Can We Assess Early DNA Damage at the Molecular Scale by Radiation Track Structure Simulations? A Tetranucleosome Scenario in Geant4-DNA by Lorenzo Petrolli, Lorenzo Petrolli, Francesco Tommasino, Francesco Tommasino, Emanuele Scifoni, Gianluca Lattanzi, Gianluca Lattanzi

“…In this work, we extend the PDB4DNA example of the Geant4-DNA toolkit, to briefly assess the hit and DSB scores over a nucleosome tetramer framework (Protein Data Bank entry: 1zbb). We describe a critical scenario that biases the statistical significance for an event-by-event track structure assessment at the nanometric scale, based on a Shannon's entropy estimate of the volumetric hit score; finally, we draw a tentative correlation between the mean DSB quality and a proton track, and conclude that short-distanced DSBs by direct effect are favored within a Bragg peak-relevant energy range.…”
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Crystal structure and computational modeling of the fab fragment from a protective anti-ricin monoclonal antibody. by Zhiyu Zhao, David Worthylake, Louis LeCour, Grace A Maresh, Seth H Pincus

“…Because of the problem of self-reference, the accuracy and utility of these predictions can only be tested when a new structure has not yet been deposited in the Protein Data Bank.We have solved the crystal structure of the Fab fragment of RAC18, a protective anti-ricin mAb, to 1.9 Å resolution. …”
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ProtozoaDB 2.0: A Trypanosoma Brucei Case Study by Rodrigo Jardim, Diogo Tschoeke, Alberto M. R. Dávila

“…The system has been fully remodeled to allow for new tools and a more expanded view of data, and now includes a number of analyses such as: (i) similarities with other databases (model organisms, the Conserved Domains Database, and the Protein Data Bank); (ii) visualization of KEGG metabolic pathways; (iii) the protein structure from PDB; (iv) homology inferences; (v) the search for related publications in PubMed; (vi) superfamily classification; and (vii) phenotype inferences based on comparisons with model organisms. …”
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A general and robust ray-casting-based algorithm for triangulating surfaces at the nanoscale. by Sergio Decherchi, Walter Rocchia

“…To test the viability of our method on large systems, we chose one of the biggest molecular structures in the Protein Data Bank, namely the 1VSZ entry, which corresponds to the human adenovirus (180,000 atoms after Hydrogen addition). …”
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Investigation of the Importance of Protein 3D Structure for Assessing Conservation of Lysine Acetylation Sites in Protein Homologs by Kristen M. Jew, Van Thi Bich Le, Kiana Amaral, Allysa Ta, Nina M. Nguyen May, Melissa Law, Nicole Adelstein, Misty L. Kuhn

“…Therefore, we designed a study to leverage the wealth of structural data in the Protein Data Bank (PDB) to determine: (1) the 3D location of lysine residues on substrate proteins that are acetylated by E. coli KATs, and (2) investigate whether these residues are conserved on 3D structures of their homologs. …”
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Probing the Pharmacological Parameters, Molecular Docking and Quantum Computations of Plant Derived Compounds Exhibiting Strong Inhibitory Potential Against NS5 from Zika Virus by Nouman Rasool, Amir Jalal, Adnan Amjad, Waqar Hussain

“…The crystal structure of the protein is retrieved from RCSB protein data bank. A total of 2035 phytochemicals from 505 various medicinal plants are analysed for their pharmacological properties and pharmacokinetics. …”
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Epitope predictions indicate the presence of two distinct types of epitope-antibody-reactivities determined by epitope profiling of intravenous immunoglobulins. by Mitja Luštrek, Peter Lorenz, Michael Kreutzer, Zilliang Qian, Felix Steinbeck, Di Wu, Nadine Born, Bjoern Ziems, Michael Hecker, Miri Blank, Yehuda Shoenfeld, Zhiwei Cao, Michael O Glocker, Yixue Li, Georg Fuellen, Hans-Jürgen Thiesen

“…Representative crystal structures present in the Protein Data Bank (PDB) of Type I EAR are PDB 1TZI and PDB 2DD8, while PDB 2FD6 and 2J4W are typical for Type II EAR. …”
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Physicochemical characteristics of structurally determined metabolite-protein and drug-protein binding events with respect to binding specificity. by Paula eKorkuć, Dirk eWalther

“…Focusing in particular on protein binding specificity vs. promiscuity, we performed a comprehensive analysis of the physicochemical properties of compound-protein binding events as reported in the Protein Data Bank (PDB). We compared the molecular and structural characteristics obtained for metabolites to those of the well-studied interactions of drug compounds with proteins. …”
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Extended antibody-framework-to-antigen distance observed exclusively with broad HIV-1-neutralizing antibodies recognizing glycan-dense surfaces by Myungjin Lee, Anita Changela, Jason Gorman, Reda Rawi, Tatsiana Bylund, Cara W. Chao, Bob C. Lin, Mark K. Louder, Adam S. Olia, Baoshan Zhang, Nicole A. Doria-Rose, Susan Zolla-Pazner, Lawrence Shapiro, Gwo-Yu Chuang, Peter D. Kwong

