We are analyzing https://link.springer.com/article/10.1007/s10822-008-9188-5.

Title:
A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE) | Journal of Computer-Aided Molecular Design
Description:
Protein binding sites undergo ligand specific conformational changes upon ligand binding. However, most docking protocols rely on a fixed conformation of the receptor, or on the prior knowledge of multiple conformations representing the variation of the pocket, or on a known bounding box for the ligand. Here we described a general induced fit docking protocol that requires only one initial pocket conformation and identifies most of the correct ligand positions as the lowest score. We expanded a previously used diverse “cross-docking” benchmark to thirty ligand–protein pairs extracted from different crystal structures. The algorithm systematically scans pairs of neighbouring side chains, replaces them by alanines, and docks the ligand to each ‘gapped’ version of the pocket. All docked positions are scored, refined with original side chains and flexible backbone and re-scored. In the optimal version of the protocol pairs of residues were replaced by alanines and only one best scoring conformation was selected from each ‘gapped’ pocket for refinement. The optimal SCARE (SCan Alanines and REfine) protocol identifies a near native conformation (under 2 Å RMSD) as the lowest rank for 80% of pairs if the docking bounding box is defined by the predicted pocket envelope, and for as many as 90% of the pairs if the bounding box is derived from the known answer with ∼5 Å margin as used in most previous publications. The presented fully automated algorithm takes about 2 h per pose of a single processor time, requires only one pocket structure and no prior knowledge about the binding site location. Furthermore, the results for conformationally conserved pockets do not deteriorate due to substantial increase of the pocket variability.
Website Age:
28 years and 1 months (reg. 1997-05-29).

Matching Content Categories {📚}

Education
Technology & Computing
Cryptocurrency

Content Management System {📝}

What CMS is link.springer.com built with?

Custom-built

No common CMS systems were detected on Link.springer.com, and no known web development framework was identified.

Traffic Estimate {📈}

What is the average monthly size of link.springer.com audience?

🌠 Phenomenal Traffic: 5M - 10M visitors per month

Based on our best estimate, this website will receive around 7,643,328 visitors per month in the current month.

check SE Ranking
check Ahrefs
check Similarweb
check Ubersuggest
check Semrush

How Does Link.springer.com Make Money? {💸}

We can't see how the site brings in money.

While many websites aim to make money, others are created to share knowledge or showcase creativity. People build websites for various reasons. This could be one of them. Link.springer.com might be cashing in, but we can't detect the method they're using.

Keywords {🔍}

article, google, scholar, cas, abagyan, totrov, mol, docking, proteins, biol, ligand, pocket, chem, molecular, privacy, cookies, content, journal, binding, conformation, pairs, access, drug, publish, research, search, design, scare, kufareva, ruben, protein, alanines, soc, cavasotto, author, data, information, log, flexible, scanning, refinement, bottegoni, irina, bounding, box, protocol, algorithm, structure, chapter, discover,

Topics {✒️}

diverse “cross-docking” benchmark drug-receptor thermodynamics month download article/chapter irina kufareva pocket structure icm manual 3 dual alanine scanning protein sci 14 binding site location ligand binding docking protocols rely ligand docking docking bounding box author correspondence full article pdf privacy choices/manage cookies check access scripps research institute instant access initial pocket conformation correct ligand positions receptor conformationally conserved pockets cavasotto cn molecular biology european economic area multiple conformations representing neighbouring side chains original side chains single processor time related subjects brooks cl 3rd electronic supplementary material kufareva conditions privacy policy article bottegoni accepting optional cookies predicted pocket envelope torrey pines ct article journal journal finder publish main content log fixed conformation scoring conformation native conformation ruben abagyan article log article cite similar content privacy policy

