Search Results - "Journal of molecular biology"

A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core by Zimmermann, Lukas, Stephens, Andrew, Nam, Seung-Zin, Rau, David, Kübler, Jonas, Lozajic, Marko, Gabler, Felix, Söding, Johannes, Lupas, Andrei N., Alva, Vikram

“…The MPI Bioinformatics Toolkit (https://toolkit.tuebingen.mpg.de) is a free, one-stop web service for protein bioinformatic analysis. It currently offers 34…”
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Mutations Strengthened SARS-CoV-2 Infectivity by Chen, Jiahui, Wang, Rui, Wang, Menglun, Wei, Guo-Wei

“…Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infectivity is a major concern in coronavirus disease 2019 (COVID-19) prevention and economic…”
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AlphaFold and Implications for Intrinsically Disordered Proteins by Ruff, Kiersten M., Pappu, Rohit V.

“…[Display omitted] •Predicted structures generated by AlphaFold, highlight the importance of IDRs.•Caution is essential when using predicted “structures” for…”
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β-Lactamases and β-Lactamase Inhibitors in the 21st Century by Tooke, Catherine L., Hinchliffe, Philip, Bragginton, Eilis C., Colenso, Charlotte K., Hirvonen, Viivi H.A., Takebayashi, Yuiko, Spencer, James

“…The β-lactams retain a central place in the antibacterial armamentarium. In Gram-negative bacteria, β-lactamase enzymes that hydrolyze the amide bond of the…”
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Selective Autophagy: ATG8 Family Proteins, LIR Motifs and Cargo Receptors by Johansen, Terje, Lamark, Trond

“…Selective autophagy relies on soluble or membrane-bound cargo receptors that recognize cargo and bring about autophagosome formation at the cargo. The…”
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Moltemplate: A Tool for Coarse-Grained Modeling of Complex Biological Matter and Soft Condensed Matter Physics by Jewett, Andrew I., Stelter, David, Lambert, Jason, Saladi, Shyam M., Roscioni, Otello M., Ricci, Matteo, Autin, Ludovic, Maritan, Martina, Bashusqeh, Saeed M., Keyes, Tom, Dame, Remus T., Shea, Joan-Emma, Jensen, Grant J., Goodsell, David S.

“…[Display omitted] •Moltemplate streamlines preparation of coarse-grained molecular dynamics simulations.•Moltemplate is designed to be as general as…”
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BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences by Kanehisa, Minoru, Sato, Yoko, Morishima, Kanae

“…BlastKOALA and GhostKOALA are automatic annotation servers for genome and metagenome sequences, which perform KO (KEGG Orthology) assignments to characterize…”
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Phylogenetic Analysis and Structural Modeling of SARS-CoV-2 Spike Protein Reveals an Evolutionary Distinct and Proteolytically Sensitive Activation Loop by Jaimes, Javier A., André, Nicole M., Chappie, Joshua S., Millet, Jean K., Whittaker, Gary R.

“…The 2019 novel coronavirus (2019-nCoV/SARS-CoV-2) originally arose as part of a major outbreak of respiratory disease centered on Hubei province, China. It is…”
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The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes by van Zundert, G.C.P., Rodrigues, J.P.G.L.M., Trellet, M., Schmitz, C., Kastritis, P.L., Karaca, E., Melquiond, A.S.J., van Dijk, M., de Vries, S.J., Bonvin, A.M.J.J.

