Molecular Modifications and Control of Processes to Facilitate the Synergistic Degradation of Polybrominated Diphenyl Ethers in Soil by Plants and Microorganisms Based on Queuing S... by Tong Wu, Yu Li, Hailin Xiao, Mingli Fu

“…First, the key proteins that can degrade PBDEs in plants and microorganisms were searched in the PDB (Protein Data Bank), and a molecular docking method was used to characterize the binding ability of PBDEs to two key proteins. …”
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dConsensus: a tool for displaying domain assignments by multiple structure-based algorithms and for construction of a consensus assignment by Bourne Philip E, Veretnik Stella, Alden Kieran

“…The assignments are available for all protein chains in the Protein Data Bank (PDB). A consensus domain assignment is built by either allowing each algorithm to contribute equally (simple approach) or by weighting the contribution of each method by its prior performance and observed tendencies. …”
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Combination of in silico methods in the search for potential CD4+ and CD8+ T cell epitopes in the proteome of Leishmania braziliensis by Rafael de Freitas e Silva, Rafael de Freitas e Silva, Luiz Felipe Gomes Rebello Ferreira, Marcelo Zaldini Hernandes, Maria Edileuza Felinto De Brito, Beatriz Coutinho De Oliveira, Ailton Alvaro Da Silva, Osvaldo Pompilio De Melo Neto, Antonio Mauro Rezende, Valéria Rêgo Alves Pereira

“…These were used for molecular modeling and docking with MHC structures retrieved from the Protein Data Bank (PDB). Molecular docking then ranked epitopes based on their predicted binding affinity to both MHC I and II. …”
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DAMPAK KADMIUM DAN MERKURI TERHADAP METABOLISME KARBOHIDRAT: KAJIAN IN SILICO PADA ENZIM GLIKOGEN SINTASE DAN FOSFOFRUKTOKINASE by Azka Lahdimawan, Siti Arika Bulan, Eko Suhartono, Bambang Setiawan

“…Struktur enzim diperoleh dari RCSB Protein Data Bank (http://www.rcsb.org) dengan kode berikut, GS (PDB ID: 1RZV) dan PFK (PDB ID: 4WLO). …”
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Modeling, molecular dynamics, and docking assessment of transcription factor rho: a potential drug target in Brucella melitensis 16M by Pradeepkiran JA, Kumar KK, Kumar YN, Bhaskar M

“…In view the unknown nature of its crystal structure, we constructed a robust three-dimensional homology model of TtFRho’s structure by comparative modeling with the crystal structure of the Escherichia coli TtFRho (Protein Data Bank ID: 1PVO) as a template in MODELLER (v 9.10). …”
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Identification of potential biological targets of oxindole scaffolds via in silico repositioning strategies [version 2; peer review: 2 approved] by Luca Pinzi, Guido Gambacorta, Annachiara Tinivella, Giulio Rastelli, Ian Baxendale

“…To this aim, ligand-based approaches were firstly applied to evaluate the similarity degree of the investigated compound library, with respect to ligands extracted from the DrugBank, Protein Data Bank (PDB) and ChEMBL databases. In particular, the 2D fingerprint-based and 3D shape-based similarity profiles were evaluated and compared for the oxindole derivates. …”
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Inverse Molecular Docking Elucidating the Anticarcinogenic Potential of the Hop Natural Product Xanthohumol and Its Metabolites by Katarina Kores, Zala Kolenc, Veronika Furlan, Urban Bren

“…The investigated compounds were docked into the predicted binding sites of all human protein structures from the Protein Data Bank, and the best docking poses were examined. …”
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Homology modeling and molecular docking simulation of some novel imidazo[1,2-a]pyridine-3-carboxamide (IPA) series as inhibitors of Mycobacterium tuberculosis by Mustapha Abdullahi, Shola Elijah Adeniji, David Ebuka Arthur, Abdurrashid Haruna

“…Mycobacterium tuberculosis cytochrome b subunit of the cytochrome bc1 complex (QcrB) was recognized as a potential drug target in M. tuberculosis (25618/H37Rv) for imidazo[1,2-a]pyridine-3-carboxamides whose crystal strucuture is not yet reported in the Protein Data Bank (PDB). The concept of homology modeling as a powerful and useful computational method can be applied, since the M. tuberculosis QcrB protein sequence data are available. …”
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NMR-Chemical-Shift-Driven Protocol Reveals the Cofactor-Bound, Complete Structure of Dynamic Intermediates of the Catalytic Cycle of Oncogenic KRAS G12C Protein and the Significanc... by Márton Gadanecz, Zsolt Fazekas, Gyula Pálfy, Dóra Karancsiné Menyhárd, András Perczel

“…There are several Mg²⁺-bound G12C KRAS/GDP structures deposited in the Protein Data Bank (PDB), so this system was used as a reference, while the structure of the Mg²⁺-free but GDP-bound state of the RAS cycle has not been determined previously. …”
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R3D-BLAST2: an improved search tool for similar RNA 3D substructures by Ching-Yu Yen, Jian-Cheng Lin, Kun-Tze Chen, Chin Lung Lu

