Quick Guideline for Computational Drug Design (Revised Edition)

Introduction to Structural Bioinformatics

Author(s): Sheikh Arslan Sehgal*, Rana Adnan Tahir and Muhammad Waqas

Pp: 1-11 (11)

DOI: 10.2174/9789814998697121010004

* (Excluding Mailing and Handling)

Abstract

Bioinformatics is an emerging field of modern biology that solves biological problems with the help of computational approaches by utilizing mathematical and statistical techniques. There are many available databases of protein and gene sequences. The protein sequence can be retrieved from UniProt and 3D structure prediction can be performed by utilizing homology modeling, threading, and ab initio. The predicted structures can be evaluated by utilizing numerous model evaluation tools.


Keywords: Bioinformatics tools, Evolutionary biology, Homology modeling, Molecular docking, Sequence retrieval, Structural bioinformatics, Virtual screening.

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      • 15. middleware::check_user_access:114
      • 16. vendor/laravel/framework/src/Illuminate/Pipeline/Pipeline.php:183
      • 17. vendor/laravel/framework/src/Illuminate/Routing/Middleware/SubstituteBindings.php:50
      • 18. vendor/laravel/framework/src/Illuminate/Pipeline/Pipeline.php:183
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      • 17. vendor/laravel/framework/src/Illuminate/Routing/Controller.php:54
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      • 18. vendor/laravel/framework/src/Illuminate/Routing/ControllerDispatcher.php:43
      • 19. vendor/laravel/framework/src/Illuminate/Routing/Route.php:260
      • 20. vendor/laravel/framework/src/Illuminate/Routing/Route.php:206
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      • 16. app/Models/Subject.php:238
      • 17. app/Http/Controllers/ChapterController.php:1434
      • 18. vendor/laravel/framework/src/Illuminate/Routing/Controller.php:54
      • 19. vendor/laravel/framework/src/Illuminate/Routing/ControllerDispatcher.php:43
      • 20. vendor/laravel/framework/src/Illuminate/Routing/Route.php:260
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      700μsalphaeurekaselec_live_10_06_2022Subject.php#238
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      • 14. app/Models/Subject.php:238
      • 15. app/Http/Controllers/ChapterController.php:1434
      • 16. vendor/laravel/framework/src/Illuminate/Routing/Controller.php:54
      • 17. vendor/laravel/framework/src/Illuminate/Routing/ControllerDispatcher.php:43
      • 18. vendor/laravel/framework/src/Illuminate/Routing/Route.php:260
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      370μsalphaeurekaselec_live_10_06_2022Subject.php#255
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      • 16. app/Models/Subject.php:255
      • 17. app/Http/Controllers/ChapterController.php:1435
      • 18. vendor/laravel/framework/src/Illuminate/Routing/Controller.php:54
      • 19. vendor/laravel/framework/src/Illuminate/Routing/ControllerDispatcher.php:43
      • 20. vendor/laravel/framework/src/Illuminate/Routing/Route.php:260
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      410μsalphaeurekaselec_live_10_06_2022Subject.php#255
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      • 14. app/Models/Subject.php:255
      • 15. app/Http/Controllers/ChapterController.php:1435
      • 16. vendor/laravel/framework/src/Illuminate/Routing/Controller.php:54
      • 17. vendor/laravel/framework/src/Illuminate/Routing/ControllerDispatcher.php:43
