Molecular Mingling: Multimodal Predictions of Ligand Promiscuity in Pentameric Ligand-Gated Ion Channels by Filip Koniuszewski, Florian D. Vogel, Konstantina Bampali, Jure Fabjan, Thomas Seidel, Petra Scholze, Philip B. Schmiedhofer, Thierry Langer, Margot Ernst

“…Currently, approximately 100 experimental structures of pLGICs with ligands bound exist in the protein data bank (PDB). These atomic-level 3D structures enable the generation of a comprehensive binding site inventory for the superfamily and the in silico prediction of binding site properties.Methods: A panel of high throughput in silico methods including pharmacophore screening, conformation analysis and descriptor calculation was applied to a selection of allosteric binding sites for which in vitro screens are lacking. …”
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Galantamine Based Novel Acetylcholinesterase Enzyme Inhibitors: A Molecular Modeling Design Approach by Luciane B. Silva, Elenilze F. B. Ferreira, Maryam, José M. Espejo-Román, Glauber V. Costa, Josiane V. Cruz, Njogu M. Kimani, Josivan S. Costa, José A. H. M. Bittencourt, Jorddy N. Cruz, Joaquín M. Campos, Cleydson B. R. Santos

“…A bioactive pose on the <i>h</i>AChE B site of the human acetylcholinesterase (<i>h</i>AChE) enzyme employed in this investigation, which was obtained from the Protein Data Bank (PDB ID 4EY6), allowed for the prediction of the binding affinity and free binding energy between the protein and the ligand. …”
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Peptides for Coating TiO₂ Implants: An In Silico Approach by Almerinda Agrelli, Niedja Fittipaldi Vasconcelos, Rayane Cristine Santos da Silva, Carina Lucena Mendes-Marques, Isabel Renata de Souza Arruda, Priscilla Stela Santana de Oliveira, Luzia Rejane Lisbôa Santos, Audrey Nunes de Andrade, Ronald Rodrigues de Moura, Lucas Coelho Bernardo-Menezes, Natália Pereira da Silva, Giovanna Machado

“…To do so, we downloaded PDB structures of integrins α5β1, αvβ3, and αIIbβ3; their biological ligands; and low-cost proteins from the Protein Data Bank, and then we performed a primary (integrin-protein) docking analysis. …”
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Aromatic Rings as Molecular Determinants for the Molecular Recognition of Protein Kinase Inhibitors by Yan Zhu, Saad Alqahtani, Xiche Hu

“…Large-scale data mining of the Protein Data Bank resulted in a database of 2139 non-redundant high-resolution X-ray crystal structures of PKIs bound to protein kinases. …”
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Expression, characterization and structure elucidation of thermotolerant lipase with broad pH isolated from Antarctic Pseudomonas sp. strain AMS3 by Latip, Wahhida

“…The 3D structure was refined, validated and deposited to Protein Data Bank (PDB no. 5XPX). The refined truncated AMS3 lipase structure revealed a common α/β hydrolase fold with bound calcium and zinc ions. …”
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In silico study on anti-Chikungunya virus activity of hesperetin by Adrian Oo, Pouya Hassandarvish, Sek Peng Chin, Vannajan Sanghiran Lee, Sazaly Abu Bakar, Keivan Zandi

“…Methods 3D structures of CHIKV nsP2 (3TRK) and nsP3 (3GPG) were retrieved from Protein Data Bank (PDB), whereas nsP1, nsP4 and cellular factor SPK2 were modeled using Iterative Threading Assembly Refinement (I-TASSER) server based on respective amino acids sequence. …”
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Inhibitory potential of rutin and rutin nano-crystals against Helicobacter pylori, colon cancer, hemolysis and Butyrylcholinesterase in vitro and in silico by Husam Qanash, Aisha M. H. Al-Rajhi, Majed N. Almashjary, Ammar A. Basabrain, Mohannad S. Hazzazi, Tarek M. Abdelghany

“…The target molecule underwent molecular docking research against H. pylori [Protein Data Bank (PDB) code: 4HI0], HT-29 cells (PDB code: 2HQ6), and BChE (PDB code: 6EMI) in order to enhance the interactions between rutin and the chosen receptors and to estimate its molecular operating environment (MOE) affinity scoring. …”
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Cytotoxic Activity of Indonesian Pogonatum neesii Dozy from Cibodas Botanical Garden: In Silico Molecular Docking and In Vitro Evaluation by Rizky Nurdiansyah, Agus Budiawan Naro Putra, Ainun Nadhifah, Erika Chriscensia, Ulung Khoe Gondo Kusumo, Stephanie Angela Yosiano, Anastasia Beatrix Musung, Sintikhe A Wenas, Steve Makalew, Patricia Lovina, Intani Quarta Lailaty, Fransisca Aurelia Rahmad, Fandi Sutanto, Pietradewi Hartrianti

