Anthony A. Armstrong, Ph.D. - Related publications

2007 Johns Hopkins University, Baltimore, MD 
General Biophysics
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50 most relevant papers in past 60 days:
Year Citation  Score
2021 Li Y, Bedi RK, Wiedmer L, Sun X, Huang D, Caflisch A. Atomistic and Thermodynamic Analysis of N6-Methyladenosine (mA) Recognition by the Reader Domain of YTHDC1. Journal of Chemical Theory and Computation. PMID 33472367 DOI: 10.1021/acs.jctc.0c01136   
2021 Arouche TDS, Martins AY, Ramalho TC, Júnior RNC, Costa FLP, Filho TSA, Neto AMJC. Molecular Docking of Azithromycin, Ritonavir, Lopinavir, Oseltamivir, Ivermectin and Heparin Interacting with Coronavirus Disease 2019 Main and Severe Acute Respiratory Syndrome Coronavirus-2 3C-Like Proteases. Journal of Nanoscience and Nanotechnology. 21: 2075-2089. PMID 33500022 DOI: 10.1166/jnn.2021.19029   
2021 Khan S, Fakhar Z, Ahmad A. Targeting ebola virus VP40 protein through novel inhibitors: exploring the structural and dynamic perspectives on molecular landscapes. Journal of Molecular Modeling. 27: 49. PMID 33495861 DOI: 10.1007/s00894-021-04682-8   
2021 Escalante DE, Ferguson DM. Structural modeling and analysis of the SARS-CoV-2 cell entry inhibitor camostat bound to the trypsin-like protease TMPRSS2. Medicinal Chemistry Research : An International Journal For Rapid Communications On Design and Mechanisms of Action of Biologically Active Agents. 1-11. PMID 33564221 DOI: 10.1007/s00044-021-02708-7   
2021 Yadav S, Pandey V, Kumar Tiwari R, Ojha RP, Dubey KD. Does Antibody Stabilize the Ligand Binding in GP120 of HIV-1 Envelope Protein? Evidence from MD Simulation. Molecules (Basel, Switzerland). 26. PMID 33466381 DOI: 10.3390/molecules26010239   
2021 Dandekar PD, Kotmale AS, Chavan SR, Kadlag PP, Sawant SV, Dhavale DD, RaviKumar A. Insights into the Inhibition Mechanism of Human Pancreatic α-Amylase, a Type 2 Diabetes Target, by Dehydrodieugenol B Isolated from . Acs Omega. 6: 1780-1786. PMID 33521419 DOI: 10.1021/acsomega.0c00617   
2021 Gonda A, Takada K, Yanagita RC, Dan S, Irie K. Effects of side chain length of 10-methyl-aplog-1, a simplified analog of debromoaplysiatoxin, on PKC binding, anti-proliferative, and pro-inflammatory activities. Bioscience, Biotechnology, and Biochemistry. 85: 168-180. PMID 33577665 DOI: 10.1093/bbb/zbaa024   
2021 Wang X, Li W. Comparative Study of Interactions between Human cGAS and Inhibitors: Insights from Molecular Dynamics and MM/PBSA Studies. International Journal of Molecular Sciences. 22. PMID 33503880 DOI: 10.3390/ijms22031164   
2021 Liu Y, Parks FC, Sheetz EG, Chen CH, Flood AH. Polarity-Tolerant Chloride Binding in Foldamer Capsules by Programmed Solvent-Exclusion. Journal of the American Chemical Society. PMID 33596052 DOI: 10.1021/jacs.0c12562   
2021 Labra-Núñez A, Cofas-Vargas LF, Gutiérrez-Magdaleno G, Gómez-Velasco H, Rodríguez-Hernández A, Rodríguez-Romero A, García-Hernández E. Energetic and structural effects of the Tanford transition on ligand recognition of bovine β-lactoglobulin. Archives of Biochemistry and Biophysics. 699: 108750. PMID 33421379 DOI: 10.1016/   
2021 Labra-Núñez A, Cofas-Vargas LF, Gutiérrez-Magdaleno G, Gómez-Velasco H, Rodríguez-Hernández A, Rodríguez-Romero A, García-Hernández E. Energetic and structural effects of the Tanford transition on ligand recognition of bovine β-lactoglobulin. Archives of Biochemistry and Biophysics. 699: 108750. PMID 33421379 DOI: 10.1016/   
