Tag: pymol

GROMACS version: 2021.1GROMACS modification: Yes/NoDear colleagues,I have done clustering with 1,2- hexanediol molecule using gmx cluster and got a index file out put from cluster frames. Using that index file when I am extracting the cluster members as a trajectory using trajcov I am getting the output file but it…

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…

GROMACS version:2021.4-UbuntuGROMACS modification: Yes/NoHere post your question: I run 100nsec simulation with all ‘default’ parameter suggested by the tutorial Protein-Ligand Complex. After 10 days the simulation was finally over. To visualize the results prior to the analysis step, i uploaded into Pymol start.pdb(dump0) and md_0_100.gro. What I saw was that…

Bentes B, Martinelli J, Souza L, Cavalcante D, Almeida M, Isaac V. Spatial distribution of the amazon river prawn Macrobrachium Amazonicum (Heller, 1862) (Decapoda, Caridea, Palaemonidae) in two perennial creeks of an estuary on the northern coast of Brazil (Guajará Bay, Belém, Pará). Brazilian J Biol. 2011;71:925–35. Article  Google Scholar …

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…

Need assistance in proper binding of cysteines 0 Hello! I am newbie in protein building and i need to create disulfide bond between newly builded cysteine and another one to form active site for my ligand. Further i need to dock small molecule in this site. Is there any tools…

Greetings Under the overarching framework of structural bioinformatics, a comprehensive understanding of basic proteomics is essential. Proteomics is the study of proteins on a large scale, encompassing their structure, function, and interactions within biological systems. Within this context, molecular docking plays a pivotal role. Molecular docking is a computational method…

Installer Bundles Here you will find the Installer Bundles through which you can easily install PyMod 2.0 and all its dependencies. Please refer to the Installation Instructions of PyMod 2.0 User’s Guide to know how to use them. Windows Windows Installer Bundle (version 2.0.8, last updated: 3/11/2017).PLEASE NOTE: PyMod 2…

We are seeking a Senior Bioinformatics Scientist to support our ongoing antibody discovery and genetic engineering efforts. The role includes refining custom tools and algorithms to facilitate identification of therapeutic leads from OmniAb immune repertoires and applying cutting edge computational biology approaches to all stages of antibody discovery, from antigen…

Generation and purification of recombinant fiber knob proteins pQE expression plasmids (Qiagen, Manchester, UK) containing DNA encoding species D fiber knob proteins were produced by TWIST Biosciences (San Francisco, USA). The vectors were transformed by heat shock into competent SG13009 Escherichia coli (E.coli) bacteria containing a pREP4–4 plasmid. Heat shock…

How to find the most representative protein data base ID for your protein? 0 Hello, I am trying to find the most representative protein model for a set of genes – for example DNA polymerase epsilon catalytic subunit A from the human gene POLE. I have searched the protein data…

How to seperate proteins on the same chain? 2 Hello All, I am using this structure www.rcsb.org/structure/5N2S I want to separate out just the receptor and remove the cytochrome. Problem being there are in the same chain Thanks! pdb protein • 106 views • link updated 2 hours ago by…

PyMOL: how to list all selection names? 0 Hello everyone, A colleague asked me to use PyMOL and set up different colors for her selections … there are around 200 selections, I never used PyMOL before and I can’t find in the wiki how to list all the names of…

oSalad August 21, 2023, 11:29pm 1 GROMACS version: 2022GROMACS modification: No Hello, I am trying to parameterize phenylacetic acid to the CHARMM forcefield. I used CGenFF to get the .str file and used their python script to convert to GROMACS format. I made sure to use the exact version of…

Modelling of CsaB The CsaB enzyme (Uniprot K4ZGN3; 396 amino acids) was homology-modeled by use of Phyre2 and I-Tasser as well as by AlphaFold. The first two of these programs based their modeling approach onto the only so far crystallized pyruvyltransferase, Pvg1p (pdb 5ax77), which shows a low sequence identity…

