FireDock: Fast interaction refinement in molecular docking

By Nelly Andrusier, Ruth Nussinov, Haim J. Wolfson. Proteins: Structure, Function, and Bioinformatics, 2007

681 citations recorded by the source corpus.

Subfields: Computational Theory and Mathematics, Molecular Biology, Radiology, Nuclear Medicine and Imaging

View Paper: https://www.semanticscholar.org/paper/f24b9f59ee675448417b0af7faf5867a6f7360f8

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Citations in the corpus

FireDock: a web server for fast interaction refinement in molecular docking (2008, methodology): “(16) and was previously available only for downloading.”
The scoring of poses in protein-protein docking: current capabilities and future directions (2013, methodology): “FIREDOCK_EI [59] d FIREDOCK_AB [59] d INSIDE [59] d HBOND [59] d PI_PI [59] d CAT_PI [59] d ALIPH [59] d SIPPER [67] i The SIPPER score and its amino-acid propensity and desolvation constituents. as well as a number of atomic and near-atomic potentials, which are prefixed with ‘ AP_ ’ .”
The Immune Epitope Database and Analysis Resource in Epitope Discovery and Synthetic Vaccine Design (2017, methodology): “FireDock is an efficient method for refining the rigid-body docking solutions of PatchDock.”
Contacts-based prediction of binding affinity in protein–protein complexes (2015, methodology): “…( Chaudhury et al., 2010 ), PyDock ( Cheng et al., 2007 ), FireDock (the total energy, the antibody–antigen energy and the enzyme-inhibitor energy) ( Andrusier et al., 2007 ), PISA ( Viswanath et al., 2013 ), PIE ( Ravikant and Elber, 2010 ), and SIPPER ( Pons et al., 2011 ) were obtained as…”
Principles of Flexible Protein-Protein Docking (2008, methodology): “113,118”
A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions (2011, positive): “The backbone-dependent rotamer libraries we have developed previously have found uses in many different applications in protein structure prediction (Andrusier et al., 2007; Bower et al., 1997; Hartmann et al., 2007; Krieger et al., 2009; Krivov et al., 2009; Liang and Grishin, 2002; Mendes et al., ”
An iterative knowledge‐based scoring function for protein–protein recognition (2008, background): “38–40 The fourth type of scoring methods for protein–protein docking are referred to as knowledge-based potentials,41–49 which are derived from known structures of protein–protein complexes in a database such as PDB, etc.6,50–52 The interaction potentials are directly converted from the statistical…”