Structural allele-specific patterns adopted by epitopes in the MHC-I cleft and reconstruction of MHC:peptide complexes to cross-reactivity assessment. by Dinler A Antunes, Gustavo F Vieira, Maurício M Rigo, Samuel P Cibulski, Marialva Sinigaglia, José A B Chies

“…Our strategy, to construct in silico MHC:peptide complexes, was successfully tested by reproducing four different crystal structures of MHC-I molecules available at the Protein Data Bank (PDB). An in silico study of cross-reactivity potential was also performed between the wild-type complex HLA-A2-NS31073 and nine MHC:peptide complexes presenting alanine exchange peptides. …”
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Computational Studies on Syphilis protease inhibitors by D.F. Latona

“…The protein responsible for the bacterial disease was retrieved from protein data bank and docked against tetracycline compounds. …”
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Identification of distant drug off-targets by direct superposition of binding pocket surfaces. by Marcel Schumann, Roger S Armen

“…A novel approach for identification of off-targets by direct superposition of protein binding pocket surfaces is presented and applied to a set of well-studied and highly relevant drug targets, including representative kinases and nuclear hormone receptors. The entire Protein Data Bank is searched for similar binding pockets and convincing distant off-target candidates were identified that share no significant sequence or fold similarity with the respective target structure. …”
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A topological measurement of protein compressibility by Gameiro, M, Hiraoka, Y, Izumi, S, Kramar, M, Mischaikow, K, Nanda, V

“…Due to recent advances in combinatorial topology, this measure is efficiently and directly computable from information found in the Protein Data Bank (PDB). Our main result establishes a clear linear correlation between the topological measure and the experimentally-determined compressibility of most proteins for which both PDB information and experimental compressibility data are available. …”

NeissLock provides an inducible protein anhydride for covalent targeting of endogenous proteins by Scheu, A, Lim, S, Metzner, F, Mohammed, S, Howarth, M

“…We establish a computational tool to search the Protein Data Bank, assessing proximity of amines to C-termini. …”

Thera-SAbDab: the Therapeutic Structural Antibody Database by Raybould, MIJ, Marks, C, Lewis, Alan P, Shi, J, Shi, J, Bujotzek, A, Taddese, B, Deane, C

“…Thera-SAbDab is synchronized with SAbDab to update weekly, reflecting new Protein Data Bank entries and the availability of new sequence data published by the WHO. …”

Analysis of secondary structure predictions of Dengue Virus Type 2 NS2B/NS3 against crystal structure to evaluate the predictive power of thein silico methods by Othman, R., Wahab, H.A., Yusof, R., Rahman, N.A.

“…Consensus on the one-dimensional secondary structure of Den2 protease was obtained from each approach and evaluated against data from the recently crystallised Den2 NS2B/NS3 obtained from the Protein Data Bank (PDB). Results indicated the second approach to show higher accuracy compared to the use of prediction servers only. …”

In-silico search analysis of potential inhibitors for 3-chymotrypsin-like protease of SARS-CoV-2 (Covid-19) by Rahim, Nasimah, Talib, Siti Zalita, Mokhtar, Nur Ainun, Ahmad Khairudin, Nurulbahiyah

“…The protein and the ligands were downloaded from the Protein Data Bank and Pub Chem, respectively. The docked conformations were analysed in terms of the molecular interactions such as hydrogen bonds and hydrophobic interactions. …”
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Benchmark dataset for the Voronoi diagram of 3D spherical balls by Chanyoung Song, Mokwon Lee, Seunghwan Choi, Deok-Soo Kim

“…The dataset also includes protein models downloaded from RCSB Protein Data Bank (PDB). The dataset can be used as a standard benchmark dataset to verify and validate the correctness, efficiency, and robustness of the construction algorithm. …”
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SitesIdentify: a protein functional site prediction tool by Doig Andrew J, Greaves Richard, Bougouffa Salim, Chan Pedro, Bray Tracey, Warwicker Jim

