The Binding Prediction of 6-Paradol and its Derivatives on TRPV1 Agonist as a New Compound for Treating Painful Diabetic Neuropathy by Fifteen Aprila Fajrin, Fina Rahmayanti, Dwi Koko Pratoko

“…TRPV1 was obtained from protein data bank (PDB). Ligand bond prediction and affinity was performed using Molegro Virtual Docker. …”
Get full text

Inhibition of pancreatic elastase in silico and in vitro by Rubus rosifolius leaves extract and its constituents by Yesi Desmiaty, Esti Mulatsari, Fadlina Chany Saputri, Muhammad Hanafi, Rini Prastiwi, Berna Elya

“…Selected nine constituents of R. rosifolius were evaluated on the docking behavior of elastase receptor using Protein–Ligand ANT System (PLANTS) computational software with PPE enzyme with Protein Data Bank (PDB) file 1BRU. Result: The methanol extract showed significantly inhibited elastase with IC50 186.13 μg/mL, but ethyl acetate extract showed weak activity, and n-hexane extract did not show any activity. …”
Get full text

Molecular Interaction Analysis of COX-2 Against Aryl Amino Alcohol Derivatives from Isoeugenol as Anti Breast Cancer using Molecular Docking by Zulfa Zuhrufa, Tatang Shabur Julianto

“…The molecular docking approach is carried out to see the interaction of ligands with protein compounds by using the minimized ligand energy bind with protein active site using protein data bank ID 5GMN. The docking result show that IE-Benzanilide-Cl (11) and IE-Benzanilide-OH (10) have the lowest binding energy (−8.3 kcal/mol and −8.6 kcal/mol) compare to another compounds. …”
Get full text

Discovery of potential targets of Triptolide through inverse docking in ovarian cancer cells by Qinhang Wu, Gang Bao, Yang Pan, Xiaoqi Qian, Furong Gao

“…Using a self-designed inverse molecular docking protocol, we fish the top 19 probable targets of TPL from the target library, which was built on 2,250 proteins extracted from the Protein Data Bank. The 2D-DIGE assay reveals that the expression of eight genes is affected by TPL. …”
Get full text

Kinetic analysis and structural studies of a high‐efficiency laccase from Cerrena sp. RSD1 by Meng‐Hsuan Wu, Cheng‐Chung Lee, An‐Shan Hsiao, Su‐May Yu, Andrew H.‐J. Wang, Tuan‐Hua David Ho

“…RSD1 and structural factors have been deposited in the RCSB Protein Data Bank (PDB ID: 5Z1X).…”
Get full text

Molecular Dynamics Study of Human MTHFR Wild-Type and A222V Mutant-Type: A Computational Approach by Michael Resta Surya Yanuar, Dita Maria Virginia, Enade Perdana Istyastono

“…After some preparations, the crystal structure of MTHFR with code 6FCX obtained from the Protein Data Bank was used as the input file for molecular dynamics (MD) simulations. …”
Get full text

Sequence statistics of tertiary structural motifs reflect protein stability. by Fan Zheng, Gevorg Grigoryan

“…The Protein Data Bank (PDB) has been a key resource for learning general rules of sequence-structure relationships in proteins. …”
Get full text

Distill: a suite of web servers for the prediction of one-, two- and three-dimensional structural features of proteins by Walsh Ian, Vullo Alessandro, Mooney Catherine, Martin Alberto JM, Baú Davide, Pollastri Gianluca

“…The servers are based on large-scale ensembles of recursive neural networks and trained on large, up-to-date, non-redundant subsets of the Protein Data Bank. Together with structural feature predictions, Distill includes a server for prediction of C_{<it>α </it>}traces for short proteins (up to 200 amino acids).…”
Get full text

Computer-aided discovery, design, and investigation of COVID-19 therapeutics by Chun-Chun Chang, Hao-Jen Hsu, Tien-Yuan Wu, Je-Wen Liou

“…Intensive and extensive studies on SARS-CoV-2 proteins have been carried out and three-dimensional structures of the major SARS-CoV-2 proteins have been resolved and deposited in the Protein Data Bank. These structures provide the foundations for drug discovery and design using the structure-based computations, such as molecular docking and molecular dynamics simulations. …”
Get full text

When Protein Structure Embedding Meets Large Language Models by Sarwan Ali, Prakash Chourasia, Murray Patterson

“…Within structural biology, the classification of protein structures is pivotal, employing machine learning algorithms to categorize structures based on data from databases like the Protein Data Bank (PDB). To predict protein functions, embeddings based on protein sequences have been employed. …”
Get full text

Sensing preferences for prokaryotic solute binding protein families by Jean Paul Cerna‐Vargas, Beatriz Sánchez‐Romera, Miguel A. Matilla, Álvaro Ortega, Tino Krell

“…To assess possible links between SBP sequence and the ligand recognized, we have inspected manually all SBP three‐dimensional structures deposited in the protein data bank and retrieved 748 prokaryotic structures that have been solved in complex with bound ligand. …”
Get full text