Schema {🗺️}

WebPage:
      mainEntity:
         headline:A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE)
         description:Protein binding sites undergo ligand specific conformational changes upon ligand binding. However, most docking protocols rely on a fixed conformation of the receptor, or on the prior knowledge of multiple conformations representing the variation of the pocket, or on a known bounding box for the ligand. Here we described a general induced fit docking protocol that requires only one initial pocket conformation and identifies most of the correct ligand positions as the lowest score. We expanded a previously used diverse “cross-docking” benchmark to thirty ligand–protein pairs extracted from different crystal structures. The algorithm systematically scans pairs of neighbouring side chains, replaces them by alanines, and docks the ligand to each ‘gapped’ version of the pocket. All docked positions are scored, refined with original side chains and flexible backbone and re-scored. In the optimal version of the protocol pairs of residues were replaced by alanines and only one best scoring conformation was selected from each ‘gapped’ pocket for refinement. The optimal SCARE (SCan Alanines and REfine) protocol identifies a near native conformation (under 2 Å RMSD) as the lowest rank for 80% of pairs if the docking bounding box is defined by the predicted pocket envelope, and for as many as 90% of the pairs if the bounding box is derived from the known answer with ∼5 Å margin as used in most previous publications. The presented fully automated algorithm takes about 2 h per pose of a single processor time, requires only one pocket structure and no prior knowledge about the binding site location. Furthermore, the results for conformationally conserved pockets do not deteriorate due to substantial increase of the pocket variability.
         datePublished:2008-02-14T00:00:00Z
         dateModified:2008-02-14T00:00:00Z
         pageStart:311
         pageEnd:325
         sameAs:https://doi.org/10.1007/s10822-008-9188-5
         keywords:
            Scanning docking
            Cross docking
            ICM
            Internal coordinate mechanics
            Induced fit
            Receptor flexibility
            Drug binding
            Structure based drug design
            Physical Chemistry
            Computer Applications in Chemistry
            Animal Anatomy / Morphology / Histology
         image:
            https://media.springernature.com/lw1200/springer-static/image/art%3A10.1007%2Fs10822-008-9188-5/MediaObjects/10822_2008_9188_Fig1_HTML.gif
            https://media.springernature.com/lw1200/springer-static/image/art%3A10.1007%2Fs10822-008-9188-5/MediaObjects/10822_2008_9188_Fig2_HTML.gif
            https://media.springernature.com/lw1200/springer-static/image/art%3A10.1007%2Fs10822-008-9188-5/MediaObjects/10822_2008_9188_Fig3_HTML.gif
            https://media.springernature.com/lw1200/springer-static/image/art%3A10.1007%2Fs10822-008-9188-5/MediaObjects/10822_2008_9188_Fig4_HTML.gif
            https://media.springernature.com/lw1200/springer-static/image/art%3A10.1007%2Fs10822-008-9188-5/MediaObjects/10822_2008_9188_Fig5_HTML.gif
            https://media.springernature.com/lw1200/springer-static/image/art%3A10.1007%2Fs10822-008-9188-5/MediaObjects/10822_2008_9188_Fig6_HTML.gif
            https://media.springernature.com/lw1200/springer-static/image/art%3A10.1007%2Fs10822-008-9188-5/MediaObjects/10822_2008_9188_Fig7_HTML.gif
            https://media.springernature.com/lw1200/springer-static/image/art%3A10.1007%2Fs10822-008-9188-5/MediaObjects/10822_2008_9188_Fig8_HTML.gif
         isPartOf:
            name:Journal of Computer-Aided Molecular Design
            issn:
               1573-4951
               0920-654X
            volumeNumber:22
            type:
               Periodical
               PublicationVolume
         publisher:
            name:Springer Netherlands
            logo:
               url:https://www.springernature.com/app-sn/public/images/logo-springernature.png
               type:ImageObject
            type:Organization
         author:
               name:Giovanni Bottegoni
               affiliation:
                     name:The Scripps Research Institute
                     address:
                        name:Department of Molecular Biology, TPC28, The Scripps Research Institute, La Jolla, USA
                        type:PostalAddress
                     type:Organization
               type:Person
               name:Irina Kufareva
               affiliation:
                     name:The Scripps Research Institute
                     address:
                        name:Department of Molecular Biology, TPC28, The Scripps Research Institute, La Jolla, USA
                        type:PostalAddress
                     type:Organization
               type:Person
               name:Maxim Totrov