2021 Zhu M, Song LT, Liu RR, Zhai HL, Meng YJ, Ren CL. Selective inhibition mechanism of nitroxoline to the BET family: Insight from molecular simulations. Life Sciences. 119141. PMID 33529672 DOI: 10.1016/j.lfs.2021.119141   
2021 Shah S, Chaple D, Arora S, Yende S, Mehta C, Nayak U. Prospecting for to treat COVID-19 via molecular docking models of the SARS-CoV-2. Journal of Biomolecular Structure & Dynamics. 1-9. PMID 33446077 DOI: 10.1080/07391102.2021.1872419   
2021 Naves LFN, Borges NM, Custodio JMF, Vaz WF, Bastos RM, Cunha S, Napolitano HB. Structural insights into the biological activity of a thioxopyrimidine derivative. Journal of Molecular Modeling. 27: 73. PMID 33547505 DOI: 10.1007/s00894-021-04700-9   
2021 He J, Han Z, Farooq QUA, Li C. Study on functional sites in human multidrug resistance protein 1 (hMRP1). Proteins. PMID 33469960 DOI: 10.1002/prot.26049   
2021 Fleetwood O, Carlsson J, Delemotte L. Identification of ligand-specific G-protein coupled receptor states and prediction of downstream efficacy via data-driven modeling. Elife. 10. PMID 33506760 DOI: 10.7554/eLife.60715   
2021 Yu HS, Modugula K, Ichihara O, Kramschuster K, Keng S, Abel R, Wang L. General Theory of Fragment Linking in Molecular Design: Why Fragment Linking Rarely Succeeds and How to Improve Outcomes. Journal of Chemical Theory and Computation. 17: 450-462. PMID 33372778 DOI: 10.1021/acs.jctc.0c01004   
2021 Makley LN, Johnson OT, Ghanakota P, Rauch JN, Osborn D, Wu TS, Cierpicki T, Carlson HA, Gestwicki JE. Chemical validation of a druggable site on Hsp27/HSPB1 using in silico solvent mapping and biophysical methods. Bioorganic & Medicinal Chemistry. 34: 115990. PMID 33549906 DOI: 10.1016/j.bmc.2020.115990   
2021 Mahmud S, Uddin MAR, Paul GK, Shimu MSS, Islam S, Rahman E, Islam A, Islam MS, Promi MM, Emran TB, Saleh MA. Virtual screening and molecular dynamics simulation study of plant-derived compounds to identify potential inhibitors of main protease from SARS-CoV-2. Briefings in Bioinformatics. PMID 33517367 DOI: 10.1093/bib/bbaa428   
2021 Feinberg H, Jégouzo SAF, Lasanajak Y, Smith DF, Drickamer K, Weis WI, Taylor ME. Structural analysis of carbohydrate binding by the macrophage mannose receptor CD206. The Journal of Biological Chemistry. 100368. PMID 33545173 DOI: 10.1016/j.jbc.2021.100368   
2021 Sharma A, Kumari S, Goel M. Uncovering the structure-function aspects of an archaeal CsaA protein. Biochimica Et Biophysica Acta. Proteins and Proteomics. 140615. PMID 33561579 DOI: 10.1016/j.bbapap.2021.140615   
2021 Raich L, Meier K, Günther J, Christ CD, Noé F, Olsson S. Discovery of a hidden transient state in all bromodomain families. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33468647 DOI: 10.1073/pnas.2017427118   
2021 He X, Huang N, Qiu Y, Zhang J, Liu Y, Yin XL, Lu S. Conformational Selection Mechanism Provides Structural Insights into the Optimization of APC-Asef Inhibitors. Molecules (Basel, Switzerland). 26. PMID 33670371 DOI: 10.3390/molecules26040962   
2021 Wu SL, Zhao J, Sun HB, Li HY, Yin YY, Zhang LL. Insights into interaction mechanism of inhibitors E3T, E3H and E3B with CREB binding protein by using molecular dynamics simulations and MM-GBSA calculations. Sar and Qsar in Environmental Research. 32: 221-246. PMID 33661069 DOI: 10.1080/1062936X.2021.1887351   
2021 Freidel MR, Armen RS. Mapping major SARS-CoV-2 drug targets and assessment of druggability using computational fragment screening: Identification of an allosteric small-molecule binding site on the Nsp13 helicase. Plos One. 16: e0246181. PMID 33596235 DOI: 10.1371/journal.pone.0246181   