“…As more and more RNA 3D structures are available in the Protein Data Bank (PDB), a bioinformatics tool, which is able to rapidly and accurately search the PDB database for similar RNA 3D structures or substructures, is helpful to understand the structural and functional relationships of RNAs. …”
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The Order-Disorder Continuum: Linking Predictions of Protein Structure and Disorder through Molecular Simulation by Hsu, Claire C., Buehler, Markus J., Tarakanova, Anna

“…To link secondary structure prediction algorithms developed for folded proteins and protein disorder predictors, we conduct molecular dynamics simulations on representative proteins from the Protein Data Bank, comparing secondary structure and disorder predictions with simulation results. …”
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Machine learning model for fast prediction of the natural frequencies of protein molecules by Qin, Zhao, Yu, Qingyi, Buehler, Markus J

“…000 known protein molecular structures from the Protein Data Bank and use this dataset to carefully investigate the correlation between their structural features and these natural frequencies by using a machine learning model composed of a Feedforward Neural Network made of four hidden layers that predicts the natural frequencies in excellent agreement with full-atomistic normal mode calculations, but is significantly more computationally efficient. …”
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Stereoelectronic Effects Impact Glycan Recognition by McMahon, Caitlin M, Isabella, Christine R, Windsor, Ian W, Kosma, Paul, Raines, Ronald T, Kiessling, Laura L

“…This carbohydrate conformation was present in >97% of the KDO/KO structures in the Protein Data Bank. Bioinformatic analysis revealed that KO and KDO adopt a common conformation, while heptoses prefer different conformers. …”
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Co+–H interaction inspired alternate coordination geometries of biologically important cob(I)alamin : possible structural and mechanistic consequences for methyltransferases by Kumar, Manoj, Hirao, Hajime, Kozlowski, Pawel M.

“…The QM/MM analysis of methionine synthase bound Co+Cbx (Protein Data Bank ID 1BMT, resolution 3.0 Å) indicates that the enzyme-bound Co+Cbx can also form a Co+–H bond, but can only exist in square pyramidal form because of the steric constraints imposed by the cellular environment. …”
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Guanine base stacking in G-quadruplex nucleic acids by Lech, Christopher Jacques, Heddi, Brahim, Phan, Anh Tuân

“…A structural survey of the Protein Data Bank is conducted to characterize experimentally observed guanine base stacking geometries within the core of G-quadruplexes and at the interface between stacked G-quadruplex structures. …”
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Structural studies on foot-and-mouth disease virus by Lea, S, Lea, S. M.

“…</p> <p>Analysis of structures from the Protein Data Bank reveals different patterns of amino acid use in proteins involved in the two halves of the immune recognition event i.e. immunoglobulins and viruses. …”

Technical Data of In Silico Analysis of the Interaction of Dietary Flavonoid Compounds against Spike-Glycoprotein and Proteases of SARS-CoV-2 by Nurbella Sofiana Altu, Cahyo Budiman, Rafida Razali, Ruzaidi Azli Mohd Mokhtar, Khairul Azfar Kamaruzaman

“…For this purpose, protein structures of the receptor-binding domain (RBD) of S protein (6M0J), 3CL-Pro (6LU7), and PL-Pro (6W9C) were retrieved from the RCSB Protein Data Bank (PDB). Twelve dietary flavonoid compounds were selected for the studies on their binding affinity to the targeted proteins by global and local docking. …”
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Promising reduction of de novo resistance to endocrine therapies in breast cancer by small molecules from natural origin: a structural approach by Etti, Imaobong C., Kadir, Arifah A., Uweh, Esther J., Okuku, Cecilia, Abdullah, Rasedee

“…The structure of the ligand-binding domain (LBD) of human estrogen receptor was retrieved from Protein Data Bank while the structures of the studied compounds were collected from PubChem database. …”
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Protein Structure-Based Design of Novel Semisynthetic Metallotrypsin by Misran, Azizah

“…Twenty four pockets were identified in trypsin from Protein Data Bank (PDB) file entry 1AUJ using Computed Atlas of Surface Topography of proteins (CASTp). …”
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Targeting a cell surface vitamin D receptor on tumor-associated macrophages in triple-negative breast cancer by Fernanda I Staquicini, Amin Hajitou, Wouter HP Driessen, Bettina Proneth, Marina Cardó-Vila, Daniela I Staquicini, Christopher Markosian, Maria Hoh, Mauro Cortez, Anupama Hooda-Nehra, Mohammed Jaloudi, Israel T Silva, Jaqueline Buttura, Diana N Nunes, Emmanuel Dias-Neto, Bedrich Eckhardt, Javier Ruiz-Ramírez, Prashant Dogra, Zhihui Wang, Vittorio Cristini, Martin Trepel, Robin Anderson, Richard L Sidman, Juri G Gelovani, Massimo Cristofanilli, Gabriel N Hortobagyi, Zaver M Bhujwalla, Stephen K Burley, Wadih Arap, Renata Pasqualini

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