Modulators of the p53-MDM2 interaction : search for MDM2 interactors using structural guidance by Lin, Jianqing

“…Three key residues (F19, W23 and L26) for the MDM2-p53 binding were extracted from p53 and compared against all the available Protein Data Bank (PDB) structures. 15728 candidates were identified by CLICK. …”
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Physics engine by Maung Maung Thin, Wai Yan

“…The particles can be loaded in to the system by providing a PDB (Protein Data Bank) file, specifying the type and position of each particle. …”
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Statistical analysis of the protein environment of N-glycosylation sites: implications for occupancy, structure, and folding. by Petrescu, A, Milac, A, Petrescu, S, Dwek, R, Wormald, M

“…We surveyed 506 glycoproteins in the Protein Data Bank crystallographic database, giving 2592 glycosylation sequons (1683 occupied) and generated a database of 626 nonredundant sequons with 386 occupied. …”

Structural basis for protein-protein interactions in the 14-3-3 protein family. by Yang, X, Lee, W, Sobott, F, Papagrigoriou, E, Robinson, C, Grossmann, J, Sundström, M, Doyle, D, Elkins, J

“…Previously, crystal structures of three 14-3-3 isoforms (zeta, sigma, and tau) have been reported, with structural data for two isoforms deposited in the Protein Data Bank (zeta and sigma). In this study, we provide structural detail for five 14-3-3 isoforms bound to ligands, providing structural coverage for all isoforms of a human protein family. …”

Identification Of Potential Neuraminidase Inhibitors Using Ensemble-Based Virtual Screening by Lim, Kok Keong

“…Variation of neuraminidase conformations from Protein Data Bank (PDB) and molecular dynamics (MD) simulation structures were used in this study. …”
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Exploration of natural product ingredients as inhibitors of human HMG-CoA reductase through structure-based virtual screening by Lin SH, Huang KJ, Weng CF, Shiuan D

“…We used the 3D structure 1HWK from the PDB (Protein Data Bank) database of hHMGR as the target to screen for the strongly bound compounds from the traditional Chinese medicine database. …”
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Combination of coarse-grained molecular dynamics simulations and small-angle X-ray scattering experiments by Toru Ekimoto, Yuichi Kokabu, Tomotaka Oroguchi, Mitsunori Ikeguchi

“…In the CG-MD-SAXS method, the scattering factors of CG particles for proteins and nucleic acids are evaluated using high-resolution structural data in the Protein Data Bank, and the excluded volume and the hydration shell are modeled using two adjustable parameters to incorporate solvent effects. …”
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ProDFace: A web-tool for the dissection of protein-DNA interfaces by Arumay Pal, Pinak Chakrabarti, Sucharita Dey

“…The program takes as input the structure of a protein-DNA complex in PDB (Protein Data Bank) format, and outputs various physicochemical and geometric parameters of the interface, as well as conservation of the interface residues in the protein component. …”
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Eritropoyetina, hipoxia y mal de montaña. by Luisa Fernanda Zanguña Fonseca, Manuel Alejandro Peralta González, Shirley G. Cruz Rubio

“…Materiales y métodos: se realizó una búsqueda electrónica en las bases de datos PubMed, Science Direct, Protein data Bank, NCBI. Conclusión: la EPO es un factor fundamental que marca el comienzo de la eritropoyesis, cuya finalidad es mejorar el transporte de oxígeno. …”
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Structural Analysis of Monomeric RNA-Dependent Polymerases: Evolutionary and Therapeutic Implications. by Rodrigo Jácome, Arturo Becerra, Samuel Ponce de León, Antonio Lazcano

“…The crystal structures of monomeric RNA-dependent RNA polymerases and reverse transcriptases of more than 20 different viruses are available in the Protein Data Bank. They all share the characteristic right-hand shape of DNA- and RNA polymerases formed by the fingers, palm and thumb subdomains, and, in many cases, "fingertips" that extend from the fingers towards the thumb subdomain, giving the viral enzyme a closed right-hand appearance. …”
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A general approach for stabilizing nanobodies for intracellular expression by John G Dingus, Jonathan CY Tang, Ryoji Amamoto, Grace K Wallick, Constance L Cepko

