Tag: AutoDock

computational chemistry – Troubleshooting an Autodock Vina Error on Chimera: “Could not find an atomic number for Hn Hn”

After having minimized a ligand (that I prepared on Marvinsketch), and after having prepared a target enzyme to dock said ligand onto (collected from RCSP PDB), I was met with an error by the reply log stating that it “could not find atomic number for Hn Hn”. As a new…

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Autodock as a tool for virtual screening for anti-influenza drugs

ชื่อเรื่อง Autodock as a tool for virtual screening for anti-influenza drugs Autodock as a tool for virtual screening for anti-influenza drugs [Proceedings of 10th Annual National Symposium on Computational Science and Engineering] ประเภทเอกสาร บทความในหนังสือ ดรรชนี-ไทย AutoDock;ไข้หวัดใหญ่;เครื่องมือเสมือนจริง;การตรวจคัดกรอง;ยาต้านไวรัส ดรรชนี-อังกฤษ AutoDock;Influenza;Tool for virtual;Screening;Anti drugs Authors (สังกัด) …

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Error with running AutoGrid- AutoDock4 : comp_chem

Hi! I am doing my first docking study for my undergraduate research. And I have not been able to proceed beyond running AutoGrid. I keep getting the below error. Can I please get some help with this? Thank you. Also, I am using Windows. And I have both AutoDock.exe and…

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AutoDock Vina 1.2.0 | Macs in Chemistry

  A new publication describes and update to AutoDock Vina “AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings” DOI. AutoDock Vina is arguably one of the fastest and most widely used open-source programs for molecular docking. However, compared to other programs in the AutoDock Suite, it…

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Best program for covalent docking

Best program for covalent docking 0 What is the best, free software for molecular docking of small ligands and protein? I am looking for a program that would allow me to covalently dock ester to protein. I know the exact mechanism of the binding reaction. I know that AutoDock flexible…

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Rubisco molecular docking to RuBP, CO2 and O2 and DFT calculations

Rubisco molecular docking to RuBP, CO2 and O2 and DFT calculations 0 I am writing an article about Rubisco affinity to its substrates CO2 and O2. Rubisco is an enzyme with quite complicated working mechanism. Firstly, it covalently bounds to the RuBP, forming RuBP enediolate. I believe that i can…

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How To Install autodock on Ubuntu 20.04

In this tutorial we learn how to install autodock on Ubuntu 20.04. autodock is analysis of ligand binding to protein structure Introduction In this tutorial we learn how to install autodock on Ubuntu 20.04. What is autodock AutoDock is a prime representative of the programs addressing the simulation of the…

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Autodock Vina: Parse error on line 2 in file “ligand.pdbqt”: Unknown or inappropriate tag

Autodock Vina: Parse error on line 2 in file “ligand.pdbqt”: Unknown or inappropriate tag 0 Hello, I am trying to do docking analysis using Autodock Vina for a protein and a ligand. I have generated the respective protein.pdbqt and ligand.pdbqt files using Grid>Marcromolecules>Choose, and have also generated the config.txt file:…

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AutoDock Vina Gives Wildly Different Results From Different Simulations Using Same Parameters

AutoDock Vina Gives Wildly Different Results From Different Simulations Using Same Parameters 0 Hello everyone, When I run multiple Autodock Vina independent simulations (at exhaustivness of 100) on the SAME protein and the SAME ligand using the exact SAME parameters but with different random seeds I get different results. Each…

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Active Pharmaceutical Ingredients from Brazilian Pharmacopeia in PDBQT format, for docking with AutoDock e Vina Tools

Published: 11 November 2021| Version 2 | DOI: 10.17632/dp3f425kkf.2 Contributors: Description Active Pharmaceutical Ingredients (APIs) are molecules that can be used for the manufacturing of Drugs. The Brazilian Health Regulatory Agency (Agência Nacional de Vigilância Sanitária) is responsible for the oversight and approval of production and distribution of all drugs…

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Peptris Fresher Pharma jobs in Bangalore | Pharmacy / Biotechnology /Bioinformatics Candidates

