DOI . ORG {}

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We began analyzing https://link.springer.com/protocol/10.1007/978-1-60761-274-2_11, but it redirected us to https://link.springer.com/protocol/10.1007/978-1-60761-274-2_11. The analysis below is for the second page.

Title[redir]:
The Flexible Pocketome Engine for Structural Chemogenomics | SpringerLink
Description:
Biological metabolites, substrates, cofactors, chemical probes, and drugs bind to flexible pockets in multiple biological macromolecules to exert their biological effect. The rapid growth of the structural databases and sequence data, including SNPs and...

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

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Keywords {🔍}

google, scholar, article, pubmed, cas, abagyan, docking, totrov, protein, mol, proteins, structural, kufareva, biol, molecular, binding, comput, data, information, flexible, methods, interactions, modeling, prediction, structurebased, discovery, ligand, chem, energy, privacy, cookies, content, publish, search, chemogenomics, protocol, engine, biology, small, access, kinase, journal, research, pocketome, biological, comprehensive, structures, molecules, drug, design,

Topics {✒️}

nih/nigms grants 5-r01-gm071872-02 disease-related genome modifications large-scale similarity evaluations uppsala electron-density server structure-based virtual screening optimizing hydrogen-bond networks cutting-edge 3d docking side-chain amide orientation g-protein coupled receptors g-protein-coupled receptor x-ray structural information springer science+business media peptide-mhc binding geometry multiple pocket conformations ligand-steered homology modeling flexible protein-ligand docking computational protein-protein interactions structure-based identification scripps research institute structure-based discovery modulate kinase activity privacy choices/manage cookies structure-based design structural chemogenomics protocol 1-r01-gm074832-01a1 ligand binding envelopes protein binding sites reduced side effects active kinase states protein-ligand docking accurate computational approach drug-receptor thermodynamics discrete receptor flexibility predicting molecular interactions author information authors enable accurate prediction ligand/receptor interactions european economic area multiple biological macromolecules hydrogen atom contacts pdb improvement starts polar hydrogen positions neutron diffraction comparison positioning hydrogen atoms atomic surface area dual alanine scanning nucleic acids res swiss-prot annotation deformation zone mapping induced fit effects

Schema {🗺️}

ScholarlyArticle:
      headline:The Flexible Pocketome Engine for Structural Chemogenomics
      pageEnd:279
      pageStart:249
      image:https://media.springernature.com/w153/springer-static/cover/book/978-1-60761-274-2.jpg
      genre:
         Springer Protocols
      isPartOf:
         name:Chemogenomics
         isbn:
            978-1-60761-274-2
            978-1-60761-273-5
         type:Book
      publisher:
         name:Humana Press
         logo:
            url:https://www.springernature.com/app-sn/public/images/logo-springernature.png
            type:ImageObject
         type:Organization
      author:
            name:Ruben Abagyan
            affiliation:
                  name:The Scripps Research Institute
                  address:
                     name:Department of Molecular Biology, 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, The Scripps Research Institute, La Jolla, USA
                     type:PostalAddress
                  type:Organization
            type:Person
      keywords:Pocketome, Chemical biology, Flexible docking, Ensemble docking, Drug screening, Activity prediction, SCARE algorithm, Binding site, Virtual ligand screening
      description:Biological metabolites, substrates, cofactors, chemical probes, and drugs bind to flexible pockets in multiple biological macromolecules to exert their biological effect. The rapid growth of the structural databases and sequence data, including SNPs and disease-related genome modifications, complemented by the new cutting-edge 3D docking, scoring, and profiling methods has created a unique opportunity to develop a comprehensive structural map of interactions between any small molecule and biopolymers. Here we demonstrate that a comprehensive structural genomics engine can be built using multiple pocket conformations, experimentally determined or generated with a variety of modeling methods, and new efficient ensemble docking algorithms. In contrast to traditional ligand-activity-based engines trained on known chemical structures and their activities, the structural pocketome and docking engine will allow prediction of poses and activities for new, previously unknown, protein binding sites, and new, previously uncharacterized, chemical scaffolds. This de novo structure-based activity prediction engine may dramatically accelerate the discovery of potent and specific therapeutics with reduced side effects.
      datePublished:2009
      isAccessibleForFree:
      hasPart:
         isAccessibleForFree:
         cssSelector:.main-content
         type:WebPageElement
      context:https://schema.org
Book:
      name:Chemogenomics
      isbn:
         978-1-60761-274-2
         978-1-60761-273-5
Organization:
      name:Humana Press
      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, The Scripps Research Institute, La Jolla, USA
         type:PostalAddress
      name:The Scripps Research Institute
      address:
         name:Department of Molecular Biology, The Scripps Research Institute, La Jolla, USA
         type:PostalAddress
ImageObject:
      url:https://www.springernature.com/app-sn/public/images/logo-springernature.png
Person:
      name:Ruben Abagyan
      affiliation:
            name:The Scripps Research Institute
            address:
               name:Department of Molecular Biology, 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, The Scripps Research Institute, La Jolla, USA
               type:PostalAddress
            type:Organization
PostalAddress:
      name:Department of Molecular Biology, The Scripps Research Institute, La Jolla, USA
      name:Department of Molecular Biology, The Scripps Research Institute, La Jolla, USA
WebPageElement:
      isAccessibleForFree:
      cssSelector:.main-content

External Links {🔗}(172)

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