Tag: ChimeraX

Simulating Histidine Protonation in GROMACS – Beginner Seeking Guidance – User discussions

Hello GROMACS community, I am a total beginner in using GROMACS, and I’m currently working on a project where I need to simulate the protonation state change of histidine residues in a protein, specifically to simulate an acidic environment where histidines gain a proton (NH3+). I have downloaded a protein…

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Two mitochondrial HMG-box proteins, Cim1 and Abf2, antagonistically regulate mtDNA copy number in Saccharomyces cerevisiae | Nucleic Acids Research

Abstract The mitochondrial genome, mtDNA, is present in multiple copies in cells and encodes essential subunits of oxidative phosphorylation complexes. mtDNA levels have to change in response to metabolic demands and copy number alterations are implicated in various diseases. The mitochondrial HMG-box proteins Abf2 in yeast and TFAM in mammals…

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Compare similarity of protein variants

Compare similarity of protein variants 0 I have some .pdb files with structures of variants of the same protein and I’m looking for a way to quantify how similar (or dissimilar) they are from a reference protein. I’ve tried superimposing them and calculating RMSD with ChimeraX or PyMol, the problem…

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Mechanisms of neurotransmitter transport and drug inhibition in human VMAT2

Kandel, E. R., Koester, J. D., Mack, S. H. & Siegelbaum, S. A. Principles of Neural Science 6th edn (McGraw Hill Professional, 2021). Ng, J., Papandreou, A., Heales, S. J. & Kurian, M. A. Monoamine neurotransmitter disorders—clinical advances and future perspectives. Nat. Rev. Neurol. 11, 567–584 (2015). Article  CAS  PubMed …

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Bioinformatics Scientist/Research Software Engineer – UOD1104 at University of Dundee

We are seeking an individual with strong software development skills and a passion for research to join the Jalview (www.jalview.org) development team and help advance the state-of-the-art in biomolecular alignment visualisation and analysis. Jalview is a mature platform launched nearly a million times a year by students and researchers worldwide…

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DNA-binding protein PfAP2-P regulates parasite pathogenesis during malaria parasite blood stages

Parasite culture, maintenance, synchronization and transfection The DiCre-expressing P. falciparum clone II3 (ref. 10) was maintained in human A+ erythrocytes at 37 °C in Roswell Park Memorial Institute 1640 medium containing AlbumaxII (Invitrogen) supplemented with 2 mM l-glutamine. Parasites were either synchronized by sorbitol treatment or by purifying mature schizont stages using…

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Structure of human TRPM8 channel

Reagents and chemicals pFastBac Dual His6 MBP N10 TEV LIC cloning vector (5 C) was purchased from Addgene (Addgene plasmid no. 30123; www.addgene.org/30123). All restriction enzymes, the pFastBac1 vector, and DH10Bac cells were purchased from Thermo Fisher Scientific. Sf9 cells were purchased from ATCC. Q5® High-Fidelity DNA Polymerase, the Monarch® DNA…

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Plastid-localized xanthorhodopsin increases diatom biomass and ecosystem productivity in iron-limited surface oceans

Protein sequence and prediction analysis The amino acid sequence of FcR was deduced from the F. cylindrus genome sequence33. Protein alignments with characterized microbial rhodopsins were performed using the MUSCLE algorithm implemented in Geneious (v.5.6)69. Predictions of subcellular location were performed with SignalP v.4.0 and TargetP (v.1.1)70. Putative transmembrane domains…

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Templates from alpha fold predictions – Features and Functionality

DarioSB September 20, 2023, 10:45am #1 Dear all,is it possible to use an AlphaFold predicted structure as templates for picking?BestDario Hi Dario, You could use the molmap feature in ChimeraX to generate a volume of the alphafold structure (e.g. to 6 angstrom), save as an mrc file, import to cryosparc…

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Structural conservation of antibiotic interaction with ribosomes

Yonath, A. Antibiotics targeting ribosomes: resistance, selectivity, synergism and cellular regulation. Annu. Rev. Biochem. 74, 649–679 (2005). Article  CAS  PubMed  Google Scholar  Sohmen, D., Harms, J. M., Schlunzen, F. & Wilson, D. N. SnapShot: antibiotic inhibition of protein synthesis I. Cell 138, 1248 e1241 (2009). Article  Google Scholar  Wilson, D….