“…Methods: Molecular docking analysis using Autodock VINA in PyRx softwre was conducted between natural compounds found on P. neesii and several target proteins, DNA (cytosine-5)- methyltransferase 1 (DMT-1) (Protein Data Bank (PDB) id: 4WXX) in colon cancer and B-cell lymphoma 2 (Bcl-2) (PDB id: 4LXD) in cervical cancer. …”
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Pea eggplant (Solanum torvum Swartz) is a source of plant food polyphenols with SARS-CoV inhibiting potential by Nisha Govender, Norazura Syazlin Zulkifli, Nurul Farhana Badrul Hisham, Nur Syatila Ab Ghani, Zeti-Azura Mohamed-Hussein

“…Method The SARS-CoV receptor structure files (viral structural components) were retrieved from the Protein Data Bank (PDB) database: membrane protein (PDB ID: 3I6G), main protease (PDB ID: 5RE4), and spike glycoproteins (PDB ID: 6VXX and 6VYB). …”
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Inhibitory Potential of Polyclonal Camel Antibodies against New Delhi Metallo-β-lactamase-1 (NDM-1) by Rahma Ben Abderrazek, Sarra Chammam, Ayoub Ksouri, Mariagrazia Perilli, Sayda Dhaouadi, Ines Mdini, Zakaria Benlasfar, Gianfranco Amicosante, Balkiss Bouhaouala-Zahar, Alessandra Piccirilli

“…A visualization of the 3D structural basis using the three enzyme Protein Data Bank (PDB) files supports preliminarily the recorded inhibition of the three MBLs.…”
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Synthesis of new N-alkylated 6-bromoindoline-2.3-dione derivatives: Crystal structures, spectroscopic characterizations, Hirschfeld surface analyses, molecular docking studies, DFT... by Nohaila Rharmili, Yusuf Sert, Youssef Kandri Rodi, Fouad Ouazzani Chahdi, Amal Haoudi, Joel T. Mague, Ahmed Mazzah, Naoufal El Hachlafi, Nesrine Benkhaira, Kawtar Fikri-Benbrahim, El Mokhtar Essassi, Nada Kheira Sebbar

“…Finally, molecular docking studies of 4, 7 and 8 were performed to investigate their binding patterns with inhibitory targets from the Protein Data Bank (PDB: 3G7B and PDB: 3T0T using the AutoDock Vina program. …”
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Characterization of <i>α</i>-Glucosidase Inhibitors from <i>Psychotria malayana</i> Jack Leaves Extract Using LC-MS-Based Multivariate Data Analysis and In-Silico Molecular Docking... by Tanzina Sharmin Nipun, Alfi Khatib, Zalikha Ibrahim, Qamar Uddin Ahmed, Irna Elina Redzwan, Mohd Zuwairi Saiman, Farahaniza Supandi, Riesta Primaharinastiti, Hesham R. El-Seedi

“…Molecular docking of the identified inhibitors was performed using Auto Dock Vina software against the crystal structure of <i>Saccharomyces cerevisiae</i> isomaltase (Protein Data Bank code: 3A4A). Four hydrogen bonds were detected in the docked complex, involving several residues, namely ASP352, ARG213, ARG442, GLU277, GLN279, HIE280, and GLU411. …”
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Tryptophan-based fluorescent sensor for selective Cu2+ detection in aqueous media and its docking study for anticancer effects by Ghodsi Mohammadi Ziarani, Shikofa Khorrami, Fatemeh Mohajer, Sunil V. Gaikwad, Najibullah Hassani, Alireza Badiei, Siavash Iravani, Rajender S. Varma

“…The protein three-dimensional (3D) structure of protein PDB: 5vc3 and PDB: 2xp2 were isolated from the protein data bank and docked with tryptophan derivatives. …”
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A potential implication of UDP-glucuronosyltransferase 2B10 in the detoxification of drugs used in pediatric hematopoietic stem cell transplantation setting: an in silico investiga... by Shannon Robin, Khalil Ben Hassine, Jayaraman Muthukumaran, Simona Jurkovic Mlakar, Maja Krajinovic, Tiago Nava, Chakradhara Rao S. Uppugunduri, Marc Ansari

“…The three-dimensional structure of UGT2B10 was not available from the Research Collaboratory Structural Bioinformatics - Protein Data Bank (RCSB - PDB) repository and thus we predicted the first human UGT2B10 3D model by using multiple template homology modeling with MODELLER Version 9.2 and molecular docking calculations with AutoDock Vina Version 1.2 were implemented to quantify the estimated binding affinity between selected putative substrates or ligands and UGT2B10. …”
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In silico design of novel bioactive molecules to treat breast cancer with chlorogenic acid derivatives: a computational and SAR approach by Renu Sehrawat, Priyanka Rathee, Pooja Rathee, Sarita Khatkar, Esra Küpeli Akkol, Anurag Khatkar, Eduardo Sobarzo-Sánchez, Eduardo Sobarzo-Sánchez

