Celecoxib Blocks Vasculogenic Mimicry via an Off-Target Effect to Radiosensitize Lung Cancer Cells: An Experimental Study by Kai Niu, Xie-Wan Chen, Xie-Wan Chen, Yu Qin, Lu-Ping Zhang, Rong-Xia Liao, Jian-Guo Sun

“…The potential off-targets of CXB were screened using Protein Data Bank (PDB) database, MGLTools 1.5.6, and AutoDock Vina 1.1.2 and confirmed by Western blotting, enzyme activity assay, and RNA interference in vitro experiments and by immunohistochemistry in vivo experiments. …”
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Potential of fenugreek (Trigonella foenum-graecum L.) metabolites as dental residual ridge resorption inhibitors through estrogen receptor signaling: In silico study by Ester Handayani Lodra, Muhammad Chair Effendi, Nur Permatasari, Respati Suryanto Dradjat

“…Proteins were obtained from Protein Data Bank. Molecular docking prediction was carried out using PyRx software and visualized using Discovery Studio Software. …”
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A novel quinoline-appended chalcone derivative as potential Plasmodium falciparum gametocytocide by Himank Kumar, Ishan Wadi, Vinod Devaraji, C R Pillai, Sujit Kumar Ghosh

“…The X-ray crystal structure of Pfg 27 was retrieved from protein data bank and Pfs 25 was built using the Iterative Threading ASSembly Refinement (I-TASSER) server. …”
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Design, Synthesis, Molecular Docking Studies, and Biological Evaluation of 1, 3, 4-oxadiazol-3(2<i>H</i>)-yl] Ethan-1-one Derivatives as Antimicrobial Agents by Rupali Likhar, Tabassum Khan

“…To investigate the antimicrobial data on a structural basis, in-silico docking studies of the synthesized compounds (<b>4a</b>–<b>4r</b>) into the crystal structure of <i>E. coli</i> DNA gyrase (Type-2 topoisomerase) using Autodock PyRx virtual screening program were performed to predict the affinity and orientation of the synthesized compounds at the activities by using 6rks Protein Data Bank (PDB). Inhibiting the ATPase activity of gyrase blocks the introduction of negative supercoils in DNA and traps the chromosome in a positively supercoiled state that may have a downstream impact on cell physiology and division. …”
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Molecular modeling, molecular dynamics simulation, and essential dynamics analysis of grancalcin: An upregulated biomarker in experimental autoimmune encephalomyelitis mice by Shamrat Kumar Paul, Md. Saddam, Khandoker Asiqur Rahaman, Jong-Gu Choi, Sang-Suk Lee, Mahbub Hasan

“…It is a calcium-binding protein that helps neutrophils adhere to fibronectin and the formation of focal adhesions. However, the protein data bank does not contain the crystal structure of mouse GCA. …”
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Abstract P-19: 15-Microsecond Molecular Dynamics Simulations of Nucleosome Show Structural Heterogeneity and Plasticity by Grigoriy A. Armeev, Anastasiia S. Kniazeva, Galina A. Komarova, Mikhail P. Kirpichnikov, Alexey K. Shaytan

“…Currently, there are more than 340 structures of nucleosomes and their complexes with proteins in the protein data bank, 159 of them are made with cryoEM, 60 of those in 2020 and later. …”
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PDTD: a web-accessible protein database for drug target identification by Gao Zhenting, Li Honglin, Zhang Hailei, Liu Xiaofeng, Kang Ling, Luo Xiaomin, Zhu Weiliang, Chen Kaixian, Wang Xicheng, Jiang Hualiang

“…It currently contains >1100 protein entries with 3D structures presented in the Protein Data Bank. The data are extracted from the literatures and several online databases such as TTD, DrugBank and Thomson Pharma. …”
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Comparison, Analysis, and Molecular Dynamics Simulations of Structures of a Viral Protein Modeled Using Various Computational Tools by Hemalatha Mani, Chun-Chun Chang, Hao-Jen Hsu, Chin-Hao Yang, Jui-Hung Yen, Je-Wen Liou

“…The templates for each domain were obtained through sequence-based searches on NCBI and the Protein Data Bank. Then, the modeled domains were assembled to construct the complete structure of HCVcp. …”
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Homology modeling, binding site identification, molecular docking and molecular dynamics simulation study of emerging and promising drug target of Wnt signaling – Human Porcupine e... by Vishalgiri Goswami, Dhaval Patel, Shishir Rohit, Udit Chaube, Bhumika Patel

“…To design the novel Porcupine inhibitors, there was a need of crystal structure of Porcupine but in 2019, it was not resolved and deposited in the protein data bank. So, with an aim to predict its 3D structure, homology modeling study was performed using two distinct platforms; I-TASSER and Molsoft ICMPro so that we could use the best validated model for the designing of NCEs. …”
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Repurposing of monacolin K decorated BN nanoparticle on inhibition of HMG-CoA reductase: In silico approach by Vahid Khori, Mahdi Zahedi, Hassan Mirzaei, Ali Jabbari, seyedbabak Mojaveraghili, Seyed Ghadir Hosseini

