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Software
ProS2Vi (V 1.0.1): a Python Tool for Visualizing Proteins Secondary Structure
Qasim. M. L., Alisaraie. L., DOI:10.5281/zenodo.12554830, June 26, 2024
The source code is freely available ON:GitHUb PAGE of The Alisaraie GROUP: https://github.com/Alisaraie-Group/ProS2Vi
Zenodo Page of The Alisaraie Group: https://zenodo.org/records/12554831
Dataset
PDBpepDS (V 0.1.0): This comprehensive dataset of peptides was created using all the protein files deposited in RCSB as of Nov. 2023.
Qasim. M. L., Alisaraie. L., doi:10.5281/zenodo.13625563, September 1, 2024
GitHUb PAGE of The Alisaraie GROUP: https://github.com/Alisaraie-Group/PDBpepDS
Zenodo Page of The Alisaraie Group: https://zenodo.org/records/13625563
Journal Publications
ProS2Vi: a Python Tool for Visualizing Proteins Secondary Structure
Qasim. L, Alisaraie. L.
arxiv (Biomolecules), August 6, 2024, https://doi.org/10.48550/arXiv.2408.03436PRECLINICAL EVALUATION OF PEG-MULTIWALLED CARBON NANOTUBES: RADIOLABELING, BIODISTRIBUTION, AND TOXICITY IN MICE
Lemos. J, Soares. D, Pereira. N, Gomides. L, Silva. J, Bruch. G, Cassali. G, Alisaraie. L, Alves. R, Santos. A, de Barros. A.
Journal of Drug Delivery Science and Technology, 2023, 86, September issue, 104606-104617Recruitment of Dynein and Kinesin to Viral Particles
Tati. S, Alisaraie. L.
The FASEB Journal, 2022, 36, 5, 1-18journal Front cover artwork
alisaraie. l.
RSC Molecular Systems Design & Engineering (MSDE), 2022, issue 4
Photos of the Butterfly by Eloi Roobol and the Iceberg by Oliver Stueker were used with permission.Microtubule-Inspired Functionalization of Carbon Nanotubes: A Biomimetic Carrier Design. *
Barcelos. K, Alisaraie. L.
RSC Molecular Systems Design & Engineering (MSDE), 2022, 7, 4, 330-349
*: Selected for the cover of the 2022 April issueAnalysis of The Structural Mechanism of ATP Inhibition at the AAA1 Subunit of Cytoplasmic Dynein-1 Using a Chemical "Toolkit"
Tati. S, Alisaraie. L.
International journal of molecular sciences – biochemistry section, 2021, 22, 14, 7704-7730c-terminal tail of β-tubulin and its role in the alterations of dynein binding mode
heale. k, alisaraie. l.
cell biochemistry and biophysics, 2020, 78, 331–345Journal Front Cover artwork
Heale. K, Tozer. T and Alisaraie. L.
chemical biology & drug design, 2019, Issue 5interdomain twists of human thymidine phosphorylase: binding of 5-fu and its analogues to htp vs. dpd. *
tozer. t, heale. k, manto chagas. c, de barros. a, alisaraie. l.
chemical biology & drug design, 2019, 1956-1972
*: Selected for the cover of the 2019 November issuemetabolites of vinca alkaloid vinblastine: tubulin binding and activation of nausea associated receptors
manto chagas. c, alisaraie. l.
acs omega, 2019, 4, 6, 9784–9799carboxylated versus bisphosphonate swcnt: functionalization effects on the biocompatibility and in vivo behaviors in tumor-bearing mice
fernandes. s, lemos. a, de barros. a, geraldo. v, silva. e, alisaraie. l, soares. d.
journal of drug delivery science and technology, 2019, 50, 266-277drug metabolites and their effects on the development of adverse reactions: revisiting lipinski's rule of five
manto chagas. c, moss. s, alisaraie. l.
international journal of pharmaceutics, 2018, 549, 133-149mechanism of off-target interactions and toxicity of tamoxifen and its metabolites
flynn. m, heale. k, alisaraie. l.
acs chemical research in toxicology, 2017, 30, 7, 1492-1507functionalized single-walled carbon nanotubes: cellular uptake, biodistribution and applications in drug delivery
li. z, branco de barros. a, cristian ferreira soares. d, moss. s, alisaraie. l.
international journal of pharmaceutics, 2017, 1-2, 41-45insight into the mechanism of chemical modification of antibacterial agents by antibiotic resistance enzyme o-phosphotransferase-iii
power. b, smith. n, downer. b, alisaraie. l.
chemical biology & drug design, 2017, 89, 1, 84-97molecular dynamics studies for optimization of non-covalent loading of vinblastine on single-walled carbon nanotube
li. z, tozer. t, alisaraie. l.
acs journal of physical chemistry c, 2016, 120, 7, 4061-4070molecular assembly of lethal factor enzyme and pre-pore heptameric protective antigen in early stage of translocation
alisaraie. l, rouiller. i.
journal of molecular modeling, 2016, 22, 1, 7-12microtubules dual chemo and thermo-responsive depolymerisation
li. z and alisaraie. l.
proteins: structure, function and bioinformatics, 2015, 83, 5, 970-981dynamic change of heme environment in soluble guanylate cyclase and complexation of no-independent drug agents with h-nox domains
alisaraie. l, fu. y, tuszynski. J.
j. chem. bio. drug. des., 2013, 81, 3, 359-81Modeling the Yew Tree Tubulin and a Comparison of its Interaction with Paclitaxel to Human Tubulin
Tuszynski. J, Craddock. T, Mane. J, Tseng. C, Gajewski. M, Winter. P, Alisaraie. L. et al.
Pharm. Res., 2012, 29, 11, 3007-21
Peloruside, Laulimalide, and Noscapine Interactions with Beta-Tubulin
Gajewski. M, Alisaraie. L, Tuszynski. J.
Pharm. Res., 2012, 29, 11, 2985-93full-length structural model of ret3 and sec21 in copi: identification of binding sites for accessory protein recruitment motifs
alisaraie. l, rouiller. i.
j. mol. mod., 2012, 18, 7, 3199-3212determination of noscapine’s localization and interaction with tubulin-α/β heterodimer
alisaraie. l, tuszynski. J.
j. chem. bio. drug. des., 2011, 78, 4, 535-545protein tyrosine phosphatases are regulated by mononuclear iron dicitrate
gomez. m, alisaraie. l, shio. m, berghuis. a, olivier. m.
j. biol. chem., 2010, 285, 24620-24628A QXP-based Multi-Step Docking Procedure for Accurately Prediction of Protein-Ligand Complexes
Alisaraie. L, Haller. L, Fels. GACS J. Chem. Inf. Mod., 2006, 46, 1174-1187
Molecular Docking Study on the "Back Door" Hypothesis for Product Clearance in Acetylcholinesterase
Alisaraie. L, Fels. GJ. Mol. Mod., 2006, 12, 348-354