2021 Kwofie SK, Broni E, Asiedu SO, Kwarko GB, Dankwa B, Enninful KS, Tiburu EK, Wilson MD. Cheminformatics-Based Identification of Potential Novel Anti-SARS-CoV-2 Natural Compounds of African Origin. Molecules (Basel, Switzerland). 26. PMID 33466743 DOI: 10.3390/molecules26020406   
2021 Jakhmola S, Hazarika Z, Jha AN, Jha HC. analysis of antiviral phytochemicals efficacy against Epstein-Barr virus glycoprotein H. Journal of Biomolecular Structure & Dynamics. 1-14. PMID 33438528 DOI: 10.1080/07391102.2020.1871074   
2021 Dalal V, Dhankhar P, Singh V, Singh V, Rakhaminov G, Golemi-Kotra D, Kumar P. Structure-Based Identification of Potential Drugs Against FmtA of Staphylococcus aureus: Virtual Screening, Molecular Dynamics, MM-GBSA, and QM/MM. The Protein Journal. PMID 33421024 DOI: 10.1007/s10930-020-09953-6   
2021 Sillen M, Miyata T, Vaughan DE, Strelkov SV, Declerck PJ. Structural Insight into the Two-Step Mechanism of PAI-1 Inhibition by Small Molecule TM5484. International Journal of Molecular Sciences. 22. PMID 33540702 DOI: 10.3390/ijms22031482   
2021 Gupta M, Venkatramani R, Ainavarapu SRK. Role of Ligand Binding Site in Modulating the Mechanical Stability of Proteins with β-Grasp Fold. The Journal of Physical Chemistry. B. PMID 33492970 DOI: 10.1021/acs.jpcb.0c08085   
2021 Romero-Tamayo S, Laplaza R, Velazquez-Campoy A, Villanueva R, Medina M, Ferreira P. W196 and the -Hairpin Motif Modulate the Redox Switch of Conformation and the Biomolecular Interaction Network of the Apoptosis-Inducing Factor. Oxidative Medicine and Cellular Longevity. 2021: 6673661. PMID 33510840 DOI: 10.1155/2021/6673661   
2021 Ching WY, Adhikari P, Jawad B, Podgornik R. Ultra-large-scale quantum chemical computation of bio-molecular systems: the case of Spike protein of SARS-CoV-2 virus. Computational and Structural Biotechnology Journal. PMID 33623641 DOI: 10.1016/j.csbj.2021.02.004   
2021 Rai H, Barik A, Singh YP, Suresh A, Singh L, Singh G, Nayak UY, Dubey VK, Modi G. Molecular docking, binding mode analysis, molecular dynamics, and prediction of ADMET/toxicity properties of selective potential antiviral agents against SARS-CoV-2 main protease: an effort toward drug repurposing to combat COVID-19. Molecular Diversity. PMID 33582935 DOI: 10.1007/s11030-021-10188-5   
2021 Quesada Moreno MM, Pinacho P, Perez C, Sekutor M, Schreiner PR, Schnell M. Do docking sites persist upon fluorination? The diadamantyl ether-aromatics challenge for rotational spectroscopy and theory. Chemistry (Weinheim An Der Bergstrasse, Germany). PMID 33512017 DOI: 10.1002/chem.202100078   
2021 Kumari R, Dhankhar P, Dalal V. Structure-based mimicking of hydroxylated biphenyl congeners (OHPCBs) for human transthyretin, an important enzyme of thyroid hormone system. Journal of Molecular Graphics & Modelling. 105: 107870. PMID 33647754 DOI: 10.1016/j.jmgm.2021.107870   
2021 Lopez A, Havranek B, Papadantonakis GA, Islam SM. In-Silico Screening and Molecular Dynamics Simulation of Deleterious PAH Mutations Responsible for Phenylketonuria (PKU) Genetic Disorder. Proteins. PMID 33491267 DOI: 10.1002/prot.26051   
2021 Mohapatra RK, Perekhoda L, Azam M, Suleiman M, Sarangi AK, Semenets A, Pintilie L, Al-Resayes SI. Computational investigations of three main drugs and their comparison with synthesized compounds as potent inhibitors of SARS-CoV-2 main protease (M): DFT, QSAR, molecular docking, and in silico toxicity analysis. Journal of King Saud University. Science. 33: 101315. PMID 33390681 DOI: 10.1016/j.jksus.2020.101315   
