In silico molecular docking and in vitro analysis of ethanolic extract Ocimum sanctum Linn.: Inhibitory and apoptotic effects against non-small cell lung cancer by Ulayatul Kustiati, T. S. Dewi Ratih, N. Dwi Aris Agung, Dwi Liliek Kusindarta, Hevi Wihadmadyatami

“…The known main active compounds were further analyzed for inhibitory and apoptotic effects on gene signaling using in silico molecular docking involving the downloading of active compounds from PubChem and target proteins from the Protein Data Bank; the active compounds and proteins were then prepared using the Discovery Studio software v. 19.0.0 and the PyRX 0.8 program, interacted with the HEX 8.0.0 program, and visualized with the Discovery Studio Visualizer v. 19.0. …”
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Proteome-Wide Profiling of the Covalent-Druggable Cysteines with a Structure-Based Deep Graph Learning Network by Hongyan Du, Dejun Jiang, Junbo Gao, Xujun Zhang, Lingxiao Jiang, Yundian Zeng, Zhenxing Wu, Chao Shen, Lei Xu, Dongsheng Cao, Tingjun Hou, Peichen Pan

“…Finally, we profiled the entire set of protein structures in the RCSB Protein Data Bank (PDB) with DeepCoSI to evaluate the ligandability of each cysteine for covalent ligand design, and made the predicted data publicly available on website.…”
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Herbal combination from Moringa oleifera Lam. and Curcuma longa L. as SARS-CoV-2 antiviral via dual inhibitor pathway: A viroinformatics approach. by Viol Dhea Kharisma, Aggy Agatha, Arif Nur Muhammad Ansori, Muhammad Hermawan Widyananda, Wahyu Choirur Rizky, Tim Godefridus Antonius Ding, Marina Derkho, Irina Lykasova, Yulanda Antonius, Imam Rosadi, Rahadian Zainul

“…Methods: Sample was collected from PubChem (NCBI, USA) and Protein Data Bank (PDB), then drug-likeness analysis using Lipinski rule of five in SCFBIO web server and bioactive probability analysis of bioactive compounds were conducted by PASS web server. …”
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HARP: a database of structural impacts of systematic missense mutations in drug targets of Mycobacterium leprae by Sundeep Chaitanya Vedithi, Sony Malhotra, Marcin J. Skwark, Asma Munir, Marta Acebrón-García-De-Eulate, Vaishali P Waman, Ali Alsulami, David B Ascher, Tom L Blundell

“…Experimentally solved structures of DHPS, RNAP and GYR of M. leprae are not available in the Protein Data Bank, therefore, we modelled the structures of these proteins using template-based comparative modelling and introduced systematic mutations in each model generating 80,902 mutations and mutant structures for all the three proteins. …”
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Identification of Novel Inhibitor of Enoyl-Acyl Carrier Protein Reductase (InhA) Enzyme in <i>Mycobacterium tuberculosis</i> from Plant-Derived Metabolites: An In Silico Study by Kratika Singh, Niharika Pandey, Firoz Ahmad, Tarun Kumar Upadhyay, Mohammad Hayatul Islam, Nawaf Alshammari, Mohd Saeed, Lamya Ahmed Al-Keridis, Rolee Sharma

“…The chemical structures of the 80 phytochemicals and the 3D structure of the target protein were retrieved from the PubChem database and RCSB Protein Data Bank, respectively. The evaluation of druglikeness was performed based on Lipinski’s Rule of Five, while the computed phytochemical properties and molecular descriptors were used to predict the ADMET of the compounds. …”
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Bioinformatic prediction of the molecular links between Alzheimer’s disease and diabetes mellitus by Ricardo Castillo-Velázquez, Flavio Martínez-Morales, Julio E. Castañeda-Delgado, Mariana H. García-Hernández, Verónica Herrera-Mayorga, Francisco A. Paredes-Sánchez, Gildardo Rivera, Bruno Rivas-Santiago, Edgar E. Lara-Ramírez