               affiliation:
                     name:Molsoft, LLC
                     address:
                        name:Molsoft, LLC, La Jolla, USA
                        type:PostalAddress
                     type:Organization
               type:Person
               name:Ruben Abagyan
               affiliation:
                     name:The Scripps Research Institute
                     address:
                        name:Department of Molecular Biology, TPC28, The Scripps Research Institute, La Jolla, USA
                        type:PostalAddress
                     type:Organization
                     name:Molsoft, LLC
                     address:
                        name:Molsoft, LLC, La Jolla, USA
                        type:PostalAddress
                     type:Organization
               email:[email protected]
               type:Person
         isAccessibleForFree:
         hasPart:
            isAccessibleForFree:
            cssSelector:.main-content
            type:WebPageElement
         type:ScholarlyArticle
      context:https://schema.org
ScholarlyArticle:
      headline:A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE)
      description:Protein binding sites undergo ligand specific conformational changes upon ligand binding. However, most docking protocols rely on a fixed conformation of the receptor, or on the prior knowledge of multiple conformations representing the variation of the pocket, or on a known bounding box for the ligand. Here we described a general induced fit docking protocol that requires only one initial pocket conformation and identifies most of the correct ligand positions as the lowest score. We expanded a previously used diverse “cross-docking” benchmark to thirty ligand–protein pairs extracted from different crystal structures. The algorithm systematically scans pairs of neighbouring side chains, replaces them by alanines, and docks the ligand to each ‘gapped’ version of the pocket. All docked positions are scored, refined with original side chains and flexible backbone and re-scored. In the optimal version of the protocol pairs of residues were replaced by alanines and only one best scoring conformation was selected from each ‘gapped’ pocket for refinement. The optimal SCARE (SCan Alanines and REfine) protocol identifies a near native conformation (under 2 Å RMSD) as the lowest rank for 80% of pairs if the docking bounding box is defined by the predicted pocket envelope, and for as many as 90% of the pairs if the bounding box is derived from the known answer with ∼5 Å margin as used in most previous publications. The presented fully automated algorithm takes about 2 h per pose of a single processor time, requires only one pocket structure and no prior knowledge about the binding site location. Furthermore, the results for conformationally conserved pockets do not deteriorate due to substantial increase of the pocket variability.
      datePublished:2008-02-14T00:00:00Z
      dateModified:2008-02-14T00:00:00Z
      pageStart:311
      pageEnd:325
      sameAs:https://doi.org/10.1007/s10822-008-9188-5
      keywords:
         Scanning docking
         Cross docking
         ICM
         Internal coordinate mechanics
         Induced fit
         Receptor flexibility
         Drug binding
         Structure based drug design
         Physical Chemistry
         Computer Applications in Chemistry
         Animal Anatomy / Morphology / Histology
      image:
         https://media.springernature.com/lw1200/springer-static/image/art%3A10.1007%2Fs10822-008-9188-5/MediaObjects/10822_2008_9188_Fig1_HTML.gif
         https://media.springernature.com/lw1200/springer-static/image/art%3A10.1007%2Fs10822-008-9188-5/MediaObjects/10822_2008_9188_Fig2_HTML.gif
         https://media.springernature.com/lw1200/springer-static/image/art%3A10.1007%2Fs10822-008-9188-5/MediaObjects/10822_2008_9188_Fig3_HTML.gif
         https://media.springernature.com/lw1200/springer-static/image/art%3A10.1007%2Fs10822-008-9188-5/MediaObjects/10822_2008_9188_Fig4_HTML.gif
         https://media.springernature.com/lw1200/springer-static/image/art%3A10.1007%2Fs10822-008-9188-5/MediaObjects/10822_2008_9188_Fig5_HTML.gif
         https://media.springernature.com/lw1200/springer-static/image/art%3A10.1007%2Fs10822-008-9188-5/MediaObjects/10822_2008_9188_Fig6_HTML.gif
         https://media.springernature.com/lw1200/springer-static/image/art%3A10.1007%2Fs10822-008-9188-5/MediaObjects/10822_2008_9188_Fig7_HTML.gif
         https://media.springernature.com/lw1200/springer-static/image/art%3A10.1007%2Fs10822-008-9188-5/MediaObjects/10822_2008_9188_Fig8_HTML.gif
      isPartOf:
         name:Journal of Computer-Aided Molecular Design
         issn:
            1573-4951
            0920-654X
         volumeNumber:22
         type:
            Periodical
            PublicationVolume
      publisher:
         name:Springer Netherlands