2021 Sobhia ME, Ghosh K, Sivangula S, Kumar S, Singh H. Identification of potential SARS-CoV-2 M inhibitors integrating molecular docking and water thermodynamics. Journal of Biomolecular Structure & Dynamics. 1-11. PMID 33413032 DOI: 10.1080/07391102.2020.1867642   
2021 Diallo BN, Swart T, Hoppe HC, Tastan Bishop Ö, Lobb K. Potential repurposing of four FDA approved compounds with antiplasmodial activity identified through proteome scale computational drug discovery and in vitro assay. Scientific Reports. 11: 1413. PMID 33446838 DOI: 10.1038/s41598-020-80722-2   
2021 Williams-Noonan BJ, Todorova N, Kulkarni K, Aguilar MI, Yarovsky I. An Active Site Inhibitor Induces Conformational Penalties for ACE2 Recognition by the Spike Protein of SARS-CoV-2. The Journal of Physical Chemistry. B. PMID 33657325 DOI: 10.1021/acs.jpcb.0c11321   
2021 Song G, Luo BH. Effects of the association of the α β lower legs on integrin ligand binding. Journal of Cellular Biochemistry. PMID 33619784 DOI: 10.1002/jcb.29912   
2021 Shrestha R, Fajardo JE, Fiser A. Residue-based pharmacophore approaches to study protein-protein interactions. Current Opinion in Structural Biology. 67: 205-211. PMID 33486430 DOI: 10.1016/   
2021 Wang W, Zhu Y, Abraham N, Li XZ, Kimber M, Zhou T. The Ribosome-Binding Mode of Trichothecene Mycotoxins Rationalizes Their Structure-Activity Relationships. International Journal of Molecular Sciences. 22. PMID 33562610 DOI: 10.3390/ijms22041604   
2021 Yin YY, Zhao J, Zhang LL, Xu XY, Liu JQ. Molecular mechanisms of inhibitor bindings to A-FABP deciphered by using molecular dynamics simulations and calculations of MM-GBSA. Sar and Qsar in Environmental Research. 1-23. PMID 33655818 DOI: 10.1080/1062936X.2021.1891966   
2021 Ajadi MB, Soremekun OS, Elrashedy AA, Olotu FA, Kumalo HM, Soliman MES. Probing Protein-Protein Interactions and Druggable Site Identification: Mechanistic Binding Events between Ubiquitin and Zinc Finger with UFM1-Specific Peptidase Domain Protein (ZUFSP). Combinatorial Chemistry & High Throughput Screening. PMID 33538664 DOI: 10.2174/1386207324666210203175142   
2021 Liu J, Zhai Y, Liang L, Zhu D, Zhao Q, Qiu Y. Molecular modeling evaluation of the binding effect of five protease inhibitors to COVID-19 main protease. Chemical Physics. 542: 111080. PMID 33519023 DOI: 10.1016/j.chemphys.2020.111080   
2021 Tomlinson CWE, Cornish KAS, Whiting A, Pohl E. Structure-functional relationship of cellular retinoic acid-binding proteins I and II interacting with natural and synthetic ligands. Acta Crystallographica. Section D, Structural Biology. 77: 164-175. PMID 33559606 DOI: 10.1107/S2059798320015247   
2021 Guo J, Li M, Zhang Y, Xi L, Cui F. Conformational dynamics is critical for the allosteric inhibition of cGAS upon acetyl-mimic mutations. Physical Chemistry Chemical Physics : Pccp. PMID 33438687 DOI: 10.1039/d0cp05871h   
2021 Rynkiewicz P, Babbitt GA, Cui F, Hudson AO, Lynch ML. A comparative survey of Betacoronavirus binding dynamics relevant to the functional evolution of the highly transmissible SARS-CoV-2 variant N501Y. Biorxiv : the Preprint Server For Biology. PMID 33501438 DOI: 10.1101/2020.09.11.293258   
2021 Ham D, Ahn D, Ashim J, Cho Y, Kim HR, Yu W, Chung KY. Conformational switch that induces GDP release from Gi. Journal of Structural Biology. 107694. PMID 33418033 DOI: 10.1016/j.jsb.2020.107694