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Antiviral HIV-1 SERINC restriction factors disrupt virus membrane asymmetry

Constructs and expression of human SERINC proteins SERINC3 The gene that encodes human SERINC3 (Genscript-OHu02717D) was inserted upstream of a thrombin protease cleavable linker (LVPRGS) and Strep II epitope (WSHPQFEK) in a modified pFastBac vector by In-Fusion cloning (Clontech). Mutagenesis using the QuikChange Site-Directed Mutagenesis kit (Agilent) was performed to…

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Structural and functional characteristics of the SARS-CoV-2 Omicron subvariant BA.2 spike protein

Hirotsu, Y. et al. SARS-CoV-2 Omicron sublineage BA.2 replaces BA.1.1: genomic surveillance in Japan from September 2021 to March 2022. J. Infect. 85, 174–211 (2022). Article  CAS  PubMed  PubMed Central  Google Scholar  Lyngse, F. P. et al. Household transmission of SARS-CoV-2 Omicron variant of concern subvariants BA.1 and BA.2 in…

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Regulation of the macrolide resistance ABC-F translation factor MsrD

Crowe-McAuliffe, C. et al. Structural basis for antibiotic resistance mediated by the Bacillus subtilis ABCF ATPase VmlR. PNAS 115, 8978–8983 (2018). Article  ADS  CAS  PubMed  PubMed Central  Google Scholar  Crowe-McAuliffe, C. et al. Structural basis of ABCF-mediated resistance to pleuromutilin, lincosamide, and streptogramin A antibiotics in Gram-positive pathogens. Nat. Commun….

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Structural analysis of mitochondrial rRNA gene variants identified in patients with deafness

Introduction Aminoglycoside antibiotics (AGs) are some of the most commonly prescribed antibacterials, despite their well-known capacity to cause toxic side effects to the kidneys and inner ear (Huth et al., 2011). Although their use in the industrialized world is usually limited to severe infections, they remain very popular in the…

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Nuclear export of pre-60S particles through the nuclear pore complex

Hampoelz, B., Andres-Pons, A., Kastritis, P. & Beck, M. Structure and assembly of the nuclear pore complex. Annu. Rev. Biophys. 48, 515–536 (2019). Article  CAS  PubMed  Google Scholar  Lin, D. H. & Hoelz, A. The structure of the nuclear pore complex (an update). Annu. Rev. Biochem. 88, 725–783 (2019). Article …

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[chimerax-users] How to describe methods

[chimerax-users] How to describe methods Tom Goddard goddard at sonic.net Tue May 9 14:25:27 PDT 2023 Hi Jim, As Elaine says, ChimeraX is using ColabFold, which is an optimized version of AlphaFold. So you should cite ColabFold (and AlphaFold and ChimeraX). Also your description of the template use is a…

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“Structural Analysis of Predicted Proteins Using AlphaFold” by Brydon P. Wall

Abstract The function of around 67% of predicted proteins from genes in Mycobacteriophage CheetoDust can not be confidently predicted using traditional techniques and can only be functionally labeled “hypothetical proteins”. However, a new approach using AlphaFold, an artificial intelligence tool to generate a structural prediction from a sequence, can take…

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[chimerax-users] unifold

[chimerax-users] unifold Roger Leng rleng at ualberta.ca Fri May 5 10:58:35 PDT 2023 Many thanks, Elaine. I agree with your point. I find Alphafold is very close to “exactly” detecting two or three protein interactions. I used an example ” p53-MDM2 interaction” (structure and experiments) to test Alphafold Program. Also,…

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Structural atlas of a human gut crassvirus

Shkoporov, A. N. & Hill, C. Bacteriophages of the human gut: the “known unknown” of the microbiome. Cell Host Microbe 25, 195–209 (2019). Article  CAS  PubMed  Google Scholar  Dutilh, B. E. et al. A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes. Nat. Commun. 5, 4498…

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Structural insights into the broad protection against H1 influenza viruses by a computationally optimized hemagglutinin vaccine

Centers for Disease Control and Prevention. Past Seasons Vaccine Effectiveness Estimates, www.cdc.gov/flu/vaccines-work/past-seasons-estimates.html (2022). Accessed 10 March 2022. Centers for Disease Control and Prevention. Pandemic influenza—past pandemics, www.cdc.gov/flu/pandemic-resources/basics/past-pandemics.html (2022). Accessed 10 March 2022. Erbelding, E. J. et al. A universal influenza vaccine: the strategic plan for the National Institute of Allergy…

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Mirusviruses link herpesviruses to giant viruses

Vincent, F., Sheyn, U., Porat, Z., Schatz, D. & Vardi, A. Visualizing active viral infection reveals diverse cell fates in synchronized algal bloom demise. Proc. Natl Acad. Sci. USA 118, e2021586118 (2021). Article  CAS  PubMed  PubMed Central  Google Scholar  Suttle, C. A. Marine viruses — major players in the global…

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Sensory specializations drive octopus and squid behaviour

van Giesen, L., Kilian, P. B., Allard, C. A. H. & Bellono, N. W. Molecular basis of chemotactile sensation in octopus. Cell 183, 594–604.e14 (2020). Article  PubMed  PubMed Central  Google Scholar  Noviello, C. M. et al. Structure and gating mechanism of the α7 nicotinic acetylcholine receptor. Cell 184, 2121–2134 (2021)….