      • 18. vendor/laravel/framework/src/Illuminate/Routing/Route.php:260
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      • 13. app/Models/EbookVolume.php:271
      • 14. app/Http/Controllers/ChapterController.php:1438
      • 15. vendor/laravel/framework/src/Illuminate/Routing/Controller.php:54
      • 16. vendor/laravel/framework/src/Illuminate/Routing/ControllerDispatcher.php:43
      • 17. vendor/laravel/framework/src/Illuminate/Routing/Route.php:260
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      • 14. app/Models/EbookVolume.php:999
      • 15. app/Http/Controllers/ChapterController.php:1462
      • 16. vendor/laravel/framework/src/Illuminate/Routing/Controller.php:54
      • 17. vendor/laravel/framework/src/Illuminate/Routing/ControllerDispatcher.php:43
      • 18. vendor/laravel/framework/src/Illuminate/Routing/Route.php:260
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      280μsalphaeurekaselec_live_10_06_2022ContentAccess.php#647
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      • 11. app/Models/ContentAccess.php:647
      • 12. app/Http/Controllers/ChapterController.php:1465
      • 13. vendor/laravel/framework/src/Illuminate/Routing/Controller.php:54
      • 14. vendor/laravel/framework/src/Illuminate/Routing/ControllerDispatcher.php:43
      • 15. vendor/laravel/framework/src/Illuminate/Routing/Route.php:260
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      240μsalphaeurekaselec_live_10_06_2022ContentAccess.php#647
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      • 11. app/Models/ContentAccess.php:647
      • 12. app/Http/Controllers/ChapterController.php:1478
      • 13. vendor/laravel/framework/src/Illuminate/Routing/Controller.php:54
      • 14. vendor/laravel/framework/src/Illuminate/Routing/ControllerDispatcher.php:43
      • 15. vendor/laravel/framework/src/Illuminate/Routing/Route.php:260
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      580μsalphaeurekaselec_live_10_06_2022UserAccess.php#1266
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      • 13. app/Models/UserAccess/UserAccess.php:1266
      • 14. app/Http/Controllers/ChapterController.php:1518
      • 15. vendor/laravel/framework/src/Illuminate/Routing/Controller.php:54
      • 16. vendor/laravel/framework/src/Illuminate/Routing/ControllerDispatcher.php:43
      • 17. vendor/laravel/framework/src/Illuminate/Routing/Route.php:260
    • (select j.user_access_id,j.volume_id,j.user_id,j.from_ip,j.to_ip,j.type,j.track,"Trial Access" as access_base_text, CASE j.type WHEN 111 THEN true ELSE false END as terms_popup, "S" as content_download_type, null as restricted_user_access_key, null as restricted_user_access_type, CASE j.track WHEN 0 THEN false ELSE true END as tracksAccessByVolume,"chapter" as access_level, j.chapter_id from `user_access_chapter_trail` as `j` inner join `user_access_info` as `info` on `j`.`user_access_id` = `info`.`user_access_id` where ((j.from_ip <= 873443466 and j.to_ip >=873443466 )) and ((j.from_date <= 1739835002 and j.to_date >= 1739835002 and j.perpetual= 0) or (j.from_date is null and j.to_date is null and j.perpetual= 1)) and j.chapter_id = 15437) union (select j.user_access_id,j.volume_id,j.user_id,j.from_ip,j.to_ip,j.type,j.track,"Subscribed" as access_base_text, false as terms_popup, "S" as content_download_type, null as restricted_user_access_key, null as restricted_user_access_type, CASE j.track WHEN 0 THEN false ELSE true END as tracksAccessByVolume,"chapter" as access_level, j.chapter_id from `user_access_chapter_corporate` as `j` inner join `user_access_info` as `info` on `j`.