Chromatographic analysis of selected phytosterols from Cyathea and their characterization by in silico docking to potential therapeutic targets by N. Janakiraman, J. Anne Wincy, M. Johnson, Ana Beatriz Herminia Ducati, Carlos Eduardo de Oliveira Soares, Claudia Saraiva de Alencar Beltrão, H.D.M. Coutinho

“…The 3D structure of the receptor proteins viz., 1VSN, 5BNQ, 6HN8, 7DN4 and 3TJU, and the 3D SDF structures of ligands like lupeol, stigmasterol and swertiamarin were retrieved from the Protein Data Bank (PDB) and NCBI-Pub Chem Compound database respectively. …”
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Profiling the Antidiabetic Potential of Compounds Identified from Fractionated Extracts of <i>Entada africana</i> toward Glucokinase Stimulation: Computational Insight by Sunday Amos Onikanni, Bashir Lawal, Valens Munyembaraga, Oluwafemi Shittu Bakare, Muhammad Taher, Junaidi Khotib, Deny Susanti, Babatunji Emmanuel Oyinloye, Lloyd Noriega, Ayodeji Famuti, Adewale Oluwaseun Fadaka, Basiru Olaitan Ajiboye

“…We retrieved the three-dimensional (3D) crystal structure of glucokinase (PDB ID: 4L3Q) from the online protein data bank and prepared it using the Maestro 13.5, Schrödinger Suite 2022-3. …”
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Insight into antioxidant-like activity and computational exploration of identified bioactive compounds in Talinum triangulare (Jacq.) aqueous extract as potential cholinesterase in... by Olakunle Bamikole Afolabi, Oluwaseun Ruth Olasehinde, Olutunmise Victoria Owolabi, Kikelomo Folake Jaiyesimi, Funmilayo Deborah Adewumi, Olajumoke Tolulope Idowu, Samson Olatunde Mabayoje, Adejoke Olukayode Obajuluwa, Oghenerobor Benjamin Akpor

“…Also, for computational analysis, identified bioactive compounds from AETt were docked using Schrodinger's GLIDE against human cholinesterase obtained from the protein data bank ( https://www.rcsb.org/ ). Results The results revealed that AETt exhibited a significant concentration-dependent inhibition against ABTS cation radicals (IC50 = 308.26 ± 4.36 µg/ml) with butylated hydroxytoluene (BHT) as the reference. …”
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Combinatorial approach of vitamin C derivative and anti-HIV drug-darunavir against SARS-CoV-2 by Alaka Sahoo, Shasank S. Swain, Biswaranjan Paital, Maitreyee Panda

“…Initially, the chemical structures used as ligands from PubChem and the target protein, SARS-CoV-2 main protease (PDB ID: 6Y84) from the protein data bank were retrieved for this study. Further, assess the potency, toxicity, drug-ability, and pharmacokinetics profiles using several bioinformatics tools, viz., molecular docking by the AutoDock 4.1 software with predicting activity spectra for substances, Molsoft, ProTox, and SwissADME tools. …”
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SeqCP: A sequence-based algorithm for searching circularly permuted proteins by Chi-Chun Chen, Yu-Wei Huang, Hsuan-Cheng Huang, Wei-Cheng Lo, Ping-Chiang Lyu

“…SeqCP was trained by data obtained from the Circular Permutation Database and tested with nonredundant datasets from the Protein Data Bank. It shows high reliability in CP identification and achieves an AUC of 0.9. …”
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Data for molecular dynamics simulations of B-type cytochrome c oxidase with the Amber force field by Longhua Yang, Åge A. Skjevik, Wen-Ge Han Du, Louis Noodleman, Ross C. Walker, Andreas W. Götz

“…Based on the high resolution (1.8 Å) X-ray crystal structure of the ba3-type CcO from Thermus thermophilus (Protein Data Bank ID number PDB: 3S8F), we built a model that is embedded in a POPC lipid bilayer membrane and solvated with TIP3P water molecules and counterions. …”
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In silico characterization of the GH5-cellulase family from uncultured microorganisms: physicochemical and structural studies by Rahmat Eko Sanjaya, Kartika Dwi Asni Putri, Anita Kurniati, Ali Rohman, Ni Nyoman Tri Puspaningsih