“…The prediction of the quaternary structure of biomolecular macromolecules is of paramount importance for fundamental understanding of cellular processes and…”
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Structural insights into SARS-CoV-2 proteins by Arya, Rimanshee, Kumari, Shweta, Pandey, Bharati, Mistry, Hiral, Bihani, Subhash C., Das, Amit, Prashar, Vishal, Gupta, Gagan D., Panicker, Lata, Kumar, Mukesh

“…[Display omitted] •Structures of many SARS-CoV-2 proteins have been determined in last six months.•These structures provide useful insights into the…”
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Peptide Design Principles for Antimicrobial Applications by Torres, Marcelo D.T., Sothiselvam, Shanmugapriya, Lu, Timothy K., de la Fuente-Nunez, Cesar

“…The increased incidence of bacterial resistance to available antibiotics represents a major global health problem and highlights the need for novel…”
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Recent Insights Into Mechanisms of β-Cell Lipo- and Glucolipotoxicity in Type 2 Diabetes by Lytrivi, Maria, Castell, Anne-Laure, Poitout, Vincent, Cnop, Miriam

“…The deleterious effects of chronically elevated free fatty acid (FFA) levels on glucose homeostasis are referred to as lipotoxicity, and the concurrent…”
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Can Predicted Protein 3D Structures Provide Reliable Insights into whether Missense Variants Are Disease Associated? by Ittisoponpisan, Sirawit, Islam, Suhail A., Khanna, Tarun, Alhuzimi, Eman, David, Alessia, Sternberg, Michael J.E.

“…Knowledge of protein structure can be used to predict the phenotypic consequence of a missense variant. Since structural coverage of the human proteome can be…”
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ExoCarta: A Web-Based Compendium of Exosomal Cargo by Keerthikumar, Shivakumar, Chisanga, David, Ariyaratne, Dinuka, Al Saffar, Haidar, Anand, Sushma, Zhao, Kening, Samuel, Monisha, Pathan, Mohashin, Jois, Markandeya, Chilamkurti, Naveen, Gangoda, Lahiru, Mathivanan, Suresh

“…Exosomes are membranous vesicles that are released by a variety of cells into the extracellular microenvironment and are implicated in intercellular…”
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Autophagy in Parkinson's Disease by Hou, Xu, Watzlawik, Jens O., Fiesel, Fabienne C., Springer, Wolfdieter

“…Impaired protein homeostasis and accumulation of damaged or abnormally modified protein are common disease mechanisms in many neurodegenerative disorders,…”
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Metal Toxicity Links to Alzheimer's Disease and Neuroinflammation by Huat, Tee Jong, Camats-Perna, Judith, Newcombe, Estella A., Valmas, Nicholas, Kitazawa, Masashi, Medeiros, Rodrigo

“…As the median age of the population increases, the number of individuals with Alzheimer's disease (AD) and the associated socio-economic burden are predicted…”
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Apoptosis, Pyroptosis, and Necroptosis—Oh My! The Many Ways a Cell Can Die by Ketelut-Carneiro, Natália, Fitzgerald, Katherine A.

“…[Display omitted] •Apoptosis, pyroptosis and necroptosis are programmed cell death pathways.•Pyroptosis share many features with apoptosis and…”
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Mechanisms of Gasdermin Family Members in Inflammasome Signaling and Cell Death by Feng, Shouya, Fox, Daniel, Man, Si Ming

“…The Gasdermin (GSDM) family consists of Gasdermin A (GSDMA), Gasdermin B (GSDMB), Gasdermin C (GSDMC), Gasdermin D (GSDMD), Gasdermin E (GSDME) and Pejvakin…”
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The AlphaFold Database of Protein Structures: A Biologist’s Guide by David, Alessia, Islam, Suhail, Tankhilevich, Evgeny, Sternberg, Michael J.E.

“…[Display omitted] •AlphaFold, released the three-dimensional models (3D) of the human proteome.•Accurately and poorly modelled regions may be present within a…”
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Experimental Evidence for Enhanced Receptor Binding by Rapidly Spreading SARS-CoV-2 Variants by Laffeber, Charlie, de Koning, Kelly, Kanaar, Roland, Lebbink, Joyce H.G.

“…[Display omitted] •Rapidly spreading variants of SARS-CoV-2 have mutations in the receptor binding motif of the spike protein.•The N501Y variant binds 7-fold…”
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