“…Chlorogenic acid was selected because of its known activity in the field.Methods: Several chlorogenic acid derivatives were subjected to computational studies such as molecular docking, determination of absorption, distribution, metabolism, and excretion (ADME), druglikeness, toxicity, and prediction of activity spectra for substances (PASS) to develop a potential inhibitor of breast cancer. The Protein Data Bank (PDB) IDs used for docking purposes were 7KCD, 3ERT, 6CHZ, 3HB5, and 1U72.Result: Exhaustive analysis of results has been conducted by considering various parameters, like docking score, binding energy, types of interaction with important amino acid residues in the binding pocket, ADME, and toxicity data of compounds. …”
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Design, synthesis, docking studies and antibiotic evaluation (in vitro) of some novel (E)-4-(3-(diphenylamino)phenyl)-1-(4-methoxyphenyl)-2-methylbut-3-en-1-one and their analogues by AbdulRazaq Tukur, James Dama Habila, Rachael Gbekele-Oluwa Ayo, Ogunkemi Risikat Agbeke Iyun

“…With the non-mutant X-ray Human cytochrome P450 21A2 Hydroxyprogesterone retrieved from Protein Data Bank (PDB: 5VBU), molecular docking experiments were also carried out to analyse the most favourable conformation and find the orientation that maximizes interaction and minimize energy. …”
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Structural and Biofunctional Insights into the Cyclo(Pro-Pro-Phe-Phe-) Scaffold from Experimental and In Silico Studies: Melanoma and Beyond by Joanna Bojarska, Martin Breza, Milan Remko, Malgorzata Czyz, Anna Gajos-Michniewicz, Michał Zimecki, Krzysztof Kaczmarek, Izabela D. Madura, Jakub M. Wojciechowski, Wojciech M. Wolf

“…In the Cambridge Structural Database, there is only one such cyclic tetrapeptide, cyclo((R)-β<b>²</b>homoPhe-D-Pro-Lys-Phe-), while in the Protein Data Bank—none. Therefore, we report the first crystal structure of cyclo(Pro-Pro-β³homoPhe-Phe-), denoted as 4B8M, a close analog of P11, which is crucial for drug discovery. …”
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The synthesis, antimicrobial activity and docking studies of 6-(1H-benzimidazol-2-yl)-5-methylthieno[2,3-d]pyrimidin-4(3H)-ones with acetamide and 1,2,4-oxadiazol-5-ylmethyl subst... by Sergiy V. Vlasov, Oleksandr V. Borysov, Hanna I. Severina, Sergiy M. Kovalenko, Tetiana P. Osolodchenko, Vitaliy S. Vlasov, Victoriya A. Georgiyants

“…Crystallographic data for the complexes of Streptomycin with the 16S subunit of ribosomal RNA (1NTB) and its active site, as well as for tRNA (Guanine37-N1)-methyltransferase (EC 2.1.1.228; TrmD) (5ZHN) and its active site were obtained from the Protein Data Bank. Conclusions. It has been determined that 2-[6-(1H-benzimidazol-2-yl)-5-methyl-4-oxothieno[2,3-d]pyrimidin-3(4H)-yl]-N-[4-(ethoxy)phenyl]acetamide, which is the most active as an antimicrobial agent among the compounds tested, also shows the best binding activity towards the active site of tRNA (guanine37-N1)-methyltransferase.…”
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Sea Anemones Responding to Sex Hormones, Oxybenzone, and Benzyl Butyl Phthalate: Transcriptional Profiling and in Silico Modelling Provide Clues to Decipher Endocrine Disruption in... by Michael B. Morgan, Michael B. Morgan, James Ross, James Ross, James Ross, Joseph Ellwanger, Rebecca Martin Phrommala, Hannah Youngblood, Hannah Youngblood, Hannah Youngblood, Dominic Qualley, Jacob Williams

“…In silico modelling utilized protein structures from Protein Data Bank as well as creating protein structures with SWISS-MODEL. …”
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Detection and full genome characterization of two beta CoV viruses related to Middle East respiratory syndrome from bats in Italy by Ana Moreno, Davide Lelli, Luca de Sabato, Guendalina Zaccaria, Arianna Boni, Enrica Sozzi, Alice Prosperi, Antonio Lavazza, Eleonora Cella, Maria Rita Castrucci, Massimo Ciccozzi, Gabriele Vaccari

“…The three dimensional macromolecular structure (3DMMS) of the receptor binding domain (RBD) in the S protein was predicted by sequence-homology method using the protein data bank (PDB). Results Both samples resulted positive to the pan-coronavirus RT-PCR (IT-batCoVs) and their genome organization showed identical pattern of MERS CoV. …”
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