`user_access_id` = `info`.`user_access_id` where ((j.from_ip <= 873443466 and j.to_ip >=873443466 )) and ((j.from_date <= 1739835002 and j.to_date >= 1739835002 and j.perpetual= 0) or (j.from_date is null and j.to_date is null and j.perpetual= 1)) and j.chapter_id = 15437) union (select j.user_access_id,j.volume_id,j.user_id,j.from_ip,j.to_ip,j.type,j.track,"Token Based Access" as access_base_text, false as terms_popup, "R" as content_download_type, j.uc_id as restricted_user_access_key, "v" as restricted_user_access_type, CASE j.track WHEN 0 THEN false ELSE true END as tracksAccessByVolume,"chapter" as access_level, j.chapter_id from `user_access_chapter_token` as `j` inner join `user_access_info` as `info` on `j`.`user_access_id` = `info`.`user_access_id` where ((j.from_ip <= 873443466 and j.to_ip >=873443466 )) and ((j.from_date <= 1739835002 and j.to_date >= 1739835002 and j.perpetual= 0) or (j.from_date is null and j.to_date is null and j.perpetual= 1)) and j.chapter_id = 15437)
      720μsalphaeurekaselec_live_10_06_2022UserAccess.php#1266
      Backtrace
      • 13. app/Models/UserAccess/UserAccess.php:1266
      • 14. app/Http/Controllers/ChapterController.php:1549
      • 15. vendor/laravel/framework/src/Illuminate/Routing/Controller.php:54
      • 16. vendor/laravel/framework/src/Illuminate/Routing/ControllerDispatcher.php:43
      • 17. vendor/laravel/framework/src/Illuminate/Routing/Route.php:260
    • select b.banner_link, b.banner_name, b.banner_script, b.banner_remarks, b.banner_file_name, b.banner_placement, bd.content_type, bd.content_id from `tbl_banner` as `b` inner join `tbl_banner_detail` as `bd` on `bd`.`banner_id` = `b`.`banner_id` inner join `users` as `u` on `u`.`id` = `b`.`updated_by` where `b`.`banner_ebook` = 1 and `bd`.`content_type` = 'B' and `bd`.`content_id` = 3116 and `b`.`banner_from_date` <= 1739835002 and `b`.`banner_to_date` >= 1739835002 and `b`.`banner_status` = 'A' order by `b`.`banner_id` desc
      1.08msalphaeurekaselec_live_10_06_2022Banner.php#95
      Bindings
      • 0: 1
      • 1: B
      • 2: 3116
      • 3: 1739835002
      • 4: 1739835002
      • 5: A
      Backtrace
      • 13. app/Models/Banner.php:95
      • 14. app/Http/helpers.php:404
      • 17. vendor/laravel/framework/src/Illuminate/Filesystem/Filesystem.php:124
      • 18. vendor/laravel/framework/src/Illuminate/View/Engines/PhpEngine.php:58
      • 19. vendor/laravel/framework/src/Illuminate/View/Engines/CompilerEngine.php:73
    • select count(*) as aggregate from `uc_cart_products` where cart_id='b28bc8d692738ed28c853896f1e0d2a7'
      230μsalphaeurekaselec_live_10_06_2022Cart.php#271
      Backtrace
      • 15. app/Models/Cart.php:271
      • 16. view::layouts._header:260
      • 18. vendor/laravel/framework/src/Illuminate/Filesystem/Filesystem.php:124
      • 19. vendor/laravel/framework/src/Illuminate/View/Engines/PhpEngine.php:58
      • 20. vendor/laravel/framework/src/Illuminate/View/Engines/CompilerEngine.php:73
    App\Models\Keywords
    7Keywords.php#?
    App\Models\Chapter
    1Chapter.php#?
    App\Models\Ebook
    1Ebook.php#?
        _token
        qHDpqTN8CJHfzhxuExn8JXQMC0rlDvp8x0PccZTN
        uc_cart_id
        b28bc8d692738ed28c853896f1e0d2a7
        _previous
        array:1 [ "url" => "https://alpha.eurekaselect.com/chapter/15437" ]
        _flash
        array:2 [ "old" => [] "new" => [] ]
        PHPDEBUGBAR_STACK_DATA
        []
        path_info
        /chapter/15437
        status_code
        200
        