Soft-randomization of phage-displayed hIL-2 beta chain interface revealed hotspots modulating the interaction Soft-randomization was chosen for an initial mutational scanning at hIL-2/hIL-2R beta interface, focused on solvent-exposed (>20%) hIL-2 residues close to the beta chain (<5 Å). A library of 7 × 107 members was obtained by Kunkel mutagenesis15 with spiked mutagenic oligonucleotides…

Biorender is a popular site used by students, professionals, and hobbyists alike. It offers an easy way to create diagrams on the basis of given data or figures. However, there are some alternatives available that can provide similar functionality or even better application features than what biorender has to offer….

O’Leary, N. A. et al. Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion and functional annotation. Nucleic Acids Res. 44, D733–D745 (2016). Google Scholar  Frankish, A. et al. GENCODE: reference annotation for the human and mouse genomes in 2023. Nucleic Acids Res. 51, D942–D949 (2023). Google Scholar  Pertea,…

Bailey, M. H. et al. Comprehensive characterization of cancer driver genes and mutations. Cell 173, 371–385 (2018). Article  CAS  PubMed  PubMed Central  Google Scholar  Gabriele, M., Tobon, A. L., D’Agostino, G. & Testa, G. The chromatin basis of neurodevelopmental disorders: Rethinking dysfunction along the molecular and temporal axes. Prog. Neuropsychopharmacol….

Preparation of libraries A total of 265 medicinal plants were selected and introduced into the ChEBI database to extract the effective compounds. After removing duplicates, 87 potential compounds were obtained from the 265 original plant species. The PharmMapper website has introduced 423 potential target candidates for these compounds. In addition,…

Libraries preparation A total of 265 medicinal plants were selected and introduced into the ChEBI database to extract the effective compounds. After removing duplicates, 87 potential compounds were obtained from the 265 native plant species. The PharmMapper website has introduced 423 potential target candidates for these compounds. In addition, the…

Batch coloring co-folded proteins and outputting PNG 2 I’m new to using protein visualization tools and struggling to batch process my files. I currently have hundreds of co-folded proteins using Alphafold Multimer, but it’s taking too long to go through them all and manually coloring the two chains. And in…

A UCSF Chimera option: (Taken from a more complicated script I wrote for use with pychimera here: script, pychimera) NB, pychimera takes a little more involved installation compared to pymol, but I really like it. The code below should work inside chimera’s python interpreter though I believe with no extra…

Transcribed image text: Question – Please use the given 2 docking software and do the ligand-protein docking of the provided compounds. While preparing the final report, please include docking steps in both software tools. Also, include the top 3 complexes each from both software. Please upload the report to the…

Ssb1 Alphafold secondary structure (1–609 aa) was downloaded from the Pombase (www.pombase.org/gene/SPBC660.13c) and edited using PyMOL software [64]. The α-helices, β-sheets, and loops are colored in red, yellow, and green, respectively, in the four conserved DNA binding domains F, A, B, and C. The N- and C-termini are indicated by…

Study design The overall goal of this study was to explore the molecular mechanisms of remdesivir-related cardiotoxicity in anti-COVID-19 therapy. We first performed the GPCR screening using major anti-COVID-19 drugs as ligands (n = 3 per GPCR). We validated the results of GPCR screening by concentration-response analysis and determined the EC50 and…

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…

Constructs MOTH domains of human TALI (23-123), Otoraplin (18-128), and MIA (19-131), and TANGO1 (30-139) from Drosophila melanogaster (dmTANGO1(30-139)) were expressed from codon-optimized sequences in a modified pQE40 expression vector36 in M15 pRep4 E. coli strain. Human TANGO1 (21-131) (hsTANGO1 (21-131)) and TANGO1 (21-151) (hsTANGO1 (21-151)) were expressed from codon-optimized…

Design and synthesis of indolyl pyrimidinamine inhibitors of TTBK1/2 Our lead (AMG28, Fig. 1A) emerged from examination of the off-target activity of a published Amgen NF-κB inducing kinase (NIK) inhibitor27. The potency of AMG28 was reported in the MRC Kinase Profiling Inhibitor Database as 8% activity remaining for TTBK1 and 12%…

Thank you for your kind reply. I’m sorry that my explanation is not clear. I’m speaking of ‘Plugin’ tab you see in the attached image. ![image][1] The operation I want to do, written in the format you have indicated, would look like this. ‘Plugin’ > ‘APBS Electrostatics’ > ‘options(Prepare Molecule)’…

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)….

