Structure-Based Site of Metabolism (SOM) Prediction of Ligand for CYP3A4 Enzyme: Comparison of Glide XP and Induced Fit Docking (IFD) by Deepak K. Lokwani, Aniket P. Sarkate, Kshipra S. Karnik, Anna Pratima G. Nikalje, Julio A. Seijas

“…We extend our studies toward the prediction of SOM for compounds whose experimental SOM is reported but the ligand-enzyme complex crystal structure is not available in the Protein Data Bank (PDB). The quality and accuracy of Glide XP and IFD was determined by calculating RMSD of docked ligands over the corresponding co-crystallized bound ligand and by measuring the distance between the SOM of the ligand and Fe atom of heme. …”
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Accurate determination of epitope for antibodies with unknown 3D structures by Shifa Tahir, Thomas Bourquard, Astrid Musnier, Yann Jullian, Yannick Corde, Zakaria Omahdi, Laetitia Mathias, Eric Reiter, Pascale Crépieux, Gilles Bruneau, Anne Poupon

“…Finally, we show how the MAbTope-determined epitopes for a series of antibodies targeting the same protein can be used to predict competitions, and demonstrate the accuracy with an experimentally validated example.3D: three-dimensionalRMSD: root mean square deviationCDR: complementary-determining regionCPU: central processing unitsVH: heavy chain variable regionVL: light chain variable regionscFv: single-chain variable fragmentsVHH: single-chain antibody variable regionIL4Rα: Interleukin 4 receptor alpha chainSPR: surface plasmon resonancePDB: protein data bankHEK293: Human embryonic kidney 293 cellsEDTA: Ethylenediaminetetraacetic acidFBS: Fetal bovine serumANOVA: Analysis of varianceEGFR: Epidermal growth factor receptorPE: PhycoerythrinAPC: AllophycocyaninFSC: forward scatterSSC: side scatterWT: wild typeKeywords: MAbTope, Epitope Mapping, Molecular docking, Antibody modeling, Antibody-antigen docking…”
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In silico study of inhibition effects of phytocompounds from four medicinal plants against the Staphylococcus aureus β-lactamase by Faegheh Etminani, Adibeh Etminani, Shaimaa O. Hasson, Hawraa Kareem Judi, Shahina Akter, Morteza Saki

“…The 3D structure of the β-lactamase was procured from Protein Data Bank. In silico absorption, distribution, metabolism, excretion, and toxicity (ADMET) analysis was performed using SwissADME online server to evaluate the drug likeliness of the phytochemicals. …”
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In silico screening of drug inhibitors of SARS-CoV-2 RNA-dependent RNA polymerase target by Thanh Tung Bui, Bao Kim Nguyen, Minh Ngoc Le, The Toan Nguyen, The Hai Pham

“…Methods: the 3D structure of RdRp enzyme (PDB ID:6M71, resolution of 2.90 Å) was derived from the Protein Data Bank RCSB. The ligand structures were collected from DrugBank for the RdRp target. …”
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Chalcone analogue as potent anti-malarial compounds against Plasmodium falciparum: Synthesis, biological evaluation, and docking simulation study by Jufrizal Syahri, Emmy Yuanita, Beta Achromi Nurohmah, Ria Armunanto, Bambang Purwono

“…Molecular docking studies of the prepared compounds were performed using Discovery Studio 3.1 (Accelrys, Inc., San Diego, USA) software to dihydrofolate reductases–thymidylate synthase (PfDHFR-TS) protein with Protein Data Bank ID of 1J3I.pdb (sensitive-protein) and ID: 4DP3.pdb (resistance-protein). …”
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In Silico Structural and Biochemical Functional Analysis of a Novel <i>CYP21A2</i> Pathogenic Variant by Michal Cohen, Emanuele Pignatti, Monica Dines, Adi Mory, Nina Ekhilevitch, Rachel Kolodny, Christa E. Flück, Dov Tiosano