        status_text
        OK
        format
        html
        content_type
        text/html; charset=UTF-8
        request_query
        []
        
        request_request
        []
        
        request_headers
        0 of 0
        array:17 [ "x-https" => array:1 [ 0 => "1" ] "host" => array:1 [ 0 => "alpha.eurekaselect.com" ] "priority" => array:1 [ 0 => "u=0, i" ] "cookie" => array:1 [ 0 => "wayfindertarget=eyJpdiI6IkJNZVlhcy9mbGh0MjVnUlJ5ZFJvb2c9PSIsInZhbHVlIjoiWFhyMzg3bmhySHRwWEs0cnQzSE8xVmJOR1Y0UzFVeXA4S2NCc1pLM0kwQT0iLCJtYWMiOiJlZWJlMDVkMjJhNjk2NGI2NGRkYTMwYmY0MzI1YTBiOTU0ZGM4ZDNhNzQzYmIwNjZjM2M4MGQ2MzIwMWY3MDRhIiwidGFnIjoiIn0%3Dwayfindertarget=eyJpdiI6IkJNZVlhcy9mbGh0MjVnUlJ5ZFJvb2c9PSIsInZhbHVlIjoiWFhyMzg3bmhySHRwWEs0cnQzSE8xVmJOR1Y0UzFVeXA4S2NCc1pLM0kwQT0iLCJtYWMiOiJlZWJlMDVkMjJhNjk2" ] "accept-encoding" => array:1 [ 0 => "gzip, deflate, br, zstd" ] "sec-fetch-dest" => array:1 [ 0 => "document" ] "sec-fetch-user" => array:1 [ 0 => "?1" ] "sec-fetch-mode" => array:1 [ 0 => "navigate" ] "sec-fetch-site" => array:1 [ 0 => "none" ] "accept" => array:1 [ 0 => "text/html,application/xhtml+xml,application/xml;q=0.9,image/avif,image/webp,image/apng,*/*;q=0.8,application/signed-exchange;v=b3;q=0.7" ] "user-agent" => array:1 [ 0 => "Mozilla/5.0 AppleWebKit/537.36 (KHTML, like Gecko; compatible; ClaudeBot/1.0; +claudebot@anthropic.com)" ] "upgrade-insecure-requests" => array:1 [ 0 => "1" ] "sec-ch-ua-platform" => array:1 [ 0 => ""Windows"" ] "sec-ch-ua-mobile" => array:1 [ 0 => "?0" ] "sec-ch-ua" => array:1 [ 0 => ""HeadlessChrome";v="129", "Not=A?Brand";v="8", "Chromium";v="129"" ] "cache-control" => array:1 [ 0 => "no-cache" ] "pragma" => array:1 [ 0 => "no-cache" ] ]
        request_cookies
        0 of 0
        array:1 [ "wayfindertarget" => null ]
        response_headers
        0 of 0
        array:5 [ "content-type" => array:1 [ 0 => "text/html; charset=UTF-8" ] "cache-control" => array:1 [ 0 => "no-cache, private" ] "date" => array:1 [ 0 => "Mon, 17 Feb 2025 23:30:02 GMT" ] "set-cookie" => array:2 [ 0 => "XSRF-TOKEN=eyJpdiI6Ikl1aGpxQWQrekpsTFJVNFkreTJVRHc9PSIsInZhbHVlIjoiSkxXaWtQMkF5azFzaXV3TGV3SzhVUTdabU1YcEtwaEFXaWRRY3pBd0s5MWYzUDVXVmdGcHNKTmIrZHFLeTRnelI5U0JuaU9pTHRnL1Y1ODlLTXcrT0FkdXNFaXNoL1lOMzAwRkdoRktmeUdwRWExTU9DelJDWVBGeU90T1FTNU4iLCJtYWMiOiJkNTMwOTJmOGFiMTVhMDM5MDc5YmE2NDI0ZmI2OTFhNDI5ZGUyOTNjNGEyZGI4YjQ1MDE2Y2QzYjQ1MjAyNGRkIiwidGFnIjoiIn0%3D; expires=Thu, 