Simple Ligand–Receptor Interaction Descriptor (SILIRID) for alignment-free binding site comparison by Vladimir Chupakhin, Gilles Marcou, Helena Gaspar, Alexandre Varnek

“…Efficiency of SILIRID to distinguish different protein binding sites has been examined in similarity search in sc-PDB database, a druggable portion of the Protein Data Bank, using various protein–ligand complexes as queries. …”
Get full text

Paramagpy: software for fitting magnetic susceptibility tensors using paramagnetic effects measured in NMR spectra by H. W. Orton, T. Huber, G. Otting

“…Paramagpy combines the functionalities of different currently available programs to support the fitting of magnetic susceptibility tensors using PCS, RDC, PRE and CCR data and molecular coordinates in Protein Data Bank (PDB) format, including a convenient graphical user interface. …”
Get full text

Protein NMR structures refined without NOE data. by Hyojung Ryu, Tae-Rae Kim, SeonJoo Ahn, Sunyoung Ji, Jinhyuk Lee

“…The protocol was tested on 134 NMR structures in the Protein Data Bank (PDB) that also have X-ray structures. …”
Get full text

Chemotaxonomic Fingerprinting of Chilean Lichens Through Maldi and Electrospray Ionization Mass Spectrometry by Leonardo Silva Santos, Maria del Pilar Camarantin Soriano, Yaneris Mirabal-Gallardo, Veronica Carrasco-Sanchez, Fabiane Manke Nachtigall, Iris Pereira, Eugenia Pereira

“…MALDI-TOF-MS associated with chemometric analysis was used to detect new m/z patterns of soluble proteins that were compared with Protein Data Bank of UnitPro. These data also permitted the satisfactory distinction among the families and species. …”
Get full text

Genetic algorithm with a crossover elitist preservation mechanism for protein–ligand docking by Boxin Guan, Changsheng Zhang, Jiaxu Ning

“…The performance of CEPGA is tested on sixteen molecular docking complexes from RCSB protein data bank. In comparison with GA, LGA and SODOCK in the aspects of lowest energy and highest accuracy, the results of which indicate that the CEPGA is a reliable and successful method for protein–ligand docking problems.…”
Get full text

SAFlex: A structural alphabet extension to integrate protein structural flexibility and missing data information. by Ikram Allam, Delphine Flatters, Géraldine Caumes, Leslie Regad, Vincent Delos, Gregory Nuel, Anne-Claude Camproux

“…Secondly, our new algorithm deals with the missing data in the protein structure files (concerning more than 75% of the proteins from the Protein Data Bank) in a rigorous probabilistic framework. …”
Get full text

Analysis of Fluctuation in the Heme-Binding Pocket and Heme Distortion in Hemoglobin and Myoglobin by Hiroko X. Kondo, Yu Takano

“…Here, we analyzed the fluctuation in heme distortion in the protein environment for hemoglobin and myoglobin using molecular dynamics (MD) simulations and quantum mechanical (QM) calculations as well as statistical analysis of the protein structures of hemoglobin and myoglobin stored in Protein Data Bank. Our computation and statistical analysis showed that the protein environment for hemoglobin and myoglobin prominently affects the doming distortion of heme porphyrin, which correlates with its oxygen affinity, and that the magnitude of distortion is different between hemoglobin and myoglobin. …”
Get full text

Statistical potentials from the Gaussian scaling behaviour of chain fragments buried within protein globules. by Stefano Zamuner, Flavio Seno, Antonio Trovato

“…Knowledge-based approaches use the statistics collected from protein data-bank structures to estimate effective interaction potentials between amino acid pairs. …”
Get full text

Local topology and bifurcation hot-spots in proteins with SARS-CoV-2 spike protein as an example. by Xubiao Peng, Antti J Niemi

“…The analysis combines the statistics of structurally commensurate amino acid fragments in the Protein Data Bank with general stereochemical considerations. …”
Get full text

Protein disorder prediction at multiple levels of sensitivity and specificity by Cheng Jianlin, Yang Jack Y, Hecker Joshua