Molecular Docking Study of HIV-1 Protease with Triterpenoides Compounds from Plants and Mushroom by Mokhtar Nosrati, Mandana Behbahani

“…In the present study , the structure of drugs, triterpene comounds, and HIV-1 protease enzyme was received from the databases such as Chem Spider, PubChem, Human Metabolome Database (HMDB), and Protein Data Bank (PDB). After that, molecular docking was performed by iGRMDOCK 2.1 software Results: The results confirmed that the interactions of the triterpene compounds like the standard drugs were in three safeguarded and catalytic areas including central domain, flap and carboxylic terminal domain specially amino acids Asp25, Asp27, Ala28, Asp29 and Asp30 in active sites of HIV-1 protease. …”
Get full text

Fluctuating Finite Element Analysis (FFEA): A continuum mechanics software tool for mesoscale simulation of biomolecules. by Albert Solernou, Benjamin S Hanson, Robin A Richardson, Robert Welch, Daniel J Read, Oliver G Harlen, Sarah A Harris

“…The software package includes a C ++ implementation of FFEA, together with tools to assist the user to set up the system from Electron Microscopy Data Bank (EMDB) or Protein Data Bank (PDB) data files. We also provide a PyMOL plugin to perform basic visualisation and additional Python tools for the analysis of FFEA simulation trajectories. …”
Get full text

PRELIMINARY STUDIES OF INTERACTION BETWEEN NANOTUBES AND TOLL-LIKE RECEPTORS by MAGDALENA A. MOZOLEWSKA, PAWEŁ KRUPA, BAKHTIYOR RASULEV, ADAM LIWO, JERZY LESZCZYNSKI

“…For this purpose, we used the following TLR structures downloaded from the RCSB Protein Data Bank: TLR2 (3A7C), TLR4/MD (3FXI), TLR5 (3V47), TLR3 (2A0Z), and the complexes of TLR1/TLR2 (2Z7X) and TLR2/TLR6 (3A79). …”
Get full text

Structural analysis of VirD4 a type IV ATPase encoded by transmissible plasmids of Salmonella enterica isolated from poultry products by Kuppan Gokulan, Sangeeta Khare, Steven L. Foley

“…In this process, the VirD4 ATPase is the first molecule that initiates substrate selection, which is subsequently delivered to the secretory machinery. In the protein data bank (PDB), no structural information is available for the VirD4 ATPase to understand the functional property. …”
Get full text

Using Multiscale Simulations as a Tool to Interpret Equatorial X-ray Fiber Diffraction Patterns from Skeletal Muscle by Momcilo Prodanovic, Yiwei Wang, Srboljub M. Mijailovich, Thomas Irving

“…The simulation generates families of thick–thin filament repeating units, each with their individually predicted occupancies of different populations of active and inactive myosin heads that can be used to generate 2D-projected electron density models based on known Protein Data Bank structures. We show how, by adjusting only a few selected parameters, we can achieve a good correspondence between experimental and predicted X-ray intensities. …”
Get full text

Penambatan Molekuler dan Simulasi Dinamika Molekuler Senyawa Dari Genus Nigella Terhadap Penghambatan Aktivitas Enzim Protease HIV-1 by Muhammad Sulaiman Zubair, Saipul Maulana, Alwiyah Mukaddas

“…The metabolite of the Nigella genus was obtained from the KnapSack website, and enzyme model was obtained from the Protein Data Bank (3NU3). The results of molecular docking found the lowest affinity energy of Nigella compound is Nigellidine 4-O-sulfite (-13.4 kcal/mol). …”
Get full text

A new structural arrangement in proteins involving lysine NH3 + group and carbonyl by Olga N. Rogacheva, Sergei A. Izmailov, Lyudmila V. Slipchenko, Nikolai R. Skrynnikov

“…Abstract Screening of the Protein Data Bank led to identification of a recurring structural motif where lysine NH3 + group interacts with backbone carbonyl. …”
Get full text

Intermolecular Interactions in Crystal Structures of Imatinib-Containing Compounds by Anna V. Vologzhanina, Ivan E. Ushakov, Alexander A. Korlyukov

“…Analysis of molecular conformations for this drug was carried out using density functional theory calculations of rotation potentials along single bonds and by analyzing crystal structures of imatinib-containing compounds taken from the Cambridge Structural Database and the Protein Data Bank. Rotation along the N-C bond in the region of the amide group was found to be the reason for two relatively stable molecular conformations, an extended and a folded one. …”
Get full text

GAG-DB, the New Interface of the Three-Dimensional Landscape of Glycosaminoglycans by Serge Pérez, François Bonnardel, Frédérique Lisacek, Anne Imberty, Sylvie Ricard Blum, Olga Makshakova

“…We designed the database architecture and the navigation tools to query the database with the Protein Data Bank (PDB), UniProtKB, and GlyTouCan (universal glycan repository) identifiers. …”
Get full text