Investigation of the Inhibitory Effects of CLF36 Peptide Derived from Camel Lactoferrin on NF-κB Signaling Pathway in Molecular Docking Simulation (In silico) by HojjatAllah Yami, Mojtaba Tahmoorespur, Mohammad Hadi Sekhavati, Ali Javadmanesh

“…Protein data for inhibitory combinations of the Nuclear factor kappa B (NF-kB) pathway was collected from the Protein Data Bank (PDB) And UniProt.Physico-chemical properties analysis (atomic state, isoelectric point, half-life, hydrophobicity hydrophilicity , barometric and pH) was done using Expasy Prot Param online server. …”
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Production of ovine Pancreatic Ribonuclease and investigation of enzyme characteristics by mahsa Zabetian, Mohammad reza Nasiri, Ali Javadmannesh, Shahrokh ghovati

“…The objective of this study was to produce ovine pancreatic ribonuclease enzyme in E. coli and characterize its activity.Materials and methods All structures needed for this study were downloaded from the Protein Data Bank (PDB) website (http://www.rcsb.org/). …”
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Directed search for diuretics among 6-substituted pteridine-2,4,7(1H,3H,8H)-triones by K.V. Sokolova, V.V. Stavytskyi, S.I. Kovalenko, O.A. Podpletnya

“…Macromolecular data were downloaded from the Protein Data Bank (PDB) namely, the crystal structures of Human carbonic anhydrase II (PDB ID – 3HS4) and epithelial sodium channel (ENaC) (PDB ID – 4NTX). …”
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In- silico evaluation of bioactive compounds from selected medicinal plants from Southern Nigeria against hepatitis C virus genotype 1 RNA-directed RNA polymerase by Clement I. Mboto, Uwem O. Edet, Elizabeth N. Mbim, Wilfred O. Ndifon, Eno E. Ebenso, Henry O. Egharevba, Uwem E. George, Francisca O. Nwaokorie, Samuel.I. Udo

“…List of Abbreviations and Units: AA, Amino Acid; HCV, Hepatitis C Virus; HBV, Hepatitis B Virus; GC–MS, Gas chromatograph-mass spectrophotometer; MD, Molecular docking; PDB, Protein Data Bank; RdRp, RNA directed RNA polymerase; RNA, Ribonucleic Acid; HIV, Human Immunodeficiency virus; NIST, National Institute of Standards and Technology; WHO, World Health Organization…”
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TNB-738, a biparatopic antibody, boosts intracellular NAD+ by inhibiting CD38 ecto-enzyme activity by Harshad S. Ugamraj, Kevin Dang, Laure-Hélène Ouisse, Benjamin Buelow, Eduardo N. Chini, Giulia Castello, James Allison, Starlynn C Clarke, Laura M. Davison, Roland Buelow, Rong Deng, Suhasini Iyer, Ute Schellenberger, Sankar N. Manika, Shipra Bijpuria, Astrid Musnier, Anne Poupon, Maria Cristina Cuturi, Wim van Schooten, Pranjali Dalvi

“…Overall, TNB-738 represents a novel treatment with broad therapeutic potential for metabolic and inflammatory diseases associated with NAD+ deficiencies.Abbreviations: 7-AAD: 7-aminoactinomycin D; ADCC: antibody dependent cell-mediated cytotoxicity; ADCP: antibody dependent cell-mediated phagocytosis; ADPR: adenosine diphosphate ribose; APC: allophycocyanin; cADPR: cyclic ADP-ribose; cDNA: complementary DNA; BSA: bovine serum albumin; CD38: cluster of differentiation 38; CDC: complement dependent cytotoxicity; CFA: Freund’s complete adjuvant; CHO: Chinese hamster ovary; CCP4: collaborative computational project, number 4; COOT: crystallographic object-oriented toolkit; DAPI: 4′,6-diamidino-2-phenylindole; DNA: deoxyribonucleic acid; DSC: differential scanning calorimetry; 3D: three dimensional; εNAD+: nicotinamide 1,N6-ethenoadenine dinucleotide; ECD: extracellular domain; EGF: epidermal growth factor; FACS: fluorescence activated cell sorting; FcγR: Fc gamma receptors; FITC: fluorescein isothiocyanate; HEK: human embryonic kidney; HEPES: 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid; IgG: immunoglobulin; IFA: incomplete Freund’s adjuvant; IFNγ: Interferon gamma; KB: kinetic buffer; kDa: kilodalton; KEGG: kyoto encyclopedia of genes and genomes; LDH: lactate dehydrogenase; M: molar; mM: millimolar; MFI: mean fluorescent intensity; NA: nicotinic acid; NAD: nicotinamide adenine dinucleotide; NADP: nicotinamide adenine dinucleotide phosphate; NAM: nicotinamide; NGS: next-generation sequencing; NHS/EDC: N-Hydroxysuccinimide/ ethyl (dimethylamino propyl) carbodiimide; Ni-NTA: nickel-nitrilotriacetic acid; nL: nanoliter; NK: natural killer; NMN: nicotinamide mononucleotide; OD: optical density; PARP: poly (adenosine diphosphate-ribose) polymerase; PBS: phosphate-buffered saline; PBMC: peripheral blood mononuclear cell; PDB: protein data bank; PE: phycoerythrin; PISA: protein interfaces, surfaces, and assemblies: PK: pharmacokinetics; mol: picomolar; RNA: ribonucleic acid; RLU: relative luminescence units; rpm: rotations per minute; RU: resonance unit; SEC: size exclusion chromatography; SEM: standard error of the mean; SIRT: sirtuins; SPR: surface plasmon resonance; µg: microgram; µM: micromolar; µL: microliter…”
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Mechanism of the efficient quenching of tryptophan fluorescence in human gamma crystallin by Chen, Jiejin, Ph. D. Massachusetts Institute of Technology

