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7 Result(s)

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  1. No Access

    Article

    Comparative study of several algorithms for flexible ligand docking

    We have performed a comparative assessment of several programs for flexible molecular docking: DOCK 4.0, FlexX 1.8, AutoDock 3.0, GOLD 1.2 and ICM 2.8. This was accomplished using two different studies: dockin...

    Badry D. Bursulaya, Maxim Totrov… in Journal of Computer-Aided Molecular Design (2003)

  2. Article

    Discovery of small molecule inhibitors of ubiquitin-like poxvirus proteinase I7L using homology modeling and covalent docking approaches

    Essential for viral replication and highly conserved among poxviridae, the vaccinia virus I7L ubiquitin-like proteinase (ULP) is an attractive target for development of smallpox antiviral drugs. At the same time,...

    Vsevolod Katritch, Chelsea M. Byrd… in Journal of Computer-Aided Molecular Design (2007)

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  3. No Access

    Article

    A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE)

    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 con...

    Giovanni Bottegoni, Irina Kufareva… in Journal of Computer-Aided Molecular Design (2008)

  4. No Access

    Article

    Docking and scoring with ICM: the benchmarking results and strategies for improvement

    Flexible docking and scoring using the internal coordinate mechanics software (ICM) was benchmarked for ligand binding mode prediction against the 85 co-crystal structures in the modified Astex data set. The I...

    Marco A. C. Neves, Maxim Totrov… in Journal of Computer-Aided Molecular Design (2012)

  5. Article

    Open Access

    Ligand-biased ensemble receptor docking (LigBEnD): a hybrid ligand/receptor structure-based approach

    Ligand docking to flexible protein molecules can be efficiently carried out through ensemble docking to multiple protein conformations, either from experimental X-ray structures or from in silico simulations. ...

    Polo C.-H. Lam, Ruben Abagyan, Maxim Totrov in Journal of Computer-Aided Molecular Design (2018)

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  6. No Access

    Article

    Hybrid receptor structure/ligand-based docking and activity prediction in ICM: development and evaluation in D3R Grand Challenge 3

    In context of D3R Grand Challenge 3 we have investigated several ligand activity prediction protocols that combined elements of a physics-based energy function (ICM VLS score) and the knowledge-based Atomic Pr...

    Polo C.-H. Lam, Ruben Abagyan, Maxim Totrov in Journal of Computer-Aided Molecular Design (2019)

  7. No Access

    Article

    Macrocycle modeling in ICM: benchmarking and evaluation in D3R Grand Challenge 4

    Macrocycles represent a potentially vast extension of drug chemical space still largely untapped by synthetic compounds. Sampling of flexible rings is incorporated in the ICM-dock protocol. We tested the abili...

    Polo C.-H. Lam, Ruben Abagyan, Maxim Totrov in Journal of Computer-Aided Molecular Design (2019)