Nicoleta Economou - Related publications

Affiliations: 
2007-2012 Biochemistry and Molecular Biology Drexel University College of Medicine, Philadelphia, PA, United States 
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50 most relevant papers in past 60 days:
Year Citation  Score
2021 Egbert M, Ghani U, Ashizawa R, Kotelnikov S, Nguyen T, Desta I, Hashemi N, Padhorny D, Kozakov D, Vajda S. Assessing the binding properties of CASP14 targets and models. Proteins. PMID 34368994 DOI: 10.1002/prot.26209   
2021 Tanramluk D*, Pakotiprapha D, Phoochaijaroen S, Chantravisut P, Thampradid S, Vanichtanankul J, Narupiyakul L, Akavipat R, Yuvaniyama J. MANORAA: A machine learning platform to guide protein-ligand design by anchors and influential distances. Structure. PMID 34614393 DOI: 10.1016/j.str.2021.09.004   
2021 Sun Z, Zheng S, Zhao H, Niu Z, Lu Y, Pan Y, Yang Y. To improve the predictions of binding residues with DNA, RNA, carbohydrate, and peptide via multi-task deep neural networks. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 34637380 DOI: 10.1109/TCBB.2021.3118916   
2021 Sanches K, Wai DCC, Norton RS. Conformational dynamics in peptide toxins: Implications for receptor interactions and molecular design. Toxicon : Official Journal of the International Society On Toxinology. 201: 127-140. PMID 34454969 DOI: 10.1016/j.toxicon.2021.08.020   
2021 Metz A, Wollenhaupt J, Glöckner S, Messini N, Huber S, Barthel T, Merabet A, Gerber HD, Heine A, Klebe G, Weiss MS. Frag4Lead: growing crystallographic fragment hits by catalog using fragment-guided template docking. Acta Crystallographica. Section D, Structural Biology. 77: 1168-1182. PMID 34473087 DOI: 10.1107/S2059798321008196   
2021 Hassankalhori M, Bolcato G, Bissaro M, Sturlese M, Moro S. Shedding Light on the Molecular Recognition of Sub-Kilodalton Macrocyclic Peptides on Thrombin by Supervised Molecular Dynamics. Frontiers in Molecular Biosciences. 8: 707661. PMID 34532343 DOI: 10.3389/fmolb.2021.707661   
2021 Schwarz M, Eno RFM, Freitag-Pohl S, Coxon CR, Straker HE, Wortley DJ, Hughes DJ, Mitchell G, Moore J, Cummins I, Onkokesung N, Brazier-Hicks M, Edwards R, Pohl E, Steel PG. Flavonoid-based inhibitors of the Phi-class glutathione transferase from black-grass to combat multiple herbicide resistance. Organic & Biomolecular Chemistry. PMID 34643629 DOI: 10.1039/d1ob01802g   
2021 Parker JL, Deme JC, Wu Z, Kuteyi G, Huo J, Owens RJ, Biggin PC, Lea SM, Newstead S. Cryo-EM structure of PepT2 reveals structural basis for proton-coupled peptide and prodrug transport in mammals. Science Advances. 7. PMID 34433568 DOI: 10.1126/sciadv.abh3355   
2021 Kamenik AS, Singh I, Lak P, Balius TE, Liedl KR, Shoichet BK. Energy penalties enhance flexible receptor docking in a model cavity. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34475217 DOI: 10.1073/pnas.2106195118   
2021 Ayyamperumal S, Dj D, Tallapaneni V, Mohan S, S B, Selvaraj J, Joghee NM, Mjn C. Molecular docking analysis of α-Topoisomerase II with δ-Carboline derivatives as potential anticancer agents. Bioinformation. 17: 249-265. PMID 34393444 DOI: 10.6026/97320630017249   
2021 Sheikh AY, Mattei A, Miglani Bhardwaj R, Hong RS, Abraham NS, Schneider-Rauber G, Engstrom KM, Diwan M, Henry RF, Gao Y, Juarez V, Jordan E, DeGoey DA, Hutchins CW. Implications of the Conformationally Flexible, Macrocyclic Structure of the First-Generation, Direct-Acting Anti-Viral Paritaprevir on Its Solid Form Complexity and Chameleonic Behavior. Journal of the American Chemical Society. PMID 34637297 DOI: 10.1021/jacs.1c06837   