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Structural elucidation of GDSL esterase of Photobacterium sp. J15 by Syed Mazlan, Sharifah Nur Hidayah

“…To date, the number of structure of GDSL motif enzymes deposited in the Protein Data Bank (PDB) is less than 50 and none of them came from Photobacterium. …”
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An intrinsically disordered proteins community for ELIXIR [version 1; peer review: 2 approved] by Norman E. Davey, M. Madan Babu, Martin Blackledge, Alan Bridge, Salvador Capella-Gutierrez, Zsuzsanna Dosztanyi, Rachel Drysdale, Richard J. Edwards, Arne Elofsson, Isabella C. Felli, Toby J. Gibson, Aleksandras Gutmanas, John M. Hancock, Jen Harrow, Desmond Higgins, Cy M. Jeffries, Philippe Le Mercier, Balint Mészáros, Marco Necci, Cedric Notredame, Sandra Orchard, Christos A. Ouzounis, Rita Pancsa, Elena Papaleo, Roberta Pierattelli, Damiano Piovesan, Vasilis J. Promponas, Patrick Ruch, Gabriella Rustici, Pedro Romero, Sirarat Sarntivijai, Gary Saunders, Benjamin Schuler, Malvika Sharan, Denis C. Shields, Joel L. Sussman, Jonathan A. Tedds, Peter Tompa, Michael Turewicz, Jiri Vondrasek, Wim F. Vranken, Bonnie Ann Wallace, Kanin Wichapong, Silvio C. E. Tosatto

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In SILICO дослідження 4-((5-(децилтіо)-4-метил-4н-1,2,4-триазол-3-іл)метил) морфоліну та його антимікробна активність... by M. V. Ohloblina, I. V. Bushueva, O. P. Shmatenko, V. V. Parchenko, V. V. Parchenko, T. V. Khortetska, O. V. Plіeshkova

“…Рентгенівські кристалічні структури білків з спільно кристалізованими лігандами були отримані з Protein Data Bank (PDB). Для виконання дослідження стикування білка та лігандів та їх конвертації у формат pdbqt використовувався плагін DockingPie Vina в PyMOL. …”
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Ultra-high resolution X-ray structure of orthorhombic bovine pancreatic Ribonuclease A at 100K by David R. Lisgarten, Rex A. Palmer, Jon B. Cooper, Claire E. Naylor, Rosemary C. Talbert, Brendan J. Howlin, John N. Lisgarten, Janez Konc, Shabir Najmudin, Carina M. C. Lobley

“…The refined structure was deposited in the Protein Data Bank as structure 7p4r. Conserved waters, using four high resolution structures, have been investigated. …”
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Kinetics, crystallization, and structural elucidation of thermostable D311E T1 lipase variant from Geobacillus zalihae by Ruslan, Rudzanna

“…Hence, the coordinates of D311E crystal structure was deposited to RCSB Protein Data Bank under PDB ID code 3UMJ. Structural analysis showed the existence of an additional ion pair around E311 in D311E structure which led to the formation of an ion pair network comprising of five amino acid residues (Arg274, Thr278, Gly279, Arg303 and Glu311) connected by seven ion pairs. …”
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finDr: A web server for in silico D-peptide ligand identification by Helena Engel, Felix Guischard, Fabian Krause, Janina Nandy, Paulina Kaas, Nico Höfflin, Maja Köhn, Normann Kilb, Karsten Voigt, Steffen Wolf, Tahira Aslan, Fabian Baezner, Salomé Hahne, Carolin Ruckes, Joshua Weygant, Alisa Zinina, Emir Bora Akmeriç, Enoch B. Antwi, Dennis Dombrovskij, Philipp Franke, Klara L. Lesch, Niklas Vesper, Daniel Weis, Nicole Gensch, Barbara Di Ventura, Mehmet Ali Öztürk

“…Here we present finDr, a novel web server for the computational identification and optimization of D-peptide ligands to any protein structure (https://findr.biologie.uni-freiburg.de/). finDr performs molecular docking to virtually screen a library of helical 12-mer peptides extracted from the RCSB Protein Data Bank (PDB) for their ability to bind to the target. …”
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Effects of PRPS1 I72 mutations on drug resistance in acute lymphoblastic leukemia and its mechanisms by CUI Zhiyan, CHEN Yao, TAO Yue, SHEN Shuhong, LI Hui

“…The diagrams of amino acid residues and spatial conformations of I72 locus, I72V and I72F were predicted and drawn through three-dimensional imaging and PyMOL software by using the crystal structure data of PRPS1-numbered 2HCR (PDB code 2HCR) in the PDB (Protein Data Bank) database.Results·Western blotting results showed that the transiently transfected exogenous PRPS1-mutated proteins were successfully expressed in 293T cells. …”
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The Investigation of Alpha-Tubulin Differential Expression in Oligodendroglioma Brain Tumor Aiming MALDI-TOF-TOF by Mehdi Pooladi, Mehrdad Hashemi, Saeed Hesami Tackallou, Soheila Karani

“…Primary protein detection was performed based on the differences in isoelectric pH, the molecular weight of proteins and protein data banks, which was further confirmed by Matrix Assisted Laser Desorption Ionisation-Time-of-Flight (MALDITOF-TOF). …”
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Fpga-Based Accelerator for The Generation of Pseudo-Amino Acid Composition by Ching, Chee Chow

“…. ________________________________________________________________________________________________________________________ One of the biggest challenges in protein prediction post genomic age is narrowing the gap between the number of newly discovered and uncharacterized proteins and the number of known proteins in protein data banks. This leads to increased demand for efficient techniques to accurately predict protein attributes based solely on its sequence-order information. …”
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