Short hydrogen bonds in the catalytic mechanism of serine proteases by VLADIMIR LESKOVAC, SVETLANA TRIVIC, DRAGINJA PERICIN, MIRA POPOVIC, JULIJAN KANDRAC

“…The survey of crystallographic data from the Protein Data Bank for 37 structures of trypsin and other serine proteases at a resolution of 0.78–1.28 Å revealed the presence of hydrogen bonds in the active site of the enzymes, which are formed between the catalytic histidine and aspartate residues and are on average 2.7 Å long. …”
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Modelling aptamers with nucleic acid mimics (NAM): From sequence to three-dimensional docking. by Ricardo Oliveira, Eva Pinho, Ana Luísa Sousa, Óscar Dias, Nuno Filipe Azevedo, Carina Almeida

“…Representative 2'-O-methyl (2'OMe), locked nucleic acid (LNA), DNA and RNA aptamers, with experimental data deposited in Protein Data Bank, were selected to validate the workflow. …”
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Atomic Details of Carbon-Based Nanomolecules Interacting with Proteins by Luigi Di Costanzo, Silvano Geremia

“…We provide a systematic analysis of approaches used to select proteins interacting with carbon-based nanomolecules explored from the worldwide Protein Data Bank (wwPDB) and scientific literature. The analysis of van der Waals interactions from available data provides important aspects of interactions between proteins and nanomolecules with implications on functional consequences. …”
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BoBER: web interface to the base of bioisosterically exchangeable replacements by Samo Lešnik, Blaž Škrlj, Nika Eržen, Urban Bren, Stanislav Gobec, Janez Konc, Dušanka Janežič

“…Our web server enables fast and user-friendly searches for bioisosteric and scaffold replacements which were obtained by mining the whole Protein Data Bank. The working of the web server is presented on an existing MurF inhibitor as example. …”
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Structural alphabets derived from attractors in conformational space by Kleinjung Jens, Fornili Arianna, Pandini Alessandro

“…</p> <p>Results</p> <p>A Structural Alphabet has been derived by clustering all four-residue fragments of a high-resolution subset of the protein data bank and extracting the high-density states as representative conformational states. …”
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Desain Turunan Senyawa Leonurine Sebagai Kandidat Obat Anti Inflamasi by Ruslin Beny, Nindy Rachma Az Yana, Mesi Leorita

“…The receptor code used is 6COX which is downloaded from the protein data bank site (PDB). The aims of this study was to investigate the interaction of leonurine compounds and their derivatives against COX-2 receptors. …”
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Optimization based Long Short Term Memory Network for Protein Structure Prediction by Pravinkumar Sonsare, Gunavathi C.

“…We assessed our model on a FASTA-formatted file which consists of Protein Data Bank (PDB) sequences and their relative secondary structure. …”
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Detection, characterization and evolution of internal repeats in Chitinases of known 3-D structure. by Manigandan Sivaji, Vinoth Sadasivam, Jayabalan Narayanasamy, Selvaraj Samuel, Chuanzhu Fan

“…Two Chitinase sequences, 1ITX and 3SIM, were found to be structurally similar when analyzed using secondary structure of Chitinase from secondary and 3-Dimensional structure database of Protein Data Bank. Internal repeats of 3N17 and 1O6I were also involved in the ligand-binding site of those Chitinase proteins, respectively. …”
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Impact of genetic variation on three dimensional structure and function of proteins. by Roshni Bhattacharya, Peter W Rose, Stephen K Burley, Andreas Prlić

“…The Protein Data Bank (PDB; http://wwpdb.org) was established in 1971 as the first open access digital data resource in biology with seven protein structures as its initial holdings. …”
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Sparse estimation for structural variability by Singh Rohit, Hosur Raghavendra, Berger Bonnie

“…We validate our predictions for structures in the Protein Data Bank by comparing with NMR experiments, as well as on synthetic data. …”
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Modelling aptamers with nucleic acid mimics (NAM): From sequence to three-dimensional docking by Ricardo Oliveira, Eva Pinho, Ana Luísa Sousa, Óscar Dias, Nuno Filipe Azevedo, Carina Almeida

“…Representative 2ʹ-O-methyl (2ʹOMe), locked nucleic acid (LNA), DNA and RNA aptamers, with experimental data deposited in Protein Data Bank, were selected to validate the workflow. …”
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Theoretical study of the geometric and electronic characterization of carbendazim-based drug (Nocodazole) by Muhammad Khattab

“…Computations on Nocodazole structures deposited in the Protein Data Bank (PDB) revealed possible existence of at least 6 conformers of Nocodazole. …”
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An Algorithm for Protein Helix Assignment Using Helix Geometry. by Chen Cao, Shutan Xu, Lincong Wang

“…The application to the protein structures in the PDB (protein data bank) proves that the algorithm is able to assign accurately not only regular α-helix but also 310 and π helices as well as their left-handed versions. …”
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Classification of domain movements in proteins using dynamic contact graphs. by Daniel Taylor, Gavin Cawley, Steven Hayward

“…A new method for the classification of domain movements in proteins is described and applied to 1822 pairs of structures from the Protein Data Bank that represent a domain movement in two-domain proteins. …”
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Identification of allosteric disulfides from labile bonds in X-ray structures by Aster E. Pijning, Joyce Chiu, Reichelle X. Yeo, Jason W. H. Wong, Philip J. Hogg

“…Here, we identify potential allosteric disulfides in all Protein Data Bank X-ray structures from bonds that are present in some molecules of a protein crystal but absent in others, or present in some structures of a protein but absent in others. …”
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Real-time structural motif searching in proteins using an inverted index strategy. by Sebastian Bittrich, Stephen K Burley, Alexander S Rose

“…Technically, this remains an extremely challenging problem because of the size of the Protein Data Bank (PDB) archive. Existing methods depend on a clustering by sequence similarity and can be computationally slow. …”
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Predicting residue-residue contacts and helix-helix interactions in transmembrane proteins using an integrative feature-based random forest approach. by Xiao-Feng Wang, Zhen Chen, Chuan Wang, Ren-Xiang Yan, Ziding Zhang, Jiangning Song

“…However, less than 1% of membrane protein structures are in the Protein Data Bank. In this context, it is important to develop reliable computational methods for predicting the structures of membrane proteins. …”
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From isotropic to anisotropic side chain representations: comparison of three models for residue contact estimation. by Weitao Sun, Jing He

“…This study compares three side chain contact models: the Atom Distance criteria (ADC) model, the Isotropic Sphere Side chain (ISS) model and the Anisotropic Ellipsoid Side chain (AES) model using 424 high resolution protein structures in the Protein Data Bank. The results indicate that the ADC model is the most accurate and ISS is the worst. …”
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Nucleosomes and their complexes in the cryoEM era: Trends and limitations by Grigoriy A. Armeev, Anna K. Gribkova, Alexey K. Shaytan, Alexey K. Shaytan

“…At the moment, there are more than four hundred structures containing nucleosomes in the Protein Data Bank. Many of these structures represent similar complexes, others differ in composition, conformation and quality. …”
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Atomic Details of Biomineralization Proteins Inspiring Protein Design and Reengineering for Functional Biominerals by Luigi Franklin Di Costanzo

“…With this review I provide an overview of the available structural studies of biomineralization proteins, explored from the Protein Data Bank (wwPDB) archive and scientific literature, and of how these studies are inspiring the design and engineering of proteins able to synthesize novel biominerals. …”
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