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    Alika H
    The document outlines the steps for conducting in silico drug testing: 1. Determine the bioactive compound and obtain its structure from databases 2. Create a 3D model of the compound using SwissModel and validate it with saves web 3. Use tools like wey2drug and pharmmapper to identify target proteins, then use molecular docking software like PyRx to predict binding affinity between compounds and proteins 4. Analyze results, which may include a binding affinity score of -7.2 and toxicity classification of 3, indicating safe consumption in small amounts

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    Script

    Uploaded by

    Alika H
    16 views4 pages
    The document outlines the steps for conducting in silico drug testing: 1. Determine the bioactive compound and obtain its structure from databases 2. Create a 3D model of the compound using SwissModel and validate it with saves web 3. Use tools like wey2drug and pharmmapper to identify target proteins, then use molecular docking software like PyRx to predict binding affinity between compounds and proteins 4. Analyze results, which may include a binding affinity score of -7.2 and toxicity classification of 3, indicating safe consumption in small amounts

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    The document outlines the steps for conducting in silico drug testing: 1. Determine the bioactive compound and obtain its structure from databases 2. Create a 3D model of the compound using SwissModel and validate it with saves web 3. Use tools like wey2drug and pharmmapper to identify target proteins, then use molecular docking software like PyRx to predict binding affinity between compounds and proteins 4. Analyze results, which may include a binding affinity score of -7.2 and toxicity classification of 3, indicating safe consumption in small amounts

    Copyright:

    © All Rights Reserved
    Download as DOCX, PDF, TXT or read online from Scribd
    Download as docx, pdf, or txt
    16 views4 pages

    Script

    Uploaded by

    Alika H
    The document outlines the steps for conducting in silico drug testing: 1. Determine the bioactive compound and obtain its structure from databases 2. Create a 3D model of the compound using SwissModel and validate it with saves web 3. Use tools like wey2drug and pharmmapper to identify target proteins, then use molecular docking software like PyRx to predict binding affinity between compounds and proteins 4. Analyze results, which may include a binding affinity score of -7.2 and toxicity classification of 3, indicating safe consumption in small amounts

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    © All Rights Reserved
    Download as DOCX, PDF, TXT or read online from Scribd
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    Metode
    1. Bioactive compound = Determine the bioactive compound from journals
    and them find out the canonical smiles via PubChem
    2. Molecule Structure = we get the 3D structure also from pubchem that can
    be used for moleculare docking later on
    3. Targeted protein: enter smiles to wey2drug, phrammaper,
    swisstargetprediction, superpred. To summarize the data of protein from
    those 4 website stringdb is used. From there the connestions between
    proteins can be seen then choosing a disease to target or inhibit for drug
    making using the protein will be easier.
    4. Making of 3D model: create a 3d model from the Fasta the acquired from
    ncbi that fasta then can be converted to 3D modl using Swissmodel. Form
    there validate the 3d model using saves web there are 6 parameters but
    ony Errat and Procheck is used
    5. Molecular Docking: Remove water from the macromplecule using PyMol
    and continue the molecular docking into PyRx . There we can check the
    binding affinity. Pymol can also illustrate the protein to ligand connections.
    With the model that was made by Pymol a 2D Mode can be made to see
    the connections far more clearly
    6. Bagaimana membaca grafik PSA?

    8. Hasil uji fitokimia itu kualitatif atau kuantitatif?


    = Hasil uji fitokimia umumnya bersifat kualitatif, yang berarti mengidentifikasi
    keberadaan atau ketiadaan senyawa-senyawa kimia tertentu dalam suatu sampel
    tanaman. Namun, dalam beberapa kasus, uji fitokimia juga dapat mencakup aspek
    kuantitatif, di mana konsentrasi relatif senyawa-senyawa tersebut dapat diukur,
    meskipun biasanya metode kuantitatif yang lebih spesifik digunakan untuk tujuan
    tersebut.
    The results of phytochemical tests are generally qualitative in nature, which
    means identifying the presence or absence of certain chemical compounds in a
    plant sample. In some cases, however, the phytochemical assay may also include a
    quantitative aspect, in which the relative concentrations of the compounds can be
    measured, although more specific quantitative methods are usually used for this
    purpose.