“…Here, we examined intracellular expression of 75 nanobodies from the Protein Data Bank. Surprisingly, a majority of these nanobodies were unstable in cells, illustrated by aggregation and clearance. …”
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Linking Biochemical and Structural States of SERCA: Achievements, Challenges, and New Opportunities by Rodrigo Aguayo-Ortiz, L. Michel Espinoza-Fonseca

“…X-ray crystallography has proven to be an invaluable tool in understanding the structural changes of SERCA, and more than 70 SERCA crystal structures representing major biochemical states (defined by bound ligand) have been deposited in the Protein Data Bank. Consequently, SERCA is one of the best characterized components of the calcium transport machinery in the cell. …”
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Studi In Silico: Prediksi Potensi 6-shogaol dalam Zingiber officinale sebagai Inhibitor JNK by Sri Sulystyaningsih Natalia Daeng Tiring, Yohanes Bare, Andri Maulidi, Mansur S, Fitra Arya Dwi Nugraha

“…JNK protein (ID: 464Y) was obtained from Protein Data Bank (PDB) through 6-shogaol ligand (CID: 5281794) obtained from the PubChem database. …”
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Molecular dynamics simulation of interaction of the anti-cancer drug paclitaxel with the cell membrane: investigation of changes in van der Waals energy and center of mass by Maedeh Rahimnejad, Bahman Vahidi, Bahman Ebrahimi Hoseinzadeh, Fatemeh Yazdian

“…We have done molecular dynamics simulation using NAMD and also the initial structures that were achieved from the protein data bank have been modified using VMD package. …”
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In Silico exploration of phytochemicals as potential drug candidates against dipeptidyl peptidase-4 target for the treatment of type 2 diabetes by Sanjeev Singh, Sudhakar Kancharla, Prachetha Kolli, Gowtham Mandadapu, Manoj Kumar Jena

“…In parallel, the three-dimensional structure of the target protein dipeptidyl peptidase-4 in Protein Data Bank (PDB) format was obtained from the website of the Research Collaboratory for Structural Bioinformatics-PDB. …”
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In Silico Analysis of Antiviral Activity and Pharmacokinetic Prediction of Brazilein Sappan Wood (Caesalpinia sappan L.) Against SARS-CoV-2 Spike Glycoproteins by Dwi Krihariyani, Edy Haryanto, Retno Sasongkowati

“…SARS-CoV-2 S glycoprotein with NAG ligand available in Protein Data Bank (PDB) (PDB ID: 7C01) was the receptor used. …”
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Influence of Disease-Causing Mutations on Protein Structural Networks by Vasam Manjveekar Prabantu, Nagarajan Naveenkumar, Nagarajan Naveenkumar, Nagarajan Naveenkumar, Narayanaswamy Srinivasan

“…We have used manually curated information on disease mutations from UniProtKB/Swiss-Prot and their corresponding protein structures of wildtype and disease variant from the protein data bank. The PSNs of the wildtype and disease-causing mutant are compared to analyse variation of global and local dissimilarity in the overall network and at specific sites. …”
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Penggunaan Fitur Kimia Fisik dan Posisi Atom untuk Prediksi Struktur Sekunder Protein by Toto Haryanto, Budiman Budiman

“…Data diperoleh dari Protein Data Bank (PDB) padaalamat http://www.rcsb.org/. …”
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La acelerada búsqueda de candidatos terapéuticos contra SARS-CoV-2, métodos in silico: Revisión by Oscar Cobar, Rodrigo J. Vargas

“…Se realizó una revisión extensa en las bases de datos públicas e institucionales RSCB-Protein Data Bank, ZINC, NCBI (PubMed, PMC), PubChem, Science Direct e instituciones como CDC, NIH y revistas científicas especializadas sobre los avances en la búsqueda de nuevas moléculas contra el nuevo coronavirus basadas en estudios in silico, detectándose más de 40,000 publicaciones sobre SARS-CoV-2 y cerca de 200 relacionadas a dichos estudios, las consideradas más relevantes fueron analizadas e incluidas en este artículo. …”
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In silico characterization of bacterial chitinase: illuminating its relationship with archaeal and eukaryotic cousins by Bhramar Dutta, Jan Deska, Rajib Bandopadhyay, Salem Shamekh

“…Sixty-two chitinase sequences from four different groups of organisms were collected from the RCSB Protein Data Bank. Considering one suitable exemplary sequence from each group is being compared with others. …”
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