         logo:
            url:https://www.springernature.com/app-sn/public/images/logo-springernature.png
            type:ImageObject
         type:Organization
      author:
            name:Giovanni Bottegoni
            affiliation:
                  name:The Scripps Research Institute
                  address:
                     name:Department of Molecular Biology, TPC28, The Scripps Research Institute, La Jolla, USA
                     type:PostalAddress
                  type:Organization
            type:Person
            name:Irina Kufareva
            affiliation:
                  name:The Scripps Research Institute
                  address:
                     name:Department of Molecular Biology, TPC28, The Scripps Research Institute, La Jolla, USA
                     type:PostalAddress
                  type:Organization
            type:Person
            name:Maxim Totrov
            affiliation:
                  name:Molsoft, LLC
                  address:
                     name:Molsoft, LLC, La Jolla, USA
                     type:PostalAddress
                  type:Organization
            type:Person
            name:Ruben Abagyan
            affiliation:
                  name:The Scripps Research Institute
                  address:
                     name:Department of Molecular Biology, TPC28, The Scripps Research Institute, La Jolla, USA
                     type:PostalAddress
                  type:Organization
                  name:Molsoft, LLC
                  address:
                     name:Molsoft, LLC, La Jolla, USA
                     type:PostalAddress
                  type:Organization
            email:[email protected]
            type:Person
      isAccessibleForFree:
      hasPart:
         isAccessibleForFree:
         cssSelector:.main-content
         type:WebPageElement
["Periodical","PublicationVolume"]:
      name:Journal of Computer-Aided Molecular Design
      issn:
         1573-4951
         0920-654X
      volumeNumber:22
Organization:
      name:Springer Netherlands
      logo:
         url:https://www.springernature.com/app-sn/public/images/logo-springernature.png
         type:ImageObject
      name:The Scripps Research Institute
      address:
         name:Department of Molecular Biology, TPC28, The Scripps Research Institute, La Jolla, USA
         type:PostalAddress
      name:The Scripps Research Institute
      address:
         name:Department of Molecular Biology, TPC28, The Scripps Research Institute, La Jolla, USA
         type:PostalAddress
      name:Molsoft, LLC
      address:
         name:Molsoft, LLC, La Jolla, USA
         type:PostalAddress
      name:The Scripps Research Institute
      address:
         name:Department of Molecular Biology, TPC28, The Scripps Research Institute, La Jolla, USA
         type:PostalAddress
      name:Molsoft, LLC
      address:
         name:Molsoft, LLC, La Jolla, USA
         type:PostalAddress
ImageObject:
      url:https://www.springernature.com/app-sn/public/images/logo-springernature.png
Person:
      name:Giovanni Bottegoni
      affiliation:
            name:The Scripps Research Institute
            address:
               name:Department of Molecular Biology, TPC28, The Scripps Research Institute, La Jolla, USA
               type:PostalAddress
            type:Organization
      name:Irina Kufareva
      affiliation:
            name:The Scripps Research Institute
            address:
               name:Department of Molecular Biology, TPC28, The Scripps Research Institute, La Jolla, USA
               type:PostalAddress
            type:Organization
      name:Maxim Totrov
      affiliation:
            name:Molsoft, LLC
            address:
               name:Molsoft, LLC, La Jolla, USA
               type:PostalAddress
            type:Organization
      name:Ruben Abagyan
      affiliation:
            name:The Scripps Research Institute
            address:
               name:Department of Molecular Biology, TPC28, The Scripps Research Institute, La Jolla, USA
               type:PostalAddress
            type:Organization
            name:Molsoft, LLC
            address:
               name:Molsoft, LLC, La Jolla, USA
               type:PostalAddress
            type:Organization
      email:[email protected]
PostalAddress:
      name:Department of Molecular Biology, TPC28, The Scripps Research Institute, La Jolla, USA
      name:Department of Molecular Biology, TPC28, The Scripps Research Institute, La Jolla, USA
      name:Molsoft, LLC, La Jolla, USA
      name:Department of Molecular Biology, TPC28, The Scripps Research Institute, La Jolla, USA
      name:Molsoft, LLC, La Jolla, USA
WebPageElement:
      isAccessibleForFree:
      cssSelector:.main-content

External Links {🔗}(96)

Analytics and Tracking {📊}

Google Tag Manager

Libraries {📚}

Clipboard.js
Prism.js

CDN Services {📦}

Crossref

3.97s.

LINK . SPRINGER . COM {}