20 Feb 2025 11:30:02 GMT; Max-Age=216000; path=/; secure; samesite=laxXSRF-TOKEN=eyJpdiI6Ikl1aGpxQWQrekpsTFJVNFkreTJVRHc9PSIsInZhbHVlIjoiSkxXaWtQMkF5azFzaXV3TGV3SzhVUTdabU1YcEtwaEFXaWRRY3pBd0s5MWYzUDVXVmdGcHNKTmIrZHFLeTRnelI5U0Jua" 1 => "alphaeurekaselectnet_session=eyJpdiI6IjBjNi9JU2p3QmRlSVJ6WFIvWnByRUE9PSIsInZhbHVlIjoiRnhqZzdhV2pIR3dGalpMWWxpcVo4dzFCVzRnZytqY0FmbmlHZEpvc1VNL1dBc0lpL1IxU0xDK3hBZGM2c2tCWlNsRTFKQW95TDJNMVVFWWQvT0t2SFlya3pMRkExRlRPeDN5L0gwdytQQUROL1R1d3dYYTNoREVaRWlYajZjcmQiLCJtYWMiOiJkNDIxNzI5YTBjOTBhZjg2ZjkwYzQ2NTQ3OGRhZDIyYWY2ZWFkNGQyODc4MDA4YWZiN2IyZmQ0MjhkODk1MTE1IiwidGFnIjoiIn0%3D; path=/; secure; httponly; samesite=laxalphaeurekaselectnet_session=eyJpdiI6IjBjNi9JU2p3QmRlSVJ6WFIvWnByRUE9PSIsInZhbHVlIjoiRnhqZzdhV2pIR3dGalpMWWxpcVo4dzFCVzRnZytqY0FmbmlHZEpvc1VNL1dBc0lpL1IxU0xDK3h" ] "Set-Cookie" => array:2 [ 0 => "XSRF-TOKEN=eyJpdiI6Ikl1aGpxQWQrekpsTFJVNFkreTJVRHc9PSIsInZhbHVlIjoiSkxXaWtQMkF5azFzaXV3TGV3SzhVUTdabU1YcEtwaEFXaWRRY3pBd0s5MWYzUDVXVmdGcHNKTmIrZHFLeTRnelI5U0JuaU9pTHRnL1Y1ODlLTXcrT0FkdXNFaXNoL1lOMzAwRkdoRktmeUdwRWExTU9DelJDWVBGeU90T1FTNU4iLCJtYWMiOiJkNTMwOTJmOGFiMTVhMDM5MDc5YmE2NDI0ZmI2OTFhNDI5ZGUyOTNjNGEyZGI4YjQ1MDE2Y2QzYjQ1MjAyNGRkIiwidGFnIjoiIn0%3D; expires=Thu, 20-Feb-2025 11:30:02 GMT; path=/; secureXSRF-TOKEN=eyJpdiI6Ikl1aGpxQWQrekpsTFJVNFkreTJVRHc9PSIsInZhbHVlIjoiSkxXaWtQMkF5azFzaXV3TGV3SzhVUTdabU1YcEtwaEFXaWRRY3pBd0s5MWYzUDVXVmdGcHNKTmIrZHFLeTRnelI5U0Jua" 1 => "alphaeurekaselectnet_session=eyJpdiI6IjBjNi9JU2p3QmRlSVJ6WFIvWnByRUE9PSIsInZhbHVlIjoiRnhqZzdhV2pIR3dGalpMWWxpcVo4dzFCVzRnZytqY0FmbmlHZEpvc1VNL1dBc0lpL1IxU0xDK3hBZGM2c2tCWlNsRTFKQW95TDJNMVVFWWQvT0t2SFlya3pMRkExRlRPeDN5L0gwdytQQUROL1R1d3dYYTNoREVaRWlYajZjcmQiLCJtYWMiOiJkNDIxNzI5YTBjOTBhZjg2ZjkwYzQ2NTQ3OGRhZDIyYWY2ZWFkNGQyODc4MDA4YWZiN2IyZmQ0MjhkODk1MTE1IiwidGFnIjoiIn0%3D; path=/; secure; httponlyalphaeurekaselectnet_session=eyJpdiI6IjBjNi9JU2p3QmRlSVJ6WFIvWnByRUE9PSIsInZhbHVlIjoiRnhqZzdhV2pIR3dGalpMWWxpcVo4dzFCVzRnZytqY0FmbmlHZEpvc1VNL1dBc0lpL1IxU0xDK3h" ] ]
        session_attributes
        0 of 0
        array:5 [ "_token" => "qHDpqTN8CJHfzhxuExn8JXQMC0rlDvp8x0PccZTN" "uc_cart_id" => "b28bc8d692738ed28c853896f1e0d2a7" "_previous" => array:1 [ "url" => "https://alpha.eurekaselect.com/chapter/15437" ] "_flash" => array:2 [ "old" => [] "new" => [] ] "PHPDEBUGBAR_STACK_DATA" => [] ]
        ClearShow all
        Date ↕MethodURLData
        #12025-02-17 23:30:02GET/chapter/15437112199