“…Computational analysis relied on the solved structure of the protein (Protein-data-bank ID 4Y8W), structure prediction of the mutated protein, evolutionary analysis, and manual inspection. …”
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Structural Complementarity of Bruton’s Tyrosine Kinase and Its Inhibitors for Implication in B-Cell Malignancies and Autoimmune Diseases by Asim Najmi, Neelaveni Thangavel, Anugeetha Thacheril Mohanan, Marwa Qadri, Mohammed Albratty, Safeena Eranhiyil Ashraf, Safaa Fathy Saleh, Maryam Nayeem, Syam Mohan

“…This review derives the structural complementarity of the BTK-kinase domain and its inhibitors from recent three-dimensional structures of inhibitor-bound BTK in the protein data bank (PDB). Additionally, this review analyzes BTK-mediated effector responses of B-cell development and antibody production. …”
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<it>Ab initio </it>modeling of small proteins by iterative TASSER simulations by Zhang Yang, Skolnick Jeffrey, Wu Sitao

“…However, for sequences without similar folds in the Protein Data Bank (PDB) library, the models have to be predicted from scratch. …”
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Identification of a New Potential SARS-COV-2 RNA-Dependent RNA Polymerase Inhibitor via Combining Fragment-Based Drug Design, Docking, Molecular Dynamics, and MM-PBSA Calculations by Mahmoud A. El Hassab, Aly A. Shoun, Sara T. Al-Rashood, Tarfah Al-Warhi, Wagdy M. Eldehna

“…Firstly, the crystal structure of the enzyme was retrieved from the protein data bank PDB ID (7bv2). Then, Fragment-Based Drug Design (FBDD) strategy was implemented using Discovery Studio 2016. …”
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Human aldehyde oxidase (hAOX1): structure determination of the Moco‐free form of the natural variant G1269R and biophysical studies of single nucleotide polymorphisms by Cristiano Mota, Mariam Esmaeeli, Catarina Coelho, Teresa Santos‐Silva, Martin Wolff, Alessandro Foti, Silke Leimkühler, Maria João Romão

“…Databases Structural data are available in the Protein Data Bank under the accession number 6Q6Q.…”
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Molecular docking and admet properties of anacardium occidentale methanolic nut extract against inflammatory, oxidative and apoptotic markers of diabetes by Ajao Folasade Omobolanle, Iyedupe Marcus Olaoye, Adegbola Raphael Oneosinina, Kalejaiye Noheem Olaolu, Adelusi Temitope Isaac

“…Three-dimensional crystallographic structure of selected proteins; B-cell-lymphoma-2 (Bcl-2), caspase-3, glucocorticoids, interleukin-1β, myeloperoxidase and tumor necrosis factor-alpha (TNF-α) was downloaded from Protein Data Bank. Molecular docking was performed using Autodoc kvina and the active site of binding interactions was detected with the Computed Atlas of Surface Topography of proteins (CAST-P). …”
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Structure-Based Virtual Screening: From Classical to Artificial Intelligence by Eduardo Habib Bechelane Maia, Eduardo Habib Bechelane Maia, Letícia Cristina Assis, Tiago Alves de Oliveira, Alisson Marques da Silva, Alex Gutterres Taranto

“…Some virtual databases, such as the Protein Data Bank, have been created to store the 3D structures of molecules. …”
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SeqX: a tool to detect, analyze and visualize residue co-locations in protein and nucleic acid structures by Fördös Gergely, Biro Jan C

“…Structure databases (like Protein Data Bank, PDB and Nucleic Acid Data Bank, NDB) contain all information about these co-locations; however it is not an easy task to penetrate this complex information. …”
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Comprehensive structural and functional analysis of hVEGFR1: Insights into phosphorylation, molecular interactions, and potential inhibitors through docking and dynamics simulation... by Manne Munikumar, Jangampalli Adi Pradeepkiran, Marineni Kiran Kumar, Swathi Banapuram, Akshatha Bhat Edurkala