2021 Lü Y, Bai J, Tan D, Chen T, Shan A. [The effects of hinge structure on the biological activity of antimicrobial peptides and its application in molecular design: a review]. Sheng Wu Gong Cheng Xue Bao = Chinese Journal of Biotechnology. 37: 3142-3150. PMID 34622623 DOI: 10.13345/j.cjb.200728   
2021 Koneru JK, Sinha S, Mondal J. Molecular Dynamics Simulations Elucidate Oligosaccharide Recognition Pathways by Galectin-3 at Atomic Resolution. The Journal of Biological Chemistry. 101271. PMID 34619151 DOI: 10.1016/j.jbc.2021.101271   
2021 Vasta GR, Amzel LM. In Structural Glycobiology, Deuterium provides the Details. Structure (London, England : 1993). 29: 937-939. PMID 34478636 DOI: 10.1016/j.str.2021.08.004   
2021 Zhao J, Liu M, Zang J, Yang S, Chen R, Zhao X, Ding L. Molecular docking, 3D-QASR and molecular dynamics simulations of thiazoles Pin1 inhibitors. Journal of Biomolecular Structure & Dynamics. 1-15. PMID 34499020 DOI: 10.1080/07391102.2021.1975568   
2021 Smith SO. Deconstructing the transmembrane core of class A G protein-coupled receptors. Trends in Biochemical Sciences. PMID 34538727 DOI: 10.1016/j.tibs.2021.08.006   
2021 Pradhan P, Margolin W, Beuria TK. Targeting the Achilles Heel of FtsZ: The Interdomain Cleft. Frontiers in Microbiology. 12: 732796. PMID 34566937 DOI: 10.3389/fmicb.2021.732796   
2021 Li Q, Kang C. Structure and Dynamics of Zika Virus Protease and Its Insights into Inhibitor Design. Biomedicines. 9. PMID 34440248 DOI: 10.3390/biomedicines9081044   
2021 Toyama Y, Harkness RW, Kay LE. Dissecting the role of interprotomer cooperativity in the activation of oligomeric high-temperature requirement A2 protein. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34446566 DOI: 10.1073/pnas.2111257118   
2021 Maben Z, Arya R, Georgiadis D, Stratikos E, Stern LJ. Conformational dynamics linked to domain closure and substrate binding explain the ERAP1 allosteric regulation mechanism. Nature Communications. 12: 5302. PMID 34489420 DOI: 10.1038/s41467-021-25564-w   
2021 Xiao T, Sun L, Zhang M, Li Z, Haura EB, Schonbrunn E, Ji H. Synthesis and Structural Characterization of a Monocarboxylic Inhibitor for GRB2 SH2 Domain. Bioorganic & Medicinal Chemistry Letters. 128354. PMID 34506932 DOI: 10.1016/j.bmcl.2021.128354   
2021 Wallerstein J, Ekberg V, Ignjatović MM, Kumar R, Caldararu O, Peterson K, Wernersson S, Brath U, Leffler H, Oksanen E, Logan DT, Nilsson UJ, Ryde U, Akke M. Entropy-Entropy Compensation between the Protein, Ligand, and Solvent Degrees of Freedom Fine-Tunes Affinity in Ligand Binding to Galectin-3C. Jacs Au. 1: 484-500. PMID 34467311 DOI: 10.1021/jacsau.0c00094   
2021 Oyama T, Kamata S, Ishii I, Miyachi H. Crystal Structures of the Human Peroxisome Proliferator-Activated Receptor (PPAR)α Ligand-Binding Domain in Complexes with a Series of Phenylpropanoic Acid Derivatives Generated by a Ligand-Exchange Soaking Method. Biological & Pharmaceutical Bulletin. 44: 1202-1209. PMID 34471048 DOI: 10.1248/bpb.b21-00220   
2021 Tušar L, Usenik A, Turk B, Turk D. Mechanisms Applied by Protein Inhibitors to Inhibit Cysteine Proteases. International Journal of Molecular Sciences. 22. PMID 33498210 DOI: 10.3390/ijms22030997   