Bioinformatics is a rapidly growing field that integrates biological science and computer science for the development and application of computational tools in order to analyze and interpret biological data. Programming languages are the most fundamental and versatile tool that has become essential in bioinformatics. There are various languages that are…

Purification of T7Select 10-3b phages The T7Select 10-3b phage vector (Novagen, Merck) was used in this study. Non-recombinant/recombinant T7Select 10-3b phages were purified from the lysate of infected E. coli strain BL5403 by PEG-8000 precipitation as per the method described in T7 select system manual. The pellet was suspended in…

Hi guys, I want to make a protein-ligand docking from a PREDICTED protein structure (HSD17B2, calidris pugnax) (AlphaFold and D-I-TASSER) and I decided to use HADDOCK as it has been reported by many recent papers to be the overall best. The ligand I want to use id TESTOSTERONE , so…

Figure 5. Substituting residues predicted to contact the P-site tRNA or P-codon confers Gcd− phenotypes in yeast. (A–C) Contacts between G926 of h28 (A,B) and certain other rRNA residues in the P-site (B,C) with the P-site codon or tRNA as visualized in the crystal structure of the T. thermophilus 70S…

Plasmid construction The PVCpnf structural and accessory region (pvc1-16) and payload and regulatory region (Pdp1, Pnf and regulatory genes PAU_RS16570-RS24015) were synthesized de novo (GenScript) and cloned into pAWP78 and pBR322 backbones, respectively. All manipulations involving payload and regulatory plasmids (pPayload) involved standard PCR amplification with Phusion Flash 2x Master…

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…

The Molecular Dynamics (MD) is one of the techniques incorporated into bioinformatics, specifically by structural bioinformatics. With that, it is possible to obtain kinetic and thermodynamic characteristics of biomolecular structures. For example, macromolecular stability, identification of allosteric sites, elucidation of mechanisms of enzymatic activity, molecular recognition and properties of complexes…

Bioinformatics is an interdisciplinary field that analyzes and interprets biological data by combining biology, computer science, and statistics. There are various tools and techniques available for data analysis and interpretation. The software tools used in bioinformatics range from simple command-line utilities to more complex graphical programs and standalone web-services made…

Working backwards from the end of your post… I believe you have to opt into it before you start your process so that you can collect the operaions. Go to [‘Getting Started with Commands’ here](http://pymol.sourceforge.net/newman/user/S0210start_cmds.html) and look at the sections, ‘Recording Your Work (Optional)’ and ‘Saving Your Work’, particularly the…

How do I convert GUI operations to CUI operations in pymol? 0 The following operations were performed to display the surface charge density for the target pdb file in pymol. Load pdb file Click on the “Plugin” Click on the “APBS Electrostatistics” Click on the “Options” button on the main…

Can’t open Autodock and chembio3D 0 I’m studying in bioinformatics, and the same problem occured when I’m trying to open my Autodock and chembio3D. When I clicked the software, the preloading interface occurred for a second or two, and then the software closed, without any notices of defaults or hints….