“…Materials and Methods In this work, data mining of nine databases (DisGeNET, Ensembl, OMIM, Protein Data Bank, The Human Protein Atlas, UniProt, Gene Expression Omnibus, Human Cell Atlas, and PubMed) was performed to identify gene and protein information that was shared in AD and DM2. …”
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Investigation of X-ray induced radiation damage in proteins, nucleic acids and their complexes by Bury, C

“…To clarify the radiation susceptibility of tyrosine, this thesis presents a systematic investigation on radiation damage to tyrosine in a wide range of MX protein radiation damage series retrieved from the Protein Data Bank. It is concluded that the tyrosine C – O bond remains intact following X-ray irradiation, however the aromatic side-group can undergo radiation-induced displacement.…”

Nucleocapsid and matrix proteins of nipah virus produced in Pichia pastoris and their interaction by Narcisse Mary, Sither Joseph Vesudian

“…The 3-dimensional structures of the N and M proteins of NiV are not available in the Protein Data Bank (PDB) for docking analysis and there are no similar structures available. …”
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Thermal behavioral analysis of bacillus stearothermophilus L1 lipase at elevated temperature by molecular dynamics simulation method by Abdul Rahman, Mohd Basyaruddin, Abedikargiban, Roghayeh, Basri, Mahiran, Raja Abdul Rahman, Raja Noor Zaliha, Salleh, Abu Bakar

“…The crystal structure of L1 lipase in the closed conformation (entry code 1ku0), was taken from Protein Data Bank which resolved to 2.0 Å and Chain A of the crystal structure was selected as the starting structure. …”
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Prediction of COVID-19 manipulation by selective ACE inhibitory compounds of Potentilla reptant root: In silico study and ADMET profile by Yuan Xu, Mahmood Al-Mualm, Ermias Mergia Terefe, Maksuda Ilyasovna Shamsutdinova, Maria Jade Catalan Opulencia, Fahad Alsaikhan, Abduladheem Turki Jalil, Ali Thaeer Hammid, Ayesheh Enayati, Hassan Mirzaei, Vahid Khori, Ali Jabbari, Aref Salehi, Alireza Soltani, Abdullah Mohamed

“…The protein targets of selective ACE and others obtained from Protein Data Bank (PDB). The best binding pose between amino acid residues involved in active site of the targets and compounds was discovered via molecular docking. …”
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Discovery of potential drugs for human-infecting H7N9 virus containing R294K mutation by He JY, Li C, Wu G

“…Even worse, deaths caused by such mutation after oseltamivir treatment have already been reported, indicating that the need to find substitutive neuraminidase inhibitors for currently available drugs to treat drug-resistant H7N9 is really pressing.Materials and methods: First, the structure of H7N9 containing the R294K substitution was downloaded from the Protein Data Bank, and structural information of approved drugs was downloaded from the ZINC (ZINC Is Not Commercial) database. …”
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Identification of Proteins Differentially Expressed in the Striatum by Melatonin in a Middle Cerebral Artery Occlusion Rat Model—a Proteomic and in silico Approach by Fawad Ali Shah, Fawad Ali Shah, Amir Zeb, Tahir Ali, Tahir Ali, Tahir Muhammad, Muhammad Faheem, Sayed Ibrar Alam, Kamran Saeed, Phil-Ok Koh, Keun Woo Lee, Myeong Ok Kim

“…Homology modeling was performed to build 3D structures for γ-enolase, thioredoxin (TRX), and heat shock 60 (HSP60) by the template crystal structures using a protein data bank as a sequence database. The structure refinement of each model was achieved by energy minimization via molecular dynamic simulation, and the generated models were further assessed for stability by Procheck and ProSA. …”
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Análisis in silico del mimetismo molecular entre Der p 23 contra fuentes alergénicas by Andrés Sánchez Caraballo, Valentina García Solano, Sonia Karina González Rangel, Valeria Grattz Lamadrid, Marlon Munera Gomez

“…Los antígenos con estructura experimental resuelta se obtuvieron de Protein Data Bank, y aquellos no informados, se generaron mediante Swiss Model Server y ALPHAFOLD 2. …”
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Structural Homology-Based Drug Repurposing Approach for Targeting NSP12 SARS-CoV-2 by Abdulelah Aljuaid, Abdus Salam, Mazen Almehmadi, Soukayna Baammi, Fahad M. Alshabrmi, Mamdouh Allahyani, Khadijah M. Al-Zaydi, Abdullah M. Izmirly, Sarah Almaghrabi, Bandar K. Baothman, Muhammad Shahab