2021 Yang Y, Tang T, Li X, Michel T, Ling L, Huang Z, Mulaka M, Wu Y, Gao H, Wang L, Zhou J, Meunier B, Ke H, Jiang L, Rao Y. Design, synthesis, and biological evaluation of multiple targeting antimalarials. Acta Pharmaceutica Sinica. B. 11: 2900-2913. PMID 34589403 DOI: 10.1016/j.apsb.2021.05.008   
2021 Dey D, Ramakumar S, Conn GL. Targeted Redesign of Suramin Analogs for Novel Antimicrobial Lead Development. Journal of Chemical Information and Modeling. PMID 34516120 DOI: 10.1021/acs.jcim.1c00578   
2021 Navid A, Ahmad S, Sajjad R, Raza S, Azam SS. Structure Based in Silico Screening Revealed a Potent Acinetobacter baumannii Ftsz Inhibitor from Asinex Antibacterial Library. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 34375286 DOI: 10.1109/TCBB.2021.3103899   
2021 Debnath P, Bhaumik S, Sen D, Muttineni RK, Debnath S. Identification of SARS-CoV-2 Main Protease Inhibitors Using Structure Based Virtual Screening and Molecular Dynamics Simulation of DrugBank Database. Chemistryselect. 6: 4991-5013. PMID 34541295 DOI: 10.1002/slct.202100854   
2021 Uday RVS, Misra R, Harika A, Dolui S, Saha A, Pal U, Ravichandiran V, Maiti NC. Dabrafenib, idelalisib and nintedanib act as significant allosteric modulator for dengue NS3 protease. Plos One. 16: e0257206. PMID 34506566 DOI: 10.1371/journal.pone.0257206   
2021 Talapati SR, Goyal M, Nataraj V, Pothuganti M, Sreevidya MR, Gore S, Ramachandra M, Antony T, More SS, Rao NK. Structural and binding studies of Cyclin dependent kinase 2 with NU6140 inhibitor. Chemical Biology & Drug Design. PMID 34423559 DOI: 10.1111/cbdd.13941   
2021 Braun L, Schoen I, Vogel V. PIP-induced membrane binding of the Vinculin tail competes with its other binding partners. Biophysical Journal. PMID 34411575 DOI: 10.1016/j.bpj.2021.08.018   
2021 Abraham ET, Oecal S, Mörgelin M, Schmid PWN, Buchner J, Baumann U, Gebauer JM. Collagen's primary structure determines collagen:HSP47 complex stoichiometry. The Journal of Biological Chemistry. 101169. PMID 34487762 DOI: 10.1016/j.jbc.2021.101169   
2021 Gervasoni S, Spencer J, Hinchliffe P, Pedretti A, Vairoletti F, Mahler G, Mulholland AJ. A multiscale approach to predict the binding mode of metallo beta-lactamase inhibitors. Proteins. PMID 34455628 DOI: 10.1002/prot.26227   
2021 van Aalst E, Koneri J, Wylie BJ. In Silico Identification of Cholesterol Binding Motifs in the Chemokine Receptor CCR3. Membranes. 11. PMID 34436333 DOI: 10.3390/membranes11080570   
2021 Ascencio-Ibáñez JT, Bobay BG. Conserved Structural Motif Identified in Peptides That Bind to Geminivirus Replication Protein Rep. Biochemistry. PMID 34464102 DOI: 10.1021/acs.biochem.1c00408   
2021 Unarta IC, Xu J, Shang Y, Cheung CHP, Zhu R, Chen X, Cao S, Cheung PP, Bierer D, Zhang M, Huang X, Li X. Entropy of stapled peptide inhibitors in free state is the major contributor to the improvement of binding affinity with the GK domain. Rsc Chemical Biology. 2: 1274-1284. PMID 34458841 DOI: 10.1039/d1cb00087j   
2021 Suleman M, Yousafi Q, Ali J, Ali SS, Hussain Z, Ali S, Waseem M, Iqbal A, Ahmad S, Khan A, Wang Y, Wei DQ. Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. Computers in Biology and Medicine. 138: 104936. PMID 34655895 DOI: 10.1016/j.compbiomed.2021.104936   
2021 Behzadipour Y, Gholampour M, Pirhadi S, Seradj H, Khoshneviszadeh M, Hemmati S. Viral 3CL as a Target for Antiviral Intervention Using Milk-Derived Bioactive Peptides. International Journal of Peptide Research and Therapeutics. 1-14. PMID 34548852 DOI: 10.1007/s10989-021-10284-y   