“…The amino acid sequences and 3D-protein structures were retrieved from the GenBank Database and Protein Data Bank. The physicochemical analysis revealed the sequence length was roughly 332–751 amino acids, with the molecular weight range around 37–83 kDa, dominantly negative charges with pI values below 7. …”
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Comparison of Steroid Hormone Hydroxylations by and Docking to Human Cytochromes P450 3A4 and 3A5 by Toshiro Niwa, Kanae Narita, Ayaka Okamoto, Norie Murayama, Hiroshi Yamazaki

“…Docking simulations of these substrates to the heme moiety of reported crystal structures of CYP3A4 (Protein Data Bank code ITQN) and CYP3A5 (6MJM) were conducted. …”
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Protective Effect of the Anthocyanidin Extract of Hippophae rhamnoides L. on H1299 Cell Injury Induced by Hydrogen Peroxide and Effect of Nrf2/HO-1 Pathway by Yurong ZHENG, Long CHEN, Xiao WANG, Jun LI, Baoguo LI

“…At last, the research collaboratory for structural bioinformatics (RCSB) protein data bank and AutoDock software were used to verify the molecular docking between epicatechin and Nrf2, the key target protein of oxidative stress. …”
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Au courant computation of the PDB to audit diffraction anisotropy of soluble and membrane proteins by Xavier Robert, Josiane Kassis-Sahyoun, Nicoletta Ceres, Juliette Martin, Michael R. Sawaya, Randy J. Read, Patrice Gouet, Pierre Falson, Vincent Chaptal

“…This data article makes available the informed computation of the whole Protein Data Bank (PDB) to investigate diffraction anisotropy on a large scale and to perform statistics. …”
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Anti-Toxoplasma gondii effect of lupane-type triterpenes from the bark of black alder (Alnus glutinosa) and identification of a potential target by reverse docking by Darme Pierre, Escotte-Binet Sandie, Cordonnier Julien, Remy Simon, Hubert Jane, Sayagh Charlotte, Borie Nicolas, Villena Isabelle, Voutquenne-Nazabadioko Laurence, Dauchez Manuel, Baud Stéphanie, Renault Jean-Hugues, Aubert Dominique

“…A dataset of 87 T. gondii proteins from the Protein Data Bank was created. It identified calcium-dependent protein kinase CDPK3 as the most likely target of betulin derivatives.…”
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The antiviral activity of a small molecule drug targeting the NSP1-ribosome complex against Omicron, especially in elderly patients by Min Shen, Min Shen, Ping Ding, Guangxin Luan, Ting Du, Shanshan Deng

“…A virtual drug screening method based on the Nsp1 structure (Protein Data Bank ID: 7K5I) was constructed, 7495 compounds from three databases were collected for molecular docking and virtual screening, and the binding free energy was calculated by the MM/GBSA method.ResultsOur study shows that Nsp1 is relatively conserved and can be used as a comparatively fixed drug target and that therapies against Nsp1 will target all of these variants. …”
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Exploiting whole-PDB analysis in novel bioinformatics applications by Ramraj, V

“…<p>The Protein Data Bank (PDB) is the definitive electronic repository for experimentally-derived protein structures, composed mainly of those determined by X-ray crystallography. …”

Data driven approaches to improve the drug discovery process: a virtual screening quest in drug discovery by Ebejer, JP

“…This bodes well for Ligity's future use, especially when considering that protein structure databases such as the Protein Data Bank are growing exponentially every year.…”

Sub-atomic resolution X-ray crystallography and neutron crystallography: promise, challenges and potential by Matthew P. Blakeley, Samar S. Hasnain, Svetlana V. Antonyuk