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Intranasal trimeric sherpabody inhibits SARS-CoV-2 including recent immunoevasive Omicron subvariants

Research reported in this study complies with all relevant ethical regulations, and our animal study protocol has been approved by the Animal Experimental Board of Finland (license number ESAVI/28687/2020. Phage panning Sherpabody phage display library (size ~1011 cfu) was obtained from Next Biomed Therapies Oy. To develop sherpabodies specific for SARS-CoV-2…

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Functional metagenomics uncovers nitrile-hydrolysing enzymes in a coal metagenome

Introduction Cyanide-containing compounds are known as nitriles and are widely distributed in the natural environment. They are generated by different plants in various forms, such as ricinine, phenyl acetonitrile, cyanogenic glycosides, and β -cyanoalanine (Sewell et al., 2003). Anthropogenic activities have substantially influenced the production of vast quantities of nitrile…

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Structural basis for bacterial energy extraction from atmospheric hydrogen

Statistics and reproducibility Huc purification and PAGE analysis Huc was purified from M. smegmatis cells on eight separate occasions throughout the course of the study. The yield of purified Huc (mg per litre of culture) varied by a factor of five between purifications. The relative abundance of the Huc oligomer…

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Density mediated simulation fine refinement – User discussions

dave March 2, 2023, 7:50am 1 GROMACS version: gromacs-2022.2GROMACS modification: No Hi All,(maybe more relevant to Dr. Christian Blau) It has been long I did not do MD simulations. I came across an old Bioexcel webinar about density mediated simulation by Christian Blau. It seems to be a very helpful…

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A paralog of Pcc1 is the fifth core subunit of the KEOPS tRNA-modifying complex in Archaea

A paralog of Pcc1 is widely distributed among archaea The recent discovery of a fifth subunit of KEOPS in metazoa raised the possibility that a corresponding subunit could exist in archaea. In search for such a subunit, we noticed in the model archaeon Thermococcus kodakarensis KOD1 the existence of two…

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[chimerax-users] ChimeraX Alphafold Multiple jobs

[chimerax-users] ChimeraX Alphafold Multiple jobs Tom Goddard goddard at sonic.net Fri Dec 16 12:37:56 PST 2022 Hi Rayees, ChimeraX can only run one AlphaFold prediction at a time. I tried various tricks to run two predictions at a time and they did not work. I tried starting two copies of…

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Alpha Fold Working

AlphaFold: The making of a scientific breakthrough The inside story of the DeepMind team of scientists and engineers who created AlphaFold, an AI system that is recognised as a solution to “protein folding”, a grand scientific challenge for more than 50…

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Modeling an Enzyme Active Site using Molecular Visualization Freeware

Visualizing biological macromolecules is a critical skill for students and professionals in the biological sciences. In this protocol, we demonstrate how to model the active site of the enzyme glucokinase using four freely available programs for molecular modeling. This tutorial highlights several steps of the protocol for each program, which…

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Open multi-file AlphaFold models | ChimeraX Recipes

# # Open AlphaFold database models for proteins larger than 1400 amino acids. # These calculated in 1400 amino acid segments every 200 amino acids due to # limitations (GPU memory) of the AlphaFold software. We load and align # the segment models. This produces many clashes. # # Opening…

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alphafold colab github

for the third time worked! Found inside – Page iiThe eight-volume set comprising LNCS volumes 9905-9912 constitutes the refereed proceedings of the 14th European Conference on Computer Vision, ECCV 2016, held in Amsterdam, The Netherlands, in October 2016. Please make sure you have a large enough hard drive space, bandwidth…

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Ligand GNP bound in PDB entry 7obq ‹ Protein Data Bank in Europe (PDBe) ‹ EMBL-EBI

  The above 2D and 3D (Mol*) views of ligand interactions use quaternary structure derived from the PDB entry. Please note: Some chain IDs in the tooltip are followed by a number in square brackets. This number corresponds to the operation ID (mmCIF ‘oper_expression’) used to transform the chain. The…

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Alternative way to generate .PDBQT file for AutoDock Vina? : bioinformatics

For context: I’m using macOS Big Sur and have successfully run AutoDock Vina through my terminal, after which I’ll view the output in ChimeraX. Also, I’m an undergrad attempting to teach myself how to use docking software for a personal project and future use, so I may very well have…

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PyMol – molecule export problem

PyMol – molecule export problem 0 Dear all, I have a molecule in PyMol which I want to open in ChimeraX. But after exporting the molecule as .pdb, some structural information seems to be lost – regions that in the PyMol session file are embedded into helices are now loops…

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