    9. Apa yg dinaksud dg molekular docking?


    = Molekular docking adalah metode komputasional yang digunakan dalam ilmu
    kimia dan biologi untuk memprediksi bagaimana dua molekul, seperti protein dan
    senyawa kimia, dapat berinteraksi secara spasial. Tujuannya adalah untuk
    memahami bagaimana molekul-molekul ini berikatan bersama dan bagaimana
    interaksi tersebut dapat mempengaruhi aktivitas biologis atau fungsionalnya.
    Metode docking ini membantu para ilmuwan dalam merancang obat-obatan baru,
    memahami interaksi protein-ligand, dan mengidentifikasi potensi pengikatan
    antara molekul-molekul yang berbeda
    Molecular docking is a computational method used in chemistry and biology to
    predict how two molecules, such as proteins and chemical compounds, may
    interact spatially. The goal is to understand how these molecules bind together
    and how these interactions can affect their biological or functional activity. This
    docking method assists scientists in designing new drugs, understanding protein-
    ligand interactions, and identifying binding potentials between different
    molecules.

    11. Bagaimana proses pengujian in silico?


    = Cari senyawa bioaktif yang terkandung dalam suatu tanaman lalu cari tau
    canonical SMILES melalui pubchem. Dari sana masukan SMILES kedalam
    wey2drug, pharmmaper, dan siwsstargetprediction, superPRED untuk mengetahui
    protein target. Untuk meringkas data pada keempat sumber tersebut dapat
    menggunakan string.db agar lebih terlihat interaksi protein. Setelah menetukan
    protein target dan jenis penyakit maka yang dilakukan setelah itu adalah
    membuat model 3D melalui FASTA dan SwissModel, untuk mengecek validasi
    model gunakan saves webserver dalam opsi ERRAT dan Procheck. Lalu gunakan
    Pymol dan PyRx untuk 3D autodocking model yang dapat mengilustrasikan
    koneksi protein dengan ligand, dengan hasil ilustrasi tersebut model 2D dapat
    dibuat dengan ProteinPlus. Langkah terkahir adalah memastikan druglikeness dan
    toxicity melalui swissadme dan ProTox
    Look for bioactive compounds contained in a plant then find out about the
    canonical SMILES via pubchem. From there, enter SMILES into wey2drug,
    pharmmaper, and siwsstargetprediction, superPRED to find out the target protein.
    To summarize data from the four sources, you can use string.db to make protein
    interactions more visible. After determining the target protein and the type of
    disease, what is done after that is to create a 3D model via FASTA and SwissModel,
    to check model validation use webserver saves in the ERRAT and Procheck
    options. Then use Pymol and PyRx for 3D autodocking models that can illustrate
    protein-ligand connections, with the results of these illustrations 2D models can
    be made with ProteinPlus. The last step is to ensure drug likeness and toxicity
    through swissadme and ProTox

    12. Apa hasil dari pengujian in silico?


    = 3D model memiliki binding affinity -7,2. Bioavalability radar terlihat dibawah
    garis pink kecuali insaturation, Ukuran bagus karena dibawah 500, Hasil Protox
    diangka 3 yang berarti aman dikonsumsi dalam jumlah yang sedikit atau terkontrol
    The 3D model has a binding affinity of -7.2. Radar bioavailability can be seen
    below the pink line except for insaturation, good size because it is below 500, the
    Protox result is 3 which means it is safe to consume in small or controlled
    quantities

    4. How many scale of toxisity? Explain it.


    = There are five
    Class I: fatal if swallowed (LD50 ≤ 5)
    Class II: fatal if swallowed (5 < LD50 ≤ 50)
    Class III: toxic if swallowed (50 < LD50 ≤ 300)
    Class IV: harmful if swallowed (300 < LD50 ≤ 2000)
    Class V: may be harmful if swallowed (2000 < LD50 ≤ 5000)
    Class VI: non-toxic (LD50 > 5000)

    6. What is the meaning of LDS50?


    = LD50 stands for "lethal dose for 50% of the population." It is a measure
    commonly used in toxicology to determine the amount of a substance that is
    required to cause death in 50% of a population of test subjects. This value helps
    assess the relative toxicity of different substances and is an important factor in
    evaluating the potential dangers of various chemicals or compounds.

    8. What is the score of PyRx that means good?


    = . A lower binding affinity score typically indicates a stronger binding
    interaction.
    However, the exact "good" binding affinity score can vary depending on the
    specific context, the protein-ligand system being studied, and the goals of the
    research. Generally, a more negative binding affinity score (closer to zero)
    suggests a stronger binding interaction.

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