“…Herein, homologous proteins of NSP-12 were retrieved from Protein DataBank (PDB) and the evolutionary conserved sequence and structure similarity of the active site of the RdRp domain of NSP-12 was characterized. …”
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SARS-CoV-2 Antibody Effectiveness Is Influenced by Non-Epitope Mutation/Binding-Induced Denaturation of the Epitope 3D Architecture by Moffat M. Malisheni, Matthew Bates, Albert A. Rizvanov, Paul A. MacAry

“…However, the mechanisms by which non-epitope mutations in the RBD influence antibody specificity and function remain a mystery. We used Protein Data Bank (PDB) deposited 3D structures for the original, Beta, Delta, BA.1, and BA.2 RBD proteins in complex with either neutralizing antibodies or Angiotensin-Converting Enzyme 2 (ACE2) to elucidate the structural and mechanistic basis for neutralizing antibody evasion driven by non-epitope amino acid substitutions in the RBD. …”
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Computational modeling and functional characterization of a GgChi: A class III chitinase from corms of Gladiolus grandiflorus by Maria Rafiq, Ashiq Hussain, Kausar Hussain Shah, Qamar Saeed, Muhammad Umair Sial, Zahid Ali, Friedrich Buck, Richard E. Goodman, Binish Khaliq, Uzma Ishaq, Mirza Ahsen Baig, Aisha Munawar, Seema Mahmood, Ahmed Akrem

“…Since no structural details of GgChi were available in the Protein Data Bank (PDB), a homology model was predicted using the coordinate information of Crocus vernus chitinase (PDB ID: 3SIM). …”
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Multi-Targeting Bioactive Compounds Extracted from Essential Oils as Kinase Inhibitors by Annalisa Maruca, Delia Lanzillotta, Roberta Rocca, Antonio Lupia, Giosuè Costa, Raffaella Catalano, Federica Moraca, Eugenio Gaudio, Francesco Ortuso, Anna Artese, Francesco Trapasso, Stefano Alcaro

“…With this aim, we performed a Structure-Based Virtual Screening (SBVS) against X-ray models of several protein kinases selected from the Protein Data Bank (PDB) by using a chemoinformatics database of EOs. …”
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Statistical characterization of the GxxxG glycine repeats in the flagellar biosynthesis protein FliH and its Type III secretion homologue YscL by Moore Stanley A, Trost Brett

“…Finally, the α-helices from a non-redundant set of proteins from the Protein Data Bank were searched for GxxxG repeats similar in length to those found in FliH, however there were no helices containing more than three contiguous glycine repeat segments; thus, long glycine repeats similar to those found in FliH are presumably quite rare in nature.…”
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309 Effects of SARS-CoV-2 Variants on CD8+ T cell Epitope Diversity: Estimating Clinical Severity in the United States by Grace Kim, Jacob Elnaggar, Maya Sevalia, Najah Nicholas, Mallory Varnado, Judy Crabtree, Lucio Miele

“…In silico peptide docking was conducted on FoldX, utilizing HLA-B*15:01 structures (n= 7) from the Protein Data Bank. RESULTS/ANTICIPATED RESULTS: CD8+ epitope conservation was estimated at 87.6-96.5% in S, 92.5-99.6% in M, and 94.6-99% for N. …”
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OncoPeptVAC: A robust TCR binding algorithm to prioritize neoepitope using tumor mutation (DNAseq) and gene expression (RNAseq) data by Snigdha Majumder, Vasumathi Kode, Priyanka Shah, Anand Kumar, Ravi Gupta, Amit Chaudhuri, Papia Chakraborty

“…OncoPeptVAC algorithm uses features selected by analyzing crystal structures of TCR and HLA-peptide complex present in the Protein Data Bank. A neural network model was built to derive a composite score that includes, besides TCR binding, other features associated with the peptide, such as level of expression of the mutant allele, affinity of HLA binding, affinity of TAP binding and sensitivity to proteasomal processing. …”
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