“…<p>Abstract</p> <p>Background</p> <p>The rate of protein structures being deposited in the Protein Data Bank surpasses the capacity to experimentally characterise them and therefore computational methods to analyse these structures have become increasingly important. …”
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Assessment of Globularity of Protein Structures via Minimum Volume Ellipsoids and Voxel-Based Atom Representation by Mateusz Banach

“…Finally, the complete workflow is applied to over two thousand representatives of SCOP 2.08 domain superfamilies, surveying the landscape of tertiary structure of proteins from the Protein Data Bank.…”
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Conformational Sampling of Small Molecules With iCon: Performance Assessment in Comparison With OMEGA by Giulio Poli, Thomas Seidel, Thierry Langer

“…Two data sets of high-quality X-ray structures of drug-like small molecules originating from the Protein Data Bank (200 ligands) and the Cambridge Structural Database (481 molecules) were used to validate iCon's performance in the reproduction of experimental conformations. …”
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A refined pH-dependent coarse-grained model for peptide structure prediction in aqueous solution by Pierre Tufféry, Philippe Derreumaux, Philippe Derreumaux

“…All fast dedicated softwares perform well in aqueous solution at neutral pH.Methods: In this study, we go one step beyond by combining the Debye-Hückel formalism for charged-charged amino acid interactions and a coarse-grained potential of the amino acids to treat pH and salt variations.Results: Using the PEP-FOLD framework, we show that our approach performs as well as the machine-leaning AlphaFold2 and TrRosetta methods for 15 well-structured sequences, but shows significant improvement in structure prediction of six poly-charged amino acids and two sequences that have no homologous in the Protein Data Bank, expanding the range of possibilities for the understanding of peptide biological roles and the design of candidate therapeutic peptides.…”
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Antidiabetic Activity of Catechin from Cinnamon (Cinnamomun Burmanii) by Inhibiting Alfa Glucosidase Enzyme by St Zaenab, Zohrah Hasyim

“…This research method a docking simulation, the ligand was downloaded in the Pubmed database and the androgen receptor macromolecule was downloaded in the Protein Data Bank (PDB), the ligand structure preparation, the test ligand docking simulation and the comparison uses the pymol,pyrx program, and Lipinski test, toxicity test using the PREADMET program. …”
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Structural and Functional Insights into Human Nuclear Cyclophilins by Caroline Rajiv, Tara L. Davis

“…The eight human splicing complexes available in the Protein Data Bank (PDB) are analyzed from the viewpoint of the human spliceophilins. …”
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Data for the crystal structure of APRIL–BAFF–BAFF heterotrimer by Klaus Maskos, Alfred Lammens, Seng-Lai Tan, Henry Hess, Wolf Palinsky, Pascal Schneider, Xuliang Jiang

“…The atomic coordinates and structure factors have been deposited into the Protein Data Bank (accession code 4ZCH).…”
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A data management system for structural genomics by O'Toole Nicholas, Raymond Stéphane, Cygler Miroslaw

“…To avoid unnecessary work on targets, our data management system matches protein sequences weekly using BLAST to entries in the Protein Data Bank and to targets of other SG centers worldwide.…”
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Design and docking of novel series of hybrid xanthones as anti-cancer agent to target human DNA topoisomerase 2-alpha by Lalit Mohan Nainwal, Pratap Parida, Aparoop Das, Parth Sarathi Bairy

“…We developed the homology model of the topoisomerase (topo) IIα due to the unavailability of 3D structure in the Protein Data Bank. Structural assessment of the modeled protein and confirmed the quality of the model. …”
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A Structure-Based Mechanism for the Denaturing Action of Urea, Guanidinium Ion and Thiocyanate Ion by Antonella Paladino, Nicole Balasco, Luigi Vitagliano, Giuseppe Graziano

“…An exhaustive analysis of all the protein structures deposited in the Protein Data Bank, here performed, has allowed the identification of hundredths of protein-bound urea molecules and the structural characterization of such binding sites. …”
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BeEM: fast and faithful conversion of mmCIF format structure files to PDB format by Chengxin Zhang

“…Abstract Background Although mmCIF is the current official format for deposition of protein and nucleic acid structures to the protein data bank (PDB) database, the legacy PDB format is still the primary supported format for many structural bioinformatics tools. …”
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