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Showing 1–8 of 8 results
Advanced filters: Author: Sandor Vajda Clear advanced filters

  • ClusPro is a web server that performs rigid-body docking of two proteins by sampling billions of conformations. Low-energy docked structures are clustered, and centers of the largest clusters are used as likely models of the complex.

    • Dima Kozakov
    • David R Hall
    • Sandor Vajda
    Protocols
    Nature Protocols
    Volume: 12, P: 255-278

  • Fragment-based drug discovery employs screening of small polar compounds typically exhibiting low affinity towards protein targets. Here, the authors combine the use of protein-based binding pharmacophores with the theory of protein hotspots to develop a design protocol for fragment libraries, called SpotXplorer, and validate their approach on common and emerging drug targets.

    • Dávid Bajusz
    • Warren S. Wade
    • György M. Keserű
    ResearchOpen Access
    Nature Communications
    Volume: 12, P: 1-10

  • Macrocycles have the potential to act on currently undruggable targets, but their discovery thus far has been unsystematic. A physicochemical analysis of all nonredundant co-crystal structures now sets out guidelines for macrocycle development.

    • Elizabeth A Villar
    • Dmitri Beglov
    • Adrian Whitty
    Research
    Nature Chemical Biology
    Volume: 10, P: 723-731

  • AbEMap generates large ensembles of docked antigen–antibody structures based on the structure of an antigen and either the structure or the sequence of an antibody. For each antigen residue, a likelihood score for being part of the epitope is obtained.

    • Israel T. Desta
    • Sergei Kotelnikov
    • Dima Kozakov
    Protocols
    Nature Protocols
    Volume: 18, P: 1814-1840

  • This protocol describes the FTMap family of web servers for determining and characterizing ligand-binding hot spots of macromolecules, including FTSite for predicting ligand-binding sites, FTFlex for accounting for side chain flexibility, FTMap/param for parameterizing additional probes, and FTDyn for mapping ensembles of protein structures.

    • Dima Kozakov
    • Laurie E Grove
    • Sandor Vajda
    Protocols
    Nature Protocols
    Volume: 10, P: 733-755