“…</p> <p>Results</p> <p>Here we benchmark a state of the art disorder predictor, DISpro, on a large protein disorder dataset created from Protein Data Bank and systematically evaluate the relationship of sensitivity and specificity. …”

Monotopic Membrane Proteins Join the Fold by Entova, Sonya., Imperiali, Barbara

“…These proteins are generally underrepresented in the Protein Data Bank (PDB), but the past decade of research has revealed new examples that allow the description of generalizable features. …”
Get full text

Modeling of an ion channel in its open conformation. by Domene, C, Doyle, D, Vénien-Bryan, C

“…We have modeled the structure of KirBac1.1 in an open state using as a starting point the structure of KirBac1.1 in its closed conformation (Protein Data Bank 1P7B). To test the validity of the open-state model, molecular dynamics simulations in octane, a lipid bilayer mimetic, were carried out. …”

Variation in structural location and amino acid conservation of functional sites in protein domain families. by Pils, B, Copley, R, Schultz, J

“…RESULTS: Functional sites were extracted from experimentally determined structural complexes from the Protein Data Bank harbouring a conserved protein domain from the SMART database. …”

The MemProtMD database: A resource for membrane-embedded protein structures and their lipid interactions by Newport, T, Sansom, M, Stansfeld, P

“…In 2015, the MemProtMD pipeline was developed to allow the automated lipid bilayer assembly around new membrane protein structures, released from the Protein Data Bank. To make this data available to the scientific community, a web database (http://memprotmd.bioch.ox.ac.uk) has been developed. …”

Molecular docking studies of potential drugs for Covid-19 targeting on the coronavirus hemagglutinin esterase by Abu Samah, Farhana, Talib, Siti Zalita, Mokhtar, Nur Ainun, Ahmad Khairudin, Nurulbahiyah

“…The protein and the ligands were downloaded from the protein data bank (PDB) and PubChem website, respectively. …”
Get full text

A Deeper Insight into the Tick Salivary Protein Families under the Light of Alphafold2 and Dali: Introducing the TickSialoFam 2.0 Database by Ben J. Mans, John F. Andersen, José M. C. Ribeiro

“…The availability of the Alphafold2 program, which provides in silico predictions of the 3D polypeptide structure, coupled with the Dali program which uses the atomic coordinates of a structural model to search the Protein Data Bank (PDB) allows another layer of investigation to annotate and ascribe a functional role to proteins having so far being characterized as “unique”. …”
Get full text

Hesperidin Interaction with HMG-CoA-Reductase Enzyme in Hypercholesterolemia: A Study in Silico by Annisa Rizqi Dwi Oktaviani, Veronica Shania Aprillia, Eko Suhartono, Noer Komari

“…The receptor protein in dyslipidemia was obtained from the RCSB Protein Data Bank (https://www.rcsb.org) namely HMG-CoA-reductase receptor with code PDB: 1HW9. …”
Get full text

Visualizing the superfamily of metallo-β-lactamases through sequence similarity network neighborhood connectivity analysis by Javier M. González

“…It is shown that only 198 out of 15,292 representative nodes contain at least one experimentally obtained protein structure in the Protein Data Bank or a manually annotated SwissProt entry, that is to say, only 1.3 % of the superfamily has been functionally and/or structurally characterized. …”
Get full text

The puckering free-energy surface of proline by Di Wu

“…Our calculations are conducted using molecular simulations; we also verify our results using the proline conformations selected from the Protein Data Bank. In addition, we have compared our results with those calculated by the quantum mechanical methods.…”
Get full text

Amino acid empirical contact energy definitions for fold recognition in the space of contact maps by Fogolari Federico, Molinari Henriette, Berrera Marco

“…An important prerequisite for the applicability of the approach is that the protein structure under study should not exhibit anomalous solvent accessibility, compared to soluble proteins whose structure is deposited in the Protein Data Bank. The combined evaluation of a solvent accessibility parameter and contact energy allows for an effective gross screening of predictive models.…”
Get full text