Thomas MJ, Salsbury FR, Lively MO, Gmeiner WH. Site-specific DNA-doxorubicin conjugates display enhanced cytotoxicity to breast cancer cells. Bioconjugate Chemistry. 25: 406-13. PMID 24450459 DOI: 10.1021/bc4005427  0.138
2004 Thomas LR, Henson A, Reed JC, Salsbury FR, Thorburn A. Direct binding of Fas-associated death domain (FADD) to the tumor necrosis factor-related apoptosis-inducing ligand receptor DR5 is regulated by the death effector domain of FADD. The Journal of Biological Chemistry. 279: 32780-5. PMID 15173180 DOI: 10.1074/Jbc.M401680200  0.115
2021 Hemphill WO, Simpson SR, Liu M, Salsbury FR, Hollis T, Grayson JM, Perrino FW. TREX1 as a Novel Immunotherapeutic Target. Frontiers in Immunology. 12: 660184. PMID 33868310 DOI: 10.3389/fimmu.2021.660184  0.097
1997 Salsbury FR, Harris RA. Hydrogen chemical shieldings in small molecules: A magnetic field density functional approach Chemical Physics Letters. 279: 247-251.  0.089
2022 Ghoneum A, Gonzalez D, Afify H, Shu J, Hegarty A, Adisa J, Kelly M, Lentz S, Salsbury F, Said N. Compound C Inhibits Ovarian Cancer Progression via PI3K-AKT-mTOR-NFκB Pathway. Cancers. 14. PMID 36291886 DOI: 10.3390/cancers14205099  0.068
1998 Salsbury FR, Harris RA. A nonlocal current density functional for magnetic responses Journal of Chemical Physics. 108: 6102-6108.  0.04
1998 Salsbury FR, Harris RA. Estimation of the Fermi contact contribution to the xenon-hydrogen and xenon-xenon spin-spin coupling constants Molecular Physics. 94: 307-312.  0.04
1997 Salsbury FR, Harris RA. The current in magnetic field density functional theory and its application to the chemical shielding and magnetic susceptibility Journal of Chemical Physics. 107: 7350-7359.  0.037
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