BiGGER: A new (soft) docking algorithm for predicting protein interactions

By P. Palma, L. Krippahl, J. Wampler, J. Moura. Proteins: Structure, Function, and Bioinformatics, 2000

310 citations recorded by the source corpus.

Subfields: Computational Theory and Mathematics, Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/9aa1536c996e90b00501a8f87a804feefaca615e

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Citations in the corpus

RDOCK: Refinement of rigid‐body protein docking predictions (2003, background): “1,000 predictions for three test cases, and the ranks for the best hits were 6, 13, and 50 for the remaining test cases.(8) Totrov and Abagyan(31) developed a two-step docking proce-”
Efficient Unbound Docking of Rigid Molecules (2002, unknown): “The attractive running times of the algorithm and the high quality of the results compared to other state of the art method [26,12,3] are the outcome of several components.”
The scoring of poses in protein-protein docking: current capabilities and future directions (2013, methodology): “In these cases, flexible machine learning algorithms capable of inferring these relationships can be used to tailor scoring functions to the structures produced by the sampling methods [124], and indeed examples of this approach can be found in the literature [91-97].”
GEMDOCK: A generic evolutionary method for molecular docking (2004, methodology): “18–20 24 Most of these previous docking methods were evaluated using small test sets ( (cid:1) 20 protein–ligand complexes).”
Protein–protein docking with a reduced protein model accounting for side‐chain flexibility (2003, methodology): “…of a reduced protein model allows the search on the complete surface of the receptor protein in reasonable computer time of ∼ 4 to 8 h (single processor time), which is comparable or faster than Fourier correlation methods or real-space correlation techniques (Gabb et al. 1997; Palma et al. 2000).”
Recent progress and future directions in protein-protein docking. (2008, background): “*Address correspondence to this author at the Department of Computing Science, University of Aberdeen, Aberdeen, AB24 3UE, Scotland, UK; Tel: (+44)(–0)1224 272282; Fax: (+44)(–0)1224 273422; E-mail: dritchie@csd.abdn.ac.uk Protein docking is the task of calculating the threedimensional (3D)…”
Software for molecular docking: a review (2017, methodology): “The other programs include SOFTDOCK (Jiang and Kim 1991), BiGGER (Palma et al. 2000), and SKE-DOCK (Terashi et al. 2007).”
Prediction of protein interaction sites from sequence profile and residue neighbor list (2001, methodology): “5 Most docking methods are based on the observation that protein– protein interfaces are composed of relatively large surfaces with geometric and perhaps electrostatic complementarity.”
An iterative knowledge‐based scoring function for protein–protein recognition (2008, methodology): “8,10,54 Despite significant achievements, one hurdle in deriving knowledge-based scoring functions is the determination of the ‘‘reference state’’ q (cid”
Improved side‐chain modeling for protein–protein docking (2005, unknown): “…transform (FFT) (Katchalski-Katzir et al. 1992; Gabb et al. 1997; Chen and Weng 2002), geometrical hashing (Norel et al. 1999), Boolean operations (Palma et al. 2000), and genetic algorithms (Taylor and Burnett 2000; Gardiner et al. 2001), have been used to rapidly search rigid-body orientation…”