Unable to change torsion angles of 3D structure after loading 0 Hello everyone, I am having an issue with PyMOL’s save/load command. What I am doing is that by using PDB files of RNA structures, I am doing some perturbations to the torsion angles, saving this updated structure with cmd.save(),…

jackn March 3, 2023, 7:36pm 1 GROMACS version: 2023GROMACS modification: NoI am new to GROMACS and have been following the lysozyme in water tutorial (Lysozyme in Water). When I mdrun after making all the necessary files and run the output .gro file with the .xtc file in Pymol the waters…

How Does Structure Viewer recognize Second Structure Element? 2 How does structure viewer (like RasMol ,PyMOL, etc) recognize the second structure elements(alpha sheet, beta strand,etc)? Even though in PDB file, it do not have information about which part is alpha sheet or beta strand. Appreciate any comment and suggestion! pymol…

Introduction At present, major progress has been made to prevent and treat cardiovascular disease (CVD) through lifestyle changes and drugs, but CVD is still the main cause of death in humans, especially in developed country and developing country.1 It is worth noting that the residual risk of CVD in patients…

Recent gene duplication in the MCP gene family The MCP family of enzymes presents evidence of common ancestry, both in terms of sequence and structural homology and the chromosomal arrangement of genes. We were interested to know if any of these MCP genes continued to be duplicated more recently, and…

PyMOL: Gaps in protein structure yet shown by the sequence 0 In the screenshot below, I’m trying to determine what exactly is meant by the gap in the protein structure–depicted by dashed noodle. I’m trying to determine what is meant by the greyed out residues: VSGTNGT. The protein structure seems…

Introduction Proteases regulate various biological processes including protein synthesis and maturation, activity modification, degradation and turnover. Depending on their catalytic mechanisms, these proteases are primarily classified into cysteine, metallo-, serine, threonine and aspartic protease family (Beers et al., 2004). The latter protease family is known as acid protease family because they…

2D structure of a custom protein (not in any databases) from a PDB file. 1 Hi! I’m looking for a tool that can convert the 3D protein structure of a custom PDB file (not in any databases) into a 2D representation. So that the protein is laid out flat and…

Cells and reagents HEK293T and U87 cells were maintained in DMEM medium (Gibco) supplemented with 10% fetal bovine serum (FBS, Labtech) and 100 U ml−1 penicillin plus 100 μg ml−1 streptomycin (Pen/Strep; Gibco). THP-1-IFIT1 cells that had been modified to express Gaussia luciferase under the control of the IFIT1 promoter were described previously62. THP-1…

International Diabetes Federation (IDF). Diabetes Atlas 8th Edition 2017. www.idf.org/our-network/regions-members/africa/welcome.html. Accessed 15 July 2018 (2018). Singh, S., Usman, K. & Banerjee, M. Pharmacogenetic studies update in type 2 diabetes mellitus. World J. Diabetes. 7, 302. doi.org/10.4239/wjd.v7.i15.302 (2016). Article  PubMed  PubMed Central  Google Scholar  Inzucchi, S. E. et al. Management of…

Pérez-Serra, A. et al. Genetic basis of dilated cardiomyopathy. Int. J. Cardiol. 224, 461–472 (2016). PubMed  Article  Google Scholar  Petropoulou, E. et al. Digenic inheritance of mutations in the cardiac troponin (TNNT2) and cardiac beta myosin heavy chain (MYH7) as the cause of severe dilated cardiomyopathy. Eur. J. Med. Genet….

Hi Filip, This is already done. The update was in PyMOL 1.8.4.2 and in Open-Source PyMOL rev 4165. The object names are still the same, so it’s backwards compatible. The only difference is the file format, previously we downloaded omap format, now it’s ccp4 map format (larger files but higher…

Job Summary Illumina, is currently hiring on a vacant job post of Summer Intern – Bioinformatics based in Cambridge England United Kingdom. Please read the job detail carefully before applying. Job Title: Summer Intern – Bioinformatics Company Name: Illumina Job Type: Full Time Job Location: Cambridge England United Kingdom Salary:…

M. Madan Babus Group and the Center for Data-Driven Discovery in the Department of Structural Biology is seeking a highly driven, Full time Machine Learning Research Scientist support the Kalodimos and Babu Groups on the Blue Sky Initiative “Seeing the Invisible in Protein Kinases.” This project is supported by $35…