“…Here, the authors analyse the distance between the body of an antibody and a protein antigen denoted as the Antibody-Framework-to-Antigen Distance (AFAD) for about 2000 non-redundant antibody-protein antigen complexes in the Protein Data Bank. They observe that antibodies with exceptionally long AFADs were all broad HIV-1-neutralizing antibodies that targeted densely glycosylated regions on the HIV-1-envelope trimer. …”
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Comprehensive investigation of Co(II), Ni(II) and Cu(II) complexes derived from a novel Schiff base: Synthesis, characterization, DNA interactions, ADME profiling, molecular dockin... by K. Jagadesh Babu, Dasari Ayodhya, Shivaraj

“…Further, the biological efficiency of the ligand (HL) and complexes were verified by computational methods, including molecular docking (against protein data bank PDB ID: 2ADO.pdb) and pharmacokinetic studies, both the ligand (HL) and complexes have demonstrated significant potency. …”
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Metal based donepezil analogues designed to inhibit human acetylcholinesterase for Alzheimer's disease. by Md Junaid, Nazrul Islam, Md Kamal Hossain, M Obayed Ullah, Mohammad A Halim

“…According to ensemble based docking, D9 shows greater binding affinity compared to the parent in most conformations obtained from protein data bank and MD simulation. In addition, it is observed that the π- π stacking with the residues of Trp86, Tyr337, Tyr341, Tyr124 and Trp286 may be required for strong ligand binding. …”
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Modeling to Understand Plant Protein Structure-Function Relationships—Implications for Seed Storage Proteins by Faiza Rasheed, Joel Markgren, Mikael Hedenqvist, Eva Johansson

“…Modeling of plant proteins is increasing, but less than 9% of deposits in the Research Collaboratory for Structural Bioinformatics Protein Data Bank come from plant proteins. Although, similar tools are applied as in other proteins, modeling of plant proteins is lagging behind and innovative methods are rarely used. …”
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Profile Protein Autism Analysis Based Bioinformatics as Public Dissemination Materials in Malang about The Potensial Causes Autism by Rizki Mei Listawati, Umie Lestari, Mohammad Amin

“…Jenis penelitian ini adalah deskriptif kualitatif, menggunakan tiga database yaitu National Center for Biotechnology Information (NCBI), Uniprot, dan Protein Data Bank (PDB) serta menggunakan software Pymol. …”
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Functional metagenomics uncovers nitrile-hydrolysing enzymes in a coal metagenome by Arunmozhi Bharathi Achudhan, Priya Kannan, Lilly M. Saleena

“…Ligands were extracted from the Protein Data Bank (PDB) for molecular docking upon active site prediction using the CASTp server.Results and discussion:In silico mining of annotated metagenomic data revealed nitrilase from unclassified Alphaproteobacteria. …”
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The complexity of protein interactions unravelled from structural disorder. by Beatriz Seoane, Alessandra Carbone

“…At variance with previous works, our conclusions rely exclusively on a large-scale analysis of all the 134337 X-ray crystallographic structures of the Protein Data Bank averaged over clusters of almost identical protein sequences. …”
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Overview of Membrane Protein Sample Preparation for Single-Particle Cryo-Electron Microscopy Analysis by Catherine Vénien-Bryan, Carlos A. H. Fernandes

“…Indeed, in recent years, huge increase in the number of MPs solved via cryo-EM SPA at a resolution better than 3.0 Å in the Protein Data Bank (PDB) has been observed. However, sample preparation remains a significant challenge in the field. …”
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AlphaFold Protein Structure Database for Sequence-Independent Molecular Replacement by Lawrence Chai, Ping Zhu, Jin Chai, Changxu Pang, Babak Andi, Sean McSweeney, John Shanklin, Qun Liu

“…Molecular replacement is a commonly used phasing method for crystal structures in the protein data bank. In one form it uses a protein sequence to search a structure database to find suitable templates for phasing. …”
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A homogeneous dataset of polyglutamine and glutamine rich aggregating peptides simulations by Exequiel E. Barrera, Sergio Pantano, Francesco Zonta

“…The trajectory files are provided in Protein Data Bank (PDB) format containing the Cartesian coordinates of all heavy atoms in the aggregating peptides. …”
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SSMap: A new UniProt-PDB mapping resource for the curation of structural-related information in the UniProt/Swiss-Prot Knowledgebase by David Fabrice PA, Yip Yum L

“…The UniProt knowledgebase (UniProtKB) strives to help users on this undertaking by providing complete cross-references to Protein Data Bank (PDB) as well as coherent feature annotation using available structural information. …”
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chemalot and chemalot_knime: Command line programs as workflow tools for drug discovery by Man-Ling Lee, Ignacio Aliagas, Jianwen A. Feng, Thomas Gabriel, T. J. O’Donnell, Benjamin D. Sellers, Bernd Wiswedel, Alberto Gobbi

“…Results Use of the command line programs is demonstrated in three different workflow examples: (1) A workflow to create a data file with project-relevant data for structure–activity or property analysis and other type of investigations, (2) The creation of a quantitative structure–property-relationship model using the command line programs via KNIME nodes, and (3) The analysis of strain energy in small molecule ligand conformations from the Protein Data Bank database. Conclusions The chemalot and chemalot_knime packages provide lightweight and powerful tools for many tasks in cheminformatics. …”
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