“…The protein structures of selective HMG-COA reductase, as well as peroxisome proliferator-activated receptor-α (PPAR-α) and others, were obtained from Protein Data Bank (PDB). The binding affinity between key residues involved in the binding mode of the targets and selective complexes is identified via in silico molecular docking. …”
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Identification of NAD interacting residues in proteins by Raghava Gajendra PS, Ansari Hifzur R

“…</p> <p>Results</p> <p>We extracted 1556 proteins chains from 555 NAD binding proteins whose structure is available in Protein Data Bank. Then we removed all redundant protein chains and finally obtained 195 non-redundant NAD binding protein chains, where no two chains have more than 40% sequence identity. …”
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Snowflake: A deep learning-based human leukocyte antigen matching algorithm considering allele-specific surface accessibility by Matthias Niemann, Benedict M. Matern, Eric Spierings, Eric Spierings

“…We extracted 676 HLA Class-I experimental structures from the Protein Data Bank and supplemented it by 37 Class-I alleles for which structures were predicted. …”
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In Silico Strategies for Designing of Peptide Inhibitors of Oncogenic K-Ras G12V Mutant: Inhibiting Cancer Growth and Proliferation by Mehreen Ghufran, Haider Ali Khan, Mehran Ullah, Sabreen Ghufran, Muhammad Ayaz, Muhammad Siddiq, Syed Shams ul Hassan, Simona Bungau

“…The crystal structure of the mutant <i>K-Ras</i> G12V-H-REV107 complex was obtained from a protein data bank. Further, we used a residue scan approach to create unique peptides from the reference peptide (H-REV107). …”
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Ligand binding specificity of RutR, a member of the TetR family of transcription regulators inEscherichia coli by Phu Nguyen Le Minh, Sergio de Cima, Indra Bervoets, Dominique Maes, Vicente Rubio, Daniel Charlier

“…Although RutR structures have been determined previously, they were deposited in the Protein Data Bank without accompanying publications. All of them have uracil bound in the effector‐binding site, representing the inactive form of the regulator. …”
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How fullerene derivatives (FDs) act on therapeutically important targets associated with diabetic diseases by Natalja Fjodorova, Marjana Novič, Katja Venko, Viktor Drgan, Bakhtiyor Rasulev, Melek Türker Saçan, Safiye Sağ Erdem, Gulcin Tugcu, Alla P. Toropova, Andrey A. Toropov

“…The structures of proteins [(PDB ID: 1BMQ, 1FM6, 1GPB, 1H5U, 1US0)] belonging to the class of anti-diabetes targets were obtained from the Protein Data Bank (PDB). Protein binding activity data (binding scores) were calculated for the dataset of 169 FDs related to these five proteins. …”
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Interaction pattern of aldose reductase with β-glucogallin: Active site exploration and multiple docking analyses by Md Ashikujjaman Ashik, Tasmia Islam, Michihiko Fujii, Md Morshedul Alam, Mohammad Nazir Hossain, Ph.D.

“…High-resolution crystal structure of human aldose reductase (ALR2) (PDB ID: “1pwm”) from ‘Protein Data Bank’ was retrieved, and active site determination was done using “ CASTp” and blind docking strategies. …”
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Crystallization and Crystallographic Analysis of a <i>Bradyrhizobium Elkanii</i> USDA94 Haloalkane Dehalogenase Variant with an Eliminated Halide-Binding Site by Tatyana Prudnikova, Barbora Kascakova, Jeroen R. Mesters, Pavel Grinkevich, Petra Havlickova, Andrii Mazur, Anastasiia Shaposhnikova, Radka Chaloupkova, Jiri Damborsky, Michal Kuty, Ivana Kuta Smatanova

“…The DbeA&#916;Cl molecular structure was characterized and compared with five known haloalkane dehalogenases selected from the Protein Data Bank.…”
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Decomposing compounds enables reconstruction of interaction fingerprints for structure-based drug screening by Melissa F. Adasme, Sarah Naomi Bolz, Ali Al-Fatlawi, Michael Schroeder

“…Results We fragmented over 100,000 compounds in the Protein Data Bank (PDB) and characterized the structural binding mode of 153,000 fragments to their crystallized targets. …”
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Isolation and identification of hair growth potential fraction from active plant extract of Blumea eriantha DC grown in Western Ghat of India: In silico study by Somnath D. Bhinge, Namdeo R. Jadhav, Dheeraj S. Randive, Mangesh A. Bhutkar, Rohankumar Chavan, Bajarang V. Kumbhar

“…The PDB identifications 2PVC (DNMT3L recognizes unmethylated histone H3 lysine 4), 4U7P (Crystal structure of DNMT3A-DNMT3L complex and 2FGF (Human Basic Fibroblast Growth Factor) were downloaded from Protein Data Bank. Results: The study data revealed that B. eriantha DC alcoholic extracts exhibited prominent hair growth activity and it was affirmed that Dimethyl sulfone a phyto-constituent isolated from B. eriantha DC alcoholic extract contributed for the same. …”
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Inverse Molecular Docking as a Novel Approach to Study Anticarcinogenic and Anti-Neuroinflammatory Effects of Curcumin by Veronika Furlan, Janez Konc, Urban Bren

“…For the first time, we performed inverse molecular docking of curcumin into a collection of 13,553 available human protein structures from the Protein Data Bank resulting in prioritized target proteins of curcumin. …”
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