“…The International Year of Crystallography saw the number of macromolecular structures deposited in the Protein Data Bank cross the 100000 mark, with more than 90000 of these provided by X-ray crystallography. …”
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Functional and Structural Insights into the Human PPARα/δ/γ Targeting Preferences of Anti-NASH Investigational Drugs, Lanifibranor, Seladelpar, and Elafibranor by Shotaro Kamata, Akihiro Honda, Ryo Ishikawa, Makoto Akahane, Ayane Fujita, Chihiro Kaneko, Saeka Miyawaki, Yuki Habu, Yui Shiiyama, Kie Uchii, Yui Machida, Takuji Oyama, Isao Ishii

“…Seven high-resolution cocrystal structures (namely, those of the PPARα/δ/γ-ligand-binding domain (LBD)–lanifibranor, PPARα/δ/γ-LBD–seladelpar, and PPARα-LBD–elafibranor) were obtained through X-ray diffraction analyses, six of which represent the first deposit in the Protein Data Bank. Lanifibranor and seladelpar were found to bind to different regions of the PPARα/δ/γ-ligand-binding pockets and activated all PPAR subtypes with different potencies and efficacies in the three assays. …”
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Identification of vaccine candidates against rhodococcus equi by combining pangenome analysis with a reverse vaccinology approach by Lu Liu, Wanli Yu, Kuojun Cai, Siyuan Ma, Yanfeng Wang, Yuhui Ma, Hongqiong Zhao

“…All 12 vaccine candidates have an experimentally validated 3D structure available in the protein data bank (PDB). Epitope mapping of the candidates showed that 16 MHC I epitopes and 13 MHC II epitopes with the strongest immunogenicity were exposed on the protein surface, indicating that they could be used to develop a polypeptide vaccine. …”
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Synthesis and properties of 3-(ethylthio)-9-methyl-6-(alkylthio)pyrazolo[1,5-d][1,2,4]triazolo[3,4-f][1,2,4]triazines by S. O. Fedotov, A. S. Hotsulia

“…Cyclooxygenase-2, lanosterol-14α-demethylase and receptor tyrosine kinase were selected as model enzymes for docking, the crystal structure of which was loaded from the Protein Data Bank. Results. The synthesis of 3-(ethylthio)-9-methyl-6-(alkylthio)-pyrazolo[1,5-d][1,2,4]triazolo[3,4-f][1,2,4]triazines were carried out and the optimal conditions for the production of these substances were determined. …”
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Inhibitory activity of Enhydra fluctuans Lour. on calcium oxalate crystallisation through in silico and in vitro studies by Bornika Chattaraj, Arijit Nandi, Anwesha Das, Amit Sharma, Yadu Nandan Dey, Dharmendra Kumar, Mogana R

“…Baicalein-7-O-diglucoside and 4′,5,6,7-Tetrahydroxy-8-methoxy isoflavone-7-O-beta-D- galactopyranosyl-(1→3)-O-beta-D-xylopyranosyl-(1→4)- O-alpha-L-rhamnopyranoside showed modulatory effects on the four renal stone matrix-associated protein (Human CTP: Phosphoethanolamine Cytidylyltransferase (Protein Data Bank ID: 3ELB), UDP glucose: glycoprotein glucosyltransferase 2 (Gene: UGGT2) (AlphaFold) and RIMS-binding protein 3A (Gene: RIMBP3) (AlphaFold), and Ras GTPase activating-like protein (PDB: 3FAY) based on their docking scores which indicates that they may inhibit the crystallization process. …”
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Computation-based virtual screening for designing novel antimalarial drugs by targeting falcipain-III: A structure-based drug designing approach by Rajesh Kumar Kesharwani, Durg Vijay Singh, Krishna Misra

“…<b>Methods</b>: Protein falcipain-II and falcipain-III together with bounds inhibitors epoxysuccinate E64 (E64) and leupeptin respectively were retrieved from protein data bank (PDB) and latter leupeptin was used as lead molecule to design new analogues by using Ligbuilder software and refined the molecules on the basis of Lipinski rule of five and fitness score parameters. …”
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