Peptris is an Al / ML company working on drug discovery. Peptris has developed a platform technology to enhance efficiencies across the drug discovery/development cascade using Artificial Intelligence/Machine Learning. We are currently looking for Computational Chemistry Research Associates to be part of our team that is developing an Al/ML platform…

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Rubisco molecular docking in AutoDock Vina : bioinformatics

To begin with I have to admit I f***ed up. I chose my school essay topic, to be about how aminoacids subsitions change Rubisco affinity to oxygen and carbon dioxide in wheat Rubisco. However, I did it at the last minute without enough research about mechanism of Rubisco and right…

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docking – How can I get Vina to recognise boron atoms?

I am trying to dock a ligand that features a boron (B) atom. AutoDock Vina throws an error with the following message: ATOM syntax incorrect: “B” is not a valid AutoDock type. Note that AutoDock atom types are case-sensitive. I assumed that the error meant that I had to add…

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Improving ligand-ranking of AutoDock Vina by changing the empirical parameters

doi: 10.1002/jcc.26779. Online ahead of print. T Ngoc Han Pham  1 , Trung Hai Nguyen  2   3 , Nguyen Minh Tam  3   4 , Thien Y Vu  1 , Nhat Truong Pham  5 , Nguyen Truong Huy  1 , Binh Khanh Mai  6 , Nguyen Thanh Tung  7   8 , Minh Quan Pham  8  …

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Molecular docking considerations

I am performing molecular docking experiments but find that the results are “pre-determined” by the setting used. Therefore, I am looking for a general guideline on performing docking and subsequent interpretation. (I know docking is all hypothetical and needs further experimental validation, but in this question please assume, although might…

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(2Z)-3-hydroxy-3-(4-R-phenyl)-prop-2-enedithioic acids | IDR

Introduction Mycobacterium tuberculosis is a pathogenic bacterium that is well known to be the causative agent of tuberculosis. The World Health Organization (WHO) has pinpointed this pathogen as one of the two leading causes worldwide of higher mortality resulting from an infectious agent. The increase in the number of cases…

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Protein Evolution Inc hiring Research Scientist, Bioinformatics in Guilford, Indiana, United States

LocationThis role will be based out of Guilford, CT or Cambridge, MA. Company Description Protein Evolution Inc. (PEI) develops proteins that address problems in climate change and healthcare. We unite proprietary technology in molecular biology, artificial intelligence, and engineering to enable a high-throughput development process not possible elsewhere. Protein Evolution…

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Index error list index out of range autodock 4

Index error list index out of range autodock 4 30-09-2021 apologise, but does not of index range 4 list index error range autodock not out try all successively IndexError: list index out of range…

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Extraction and characterization of metabolites from Olea europaea pulp and their molecular docking against SARS-CoV-2 main-protease (M(pro))

This article was originally published here Nat Prod Res. 2021 Sep 28:1-7. doi: 10.1080/14786419.2021.1983813. Online ahead of print. ABSTRACT The present study is the first to extract the bioactive metabolites from Olea europaea fruit using the Soxhlet-maceration extraction method. The preliminary phytochemical; Fourier transform-infrared spectroscopy (FT-IR); gas chromatography-mass spectrometry (GC-MS)…

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AI Rx | Computer Graphics World

Today, we can produce more biomedical data in about three months than we did in the past, with petabytes from just a single hospital. There is a deluge from various sources, such as patients’ medical records, medical instruments, lab work, and more. Likewise, in the research and development space, similar…

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AutoDock Flexible Molecular Docking Tutorial

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…

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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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Vcl.ExtCtrls.TControlBar.AutoDock – RAD Studio API Documentation

Delphi property AutoDock: Boolean read FAutoDock write FAutoDock default 1; C++ __property AutoDock = {default=1}; Properties Description Determines whether the control bar temporarily docks drag clients to provide visual feedback. Vcl.ExtCtrls.TControlBar.AutoDock inherits from Vcl.ExtCtrls.TCustomControlBar.AutoDock. All content below this line refers to Vcl.ExtCtrls.TCustomControlBar.AutoDock. Determines whether the control bar temporarily docks drag…

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