“…The 3D crystal structure of the hTK domain, obtained from Protein Data Bank (PDB ID: 3HNG), has provided vital structural insights of hVEGFR1. …”
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Chromone-embedded peptidomimetics and furopyrimidines as highly potent SARS-CoV-2 infection inhibitors: docking and MD simulation study by Zahra Shakibay Senobari, Mohsen Masoumian Hosseini, Mohammad Bagher Teimouri, Ali Hossein Rezayan, Saeed Samarghandian, Azadeh Hekmat

“…The crystal structure of these proteins was obtained from the Protein Data Bank, and the inhibition site was determined using ligand binding interaction options. …”
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Patterns of database citation in articles and patents indicate long-term scientific and industry value of biological data resources [version 1; referees: 2 approved] by David Bousfield, Johanna McEntyre, Sameer Velankar, George Papadatos, Alex Bateman, Guy Cochrane, Jee-Hyub Kim, Florian Graef, Vid Vartak, Blaise Alako, Niklas Blomberg

“…Data from open access biomolecular data resources, such as the European Nucleotide Archive and the Protein Data Bank are extensively reused within life science research for comparative studies, method development and to derive new scientific insights. …”
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Molecular Docking and Dynamics Simulation of Protein β-Tubulin and Antifungal Cyclic Lipopeptides by Nubia Noemi Cob-Calan, Luz America Chi-Uluac, Filiberto Ortiz-Chi, Daniel Cerqueda-García, Gabriel Navarrete-Vázquez, Esaú Ruiz-Sánchez, Emanuel Hernández-Núñez

“…To elucidate interactions between the antifungal cyclic lipopeptides iturin A, fengycin, and surfactin produced by <i>Bacillus</i> bacteria and the microtubular protein &#946;-tubulin in plant pathogenic fungi (<i>Fusarium oxysporum</i>, <i>Colletrotrichum gloeosporioides</i>, <i>Alternaria alternata</i>, and <i>Fusarium solani</i>) in molecular docking and molecular dynamics simulations, we retrieved the structure of tubulin co-crystallized with taxol from the Protein Data Bank (PDB) (ID: 1JFF) and the structure of the cyclic lipopeptides from PubChem (Compound CID: 102287549, 100977820, 10129764). …”
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Identification of conformational epitopes on fragment crystallizable region of human Immunoglobulin G by immunoinformatic by Soheyla Rohani, Fatemeh Hajighasemi, Fatemeh Sefid

“…Methods: The amino acid residues and third structure of reference human IgG were found in protein data bank (PDB). Second IgG structure was defined by Phyre2 software (http://www.sbg.bio.ic.ac.uk/~phyre2/). …”
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Molecular Basis of Host-Virus Interactions to Explain Relative Transmission and Severity Caused by Omicron and Delta variants of SARS-CoV-2 by Vinod Joshi, B.M. Shareef, Bennet Angel, Annette Angel, Ramesh Joshi, Ambreen Shafaat Khan, Poorna Khaneja, Nuzhat Maqbool Peer, Bhawna Sharma, Neha Singh, Satinder Pal Singh, Shilpa Barthwal, Komal Tomar, Kiran Yadav

“…The Research Collaboratory Structural Bioinformatics (RCSB) and Protein Data Bank (PDB) were used to construct ACE2-Spike Protein interaction. …”
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A Statistical Method without Training Step for the Classification of Coding Frame in Transcriptome Sequences by Nicolas Carels, Diego Frías

“…Considering the protein sequences of the Protein Data Bank (RCSB PDB or more simply PDB) as a reference, we found that UFM classifies cORFs of ≥200 bp (if the coding strand is known) and cORFs of ≥300 bp (if the coding strand is unknown), and releases them in their coding strand and coding frame, which allows their automatic translation into protein sequences with a success rate equal to or higher than 95%. …”
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