Hello everyone, I recently ran some docking experiments in Maestro at a university computer. The problem is that I cannot be at that computer all the time. Is it possible to open the data in, for example, PyMOL so I can work on my personal computer? And if so, would…

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…

Question: How do I view data in pymol via Ipymol for visualisation in a Jupyter notebook? 1 I am analysing protein data using Python programming language and Jupyter notebook. In the Terminal I have put an alias in a hidden file on the home directory entitled .bash_profile, in order to…

AlphaFold2 from DeepMind has been released as an open source application.  At UNC Research Computing Center, we are able to run AlphaFold2 in our machines to provide protein 3D structure from a chain of amino acids.  Following the steps below, we will be able to invoke AlphaFold2 in Longleaf cluster….

How to open 2 separate pymol windows from a script, and run commands after pymol window closes 0 Hello, In short, I’m playing around with pymol and have come across 2 problems. How can I open 2 separate windows of pymol from the same script Closing pymol closes the entire…

Abstract The acute respiratory disease induced by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a global epidemic in just less than a year by the first half of 2020. The subsequent efficient human-to-human transmission of this virus eventually affected millions of people worldwide. The most devastating thing…

In our lab we use Profit (www.bioinf.org.uk/software/profit/) for the ligand and interface RMSD calculations. Depending on the complexity of your system this might be easy or not at all. The steps we take are: 1 – Define an interface region between both chains in the native structure. Basically, check for…

Listing Results Gromacs Contact Map Contact maps using Gromacs ResearchGate Just Now Researchgate.net View All Contact maps using Gromacs ? I used gmx mdmat in gromacs to create contact maps, but it seems that the mdmat gives the minimum average distance rather than the average centre-of-mass distance. Estimated Reading Time:…

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…

S. Both AlphaFold and Xu use simple folding engines L-BFGS (L- Broyden–Fletcher–Goldfarb– Shanno (BFGS)) and CNS (Crystallography and NMR System), respectively, i.e., improvements come from a better energy potential using distributional information. The phase problem is a problem, to the point that in the past decade, several structures, such as M-PMV…

Pymolrc settings help in pymol 0 Hello, I wanted to set up pymol, so I get the highest resolution every time it starts. this can be done in the Pymolrc file. this file can be accessed via file->edit pymolrc my code for pymolrc is bg white util.performance(0) rebuild and I…

How I can merge 2 pdb files correctly on pyMol 1 Hi there, Please, I’m not experienced in this field and I need help. I want to check the ligand-interaction of 2 molecules, but I’m not able to merge the 2 PDB files correctly, because it’s like the ligand is…

How to show intermolecular forces between two chains within the same protein in Pymol 0 Hello! Would anyone know how to show intermolecular forces such as Vanderwaal forces, hydrogen bonds etc in Pymol using a python script? I would like to analyze the forces between two chains in the same…

AutoDock Flexible Molecular Docking Tutorial Autodock is a molecular docking software package, open source and free, the official website is autodock.scripps.edu/, the latest version is AutoDock 4.2.6, including AutoDock and AutoGrid two modules, AutoDock software package download address It is autodock.scripps.edu/downloads/autodock-registration/autodock-4-2-download-page/, including Linux, Mac OS and Windows versions…

What to do with a bunch of AlphaFold2 structures? 1 I’ve ended up with the structures of a dozen or so proteins predicted by AlphaFold2 by happenstance. The proteins are all orthologs. The provenance of the sequences is transcriptomic (de novo assemblies, to be specific). I’d like to try and…

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…

how to calculate positive and negative for a given protein sequence 0 Hello, I would like to know how once could calculate positive and negative for a given sequence? The PDB of the protein is 1ak4. It has two chain A and B. I am looking to find a way…

  PYMOL: Output Polar Contacts Between Chains to Text File 0   I am new to PyMOL but have a very specific task that I need to do. I have a PDB structure file of protein homo-oligomer, and I want to use PyMol to determine polar contacts between chain A…

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…