2021 Liu Y, Shao X, Wang T, Wang X, Li N, Zhao Y, Xia W, Sun L. [Structure prediction and biological activity analysis of dybowskin-1ST antimicrobial peptide in Rana dybowskii]. Sheng Wu Gong Cheng Xue Bao = Chinese Journal of Biotechnology. 37: 2890-2902. PMID 34472306 DOI: 10.13345/j.cjb.200564   
2021 Altharawi A, Ahmad S, Alamri MA, Tahir Ul Qamar M. Structural insight into the binding pattern and interaction mechanism of chemotherapeutic agents with Sorcin by docking and molecular dynamic simulation. Colloids and Surfaces. B, Biointerfaces. 208: 112098. PMID 34509085 DOI: 10.1016/j.colsurfb.2021.112098   
2021 Dhusia K, Su Z, Wu Y. A structural-based machine learning method to classify binding affinities between TCR and peptide-MHC complexes. Molecular Immunology. 139: 76-86. PMID 34455212 DOI: 10.1016/j.molimm.2021.07.020   
2021 Johnson RM, Zhang X, Piper SJ, Nettleton TJ, Vandekolk TH, Langmead CJ, Danev R, Sexton PM, Wootten D. Cryo-EM structure of the dual incretin receptor agonist, peptide-19, in complex with the glucagon-like peptide-1 receptor. Biochemical and Biophysical Research Communications. 578: 84-90. PMID 34547628 DOI: 10.1016/j.bbrc.2021.09.016   
2021 Ngo ST, Vu KB, Pham MQ, Tam NM, Tran PT. Marine derivatives prevent MUS81 studies. Royal Society Open Science. 8: 210974. PMID 34527278 DOI: 10.1098/rsos.210974   
2021 Stenström O, Diehl C, Modig K, Nilsson UJ, Akke M. Mapping the energy landscape of protein-ligand binding linear free energy relationships determined by protein NMR relaxation dispersion. Rsc Chemical Biology. 2: 259-265. PMID 34458786 DOI: 10.1039/d0cb00229a   
2021 Essegian DJ, Cunningham TA, Zerio CJ, Chapman E, Schatz J, Schürer SC. Molecular Dynamics Simulations Identify Tractable Lead-like Phenyl-Piperazine Scaffolds as eIF4A1 ATP-competitive Inhibitors. Acs Omega. 6: 24432-24443. PMID 34604625 DOI: 10.1021/acsomega.1c02805   
2021 Tang R, Song Y, Shi M, Jiang Z, Zhang L, Xiao Y, Tian Y, Zhou S. Rational Design of a Dual-Targeting Natural Toxin-Like Bicyclic Peptide for Selective Bioenergetic Blockage in Cancer Cells. Bioconjugate Chemistry. PMID 34606715 DOI: 10.1021/acs.bioconjchem.1c00366   
2021 Heyne M, Shirian J, Cohen I, Peleg Y, Radisky ES, Papo N, Shifman JM. Climbing Up and Down Binding Landscapes through Deep Mutational Scanning of Three Homologous Protein-Protein Complexes. Journal of the American Chemical Society. PMID 34609866 DOI: 10.1021/jacs.1c08707   
2021 Egawa D, Ogiso T, Nishikata K, Yamamoto K, Itoh T. Structural Insights into the Loss-of-Function R288H Mutant of Human PPARγ. Biological & Pharmaceutical Bulletin. 44: 1196-1201. PMID 34471047 DOI: 10.1248/bpb.b21-00253   
2021 Sun L, Fu T, Zhao D, Fan H, Zhong S. Divide-and-link peptide docking: a fragment-based peptide docking protocol. Physical Chemistry Chemical Physics : Pccp. PMID 34596658 DOI: 10.1039/d1cp02098f   
2021 Pacheco-Garcia JL, Anoz-Carbonell E, Vankova P, Kannan A, Palomino-Morales R, Mesa-Torres N, Salido E, Man P, Medina M, Naganathan AN, Pey AL. Structural basis of the pleiotropic and specific phenotypic consequences of missense mutations in the multifunctional NAD(P)H:quinone oxidoreductase 1 and their pharmacological rescue. Redox Biology. 46: 102112. PMID 34537677 DOI: 10.1016/j.redox.2021.102112