Goodsell, D.S., Olson, A.J. Automated docking of substrates to proteins by simulated annealing. Proteins 8:195-- 202, 1990.  Home/Search   Document Not in Database   Summary   Related Articles   Check

....with their respective receptors, still there is a considerable extent of shape complementarity. Shape complementarity largely implicitly reflects hydrophobic and van der Waals interactions. 14 Over the last few years, a large number of docking routines have been developed and employed [15 31]. Techniques vary, according to the goals at hand. In some, the binding sites are assumed to be known, and the ligands are positioned directly in the active sites. In others, global searches are instituted. Techniques and parameters sometimes vary with the molecule size. Our computer vision based ....

Goodsell, D.; Olson, A. Automated docking of substrates to proteins by simulated annealing. P[IOTEINS: Structure, Furctior arid Geretics, 1995, $:195 202.

....algorithm, global optimization, local optimization, fast Fourier transforms. 1 Introduction Computer technology has revolutionized the way drugs are designed and analyzed. Not only do reliable methods for docking prediction exist, but there are a multitude of good techniques available (cf: [1, 6, 7, 8, 11, 13, 14, 17, 19, 20, 22, 26, 29, 35, 37, 38]. The CASP2 docking assessment compared a number of distinct techniques for studying protein interactions [4] The quality of submitted structures was quite good on the whole, and no method stood out as being exceptional in comparison with the others. Accuracy and speed are both important ....

Goodsell, D.S. and Olson, A.J. (1990), "Automated Docking of Substrates to Proteins by Simulated Annealing," Proteins: Structure, Function and Genetics, Vol. 8, No. 3, 195-202.

....range of potential hinge locations can be examined, comparing the conformational isomers, seeking the more likely chain linkers for the positioning of the hinge. Previous docking techniques have been able to allow induced hinge flexibility within relatively small ligands (e.g. drug molecules) [37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]. Partial flexibility is enabled in protein receptors only by a few workers. Leach, 1994 [48] enables side chain flexibility and Jones et al. 1995 [49] allow partial flexibility of hydrogen bonding groups. None of the currently available approaches enables full scale domain movements, although ....

D.S. Goodsell and A.J. Olson. Automated docking of substrates to proteins by simulated annealing. Proteins: Struct., Funct., Genet., 8:195, 1990.

....the docking problem. Previous flexible docking techniques account for induced hinge flexibility only within small ligands, and do not enable subparts (domain) motions in receptors [DesJarlais et al. 1986, Leach and Kuntz, 1992, Mizutani et al. 1994, Leach, 1994, Smellie et al. 1991, Goodsell and Olson, 1990, Ghose and Crippen, 1985, Jones et al. 1995, Clark and Ajay, 1995, Jones et al. 1997, Rarey et al. 1996, Welch et al. 1996] Partial receptor flexibility is allowed by Leach [Leach, 1994] which enables side chain 1 flexibility, and Jones et al. Jones et al. 1995] which allows partial ....

....ligand subparts are examined systematically, reconstructing minimal 1 A protein molecule is built up from a repertoire of 20 amino acids. The side chain (attached to the central backbone carbon atom) distinguishes between the different amino acids. 3 energy conformations. Goodsell Olson [Goodsell and Olson, 1990] employ the Metropolis (simulated annealing) for conformation searching combined with energy evaluations. Since reproducibility and convergence are not guaranteed, a global solution cannot always be obtained. The same problem exists in the method of Jones et al. Jones et al. 1995] The authors ....

Goodsell, D. and Olson, A. (1990). Automated docking of substrates to proteins by simulated annealing. Proteins: Struct., Funct., Genet., 8:195.

....will be successful in binding tightly to the active site in the enzyme. Based on the success of docking, and the resulting docked configuration, designers can refine the drug molecule. 1. 1 Autodock Autodock docks small flexible substrate molecules to large rigid macromolecules (such as proteins) [4, 11]. A candidate docking gives specific positions and orientations for the protein and small molecule. Autodock uses an approximate physical model to compute the free energy of a candidate docking, and uses a heuristic search to minimize this energy. This method makes most sense when there is a ....

....such as that described for Autodock, and use heuristic search to minimize energy. The genetic algorithm is becoming a popular choice for the heuristic search method in docking applications; see [1] for references. Earlier versions of Autodock used simulated annealing for heuristic optimization [11, 4]. There have been several successful applications of Autodock with simulated annealing [3, 9, 15, 14] and it is a good testbed for comparison with the genetic algorithm because of the effort that has gone into optimizing simulated annealing parameters. A preliminary comparison of genetic ....

Goodsell, D.S., and Olson, A.J. (1990). "Automated Docking of Substrates to Proteins by Simulated Annealing. " Proteins: Structure, Function, and Genetics 8:195-202.

....based on complementarity, packing and steric hindrance. These results were then screened using favorable interactions along the buried surface areas. FNNW93] used geometric hashing [LW88] to match features of molecular surfaces. Candidate matches were screened by voting into a 3 dimensional grid. G0] is an example of a numerical approach that used simulated annealing from a given starting position for the ligand outside of the receptor. During the procedure, the energy for each ligand atom is approximated by grid interpolation. 2 Our Approach The approach we take to solving this problem is ....

Goodsell D.S. Olson A.J. Automated docking of substrates to proteins by simulated annealing. Proteins.

....that efficiently search the conformational energy hypersurface associated with peptide docking problems. One of the most common, approaches has been based on Monte Carlo simulating annealing algorithms. This method was first applied to flexible ligand docking using molecular affinity potentials [58]. Molecular affinity potentials increase the computational efficiency of the search by employing precomputed energy grids [57] In this case, flexibility was introduced by allowing internal rotations of torsion angles, along with translational and rotational movement. However, for each docking ....

D. S. Goodsell and A. J. Olson, Automated docking of substrates to proteins by simulated annealing, Proteins, 8, (1990), 195-202.

....an energy function such as that described for Autodock, and use heuristic search to minimize energy. The genetic algorithm is becoming a popular choice for the heuristic search method in docking applications [1] Earlier versions of Autodock used simulated annealing for heuristic optimization [9, 3]. There have been several successful applications of Autodock with simulated annealing [2, 7, 13, 12] and it is a good testbed for comparison with the genetic algorithm because of the effort that has gone into optimizing simulated annealing parameters. William Hart did the original comparison of ....

David S. Goodsell and Arthur J. Olson. (1990). "Automated docking of substrates to proteins by simulated annealing." Proteins: Structure, Function, and Genetics, 8:195-202.

....[17] Energy based methods on the other hand, represent a more precise way of determing good dockings but they are more computationally demanding. Due to this fact most of the proposed approaches are based on Monte Carlo simulation and Simulated Annealing such as the works of Goodsell and Olson [12], Hart and Read [16] and Calfisch [7] Rosenfeld et al., 35] present a peptide binding study based on random selection and minimization among potential peptide structures. More recently, dynamic programming optimization, 21] is used for optimizing the overall free energy based on a fragment ....

D.S. Goodsell and A.J. Olson. Automated docking of substrates to proteins by simulated annealing. Proteins, 8:195--202, 1990.

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Goodsell, D.S., Olson, A.J. Automated docking of substrates to proteins by simulated annealing. Proteins 8:195-- 202, 1990.

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Goodsell DS, Olson AJ. Automated docking of substrates to proteins by simulated annealing. Proteins Struct Funct Genet 1990;8:195--202.

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Goodsell, D. and Olson, A. Automated docking of substrates to proteins by simulated annealing. PROTEINS: Structure, Function and Genetics, 8:195--202, 1990.

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D. Goodsell and A. Olson. Automated Docking of Substrates to Proteins by Simulated Annealing. PROTEINS:Structure, Function and Genetics, 8:195--202, 1990.

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