Camacho, J.C. and Vajda, S., Protein docking along smooth association pathways, PNAS, 98:10636--10641, 2001.  Home/Search   Document Not in Database   Summary   Related Articles   Check

....prediction. We thus examine the ligandprotein binding process using a dynamic model. In contrast, most existing methods for analyzing ligand protein binding use static models and consider only the energy of the final bound conformation of the ligand protein complex (e.g. see [21,33] Following [10], we define the funnel of a bound conformation as the set of conformations within 10 A of in RMSD. We then use SRS to compute the expected number of transitions for the ligand to reach a conformation outside of the funnel and use it as an approximation to the escape time. Given a suitable ....

C.J. Camacho and S. Vajda. Protein docking along smooth association pathways. Proc. Nat. Acad. Sci. USA, 98(19):10636--10641, 2001.

....We call such quantity the escape time. To obtain a precise definition of the escape time, we must formalize two notions: funnel of attraction and amount of time . The notion of funnel of attraction of a putative binding site has been used in other studies of ligand protein interaction, such as [CV01] where the funnel is defined as all ligand conformations within 10 A RMSD of the bound conformation. In this section, we will use a generic definition, where each putative binding conformation v is associated with a set of bound conformations F . If we use this definition, then F would ....

....grid. The energy of the ligand was also calculated as in prior work [SLB99] and the charges on each atom of each ligand were computed as a formal charge taking into account resonance structures of the molecule. In our study, we defined the funnel of attraction of a potential binding site as in [CV01] i.e. the set of conformations within 10A rmsd of the bound ligand complex. We also repeated our experiments with funnels of 6A and 8A radii, obtaining comparable results. 5 Analyzing the effects of mutations We first applied SRS to the analysis of the effects of mutations in the catalytic ....

C.J. Camacho and S. Vajda. Protein docking along smooth association pathways. PNAS, pages 10636 -- 10641, 2001. 86] A. Clarke, D. Wigley, W. Chia, D. Barstow, T. Atkinson, and J. Holbrook. Site-directed mutagenesis reveals the role of a mobile arginine residue in lactate dehydrogenase catalysis. Nature, 324:699 -- 702, 1986.

....(see, e.g. MGH 98, WKK99] Let us consider the conformation space of a ligand protein complex with a suitably defined energy function. A bound conformation generally corresponds to a local energy minimum and has a funnel of attraction around to stabilize the ligand. Following [CV01] we define the funnel of a bound conformation as the set of all conformations within 10 A of in RMSD. Figure 9 shows funnels of attraction for four potential binding sites on lactate dehydrogenase. An interesting measure of affinity of a ligand to a potential binding site is the expected ....

C.J. Camacho and S. Vajda. Protein docking along smooth association pathways. Proc. Nat. Acad. Sci. USA, 98(19):10636--10641, 2001.

....(see, e.g. MGH 98, WKK99] Let us consider the conformation space of a ligand protein complex with a suitably defined energy function. A bound conformation q generally corresponds to a local energy minimum and has a funnel of attraction around q to stabilize the ligand. Following [CV01] we define the funnel of a bound conformation q as the set of all conformations within 10 A of q in RMSD. Figure 9 shows funnels of attraction for four potential binding sites on lactate dehydrogenase. An interesting measure of affinity of a ligand to a potential binding site is the expected ....

C.J. Camacho and S. Vajda. Protein docking along smooth association pathways. Proc. Nat. Acad. Sci. USA, 98(19):10636--10641, 2001.

....around a set of putative binding sites for lactate dehydrogenase. escape time, we must formalize two notions: funnel of attraction and amount of time . The notion of funnel of attraction of a putative binding site has been used in other studies of ligand protein interaction, such as [CV01] where the funnel is defined as all ligand conformations within 10 A RMSD of the bound conformation. In this section, we will use a generic definition, where each putative binding conformation v is associated with a set of bound conformations . If we use this definition, then would ....

....grid. The energy of the ligand was also calculated as in prior work [SLB99] and the charges on each atom of each ligand were computed as a formal charge taking into account resonance structures of the molecule. In our study, we defined the funnel of attraction of a potential binding site as in [CV01] i.e. the set of conformations within 10 A rmsd of the bound ligand complex. We also repeated our experiments with funnels of 6 A and 8 A radii, obtaining comparable results. 5 ANALYZING THE EFFECTS OF MUTATIONS We first applied SRS to the analysis of the effects of mutations in the catalytic ....

C.J. Camacho and S. Vajda. Protein docking along smooth association pathways. PNAS, pages 10636 -- 10641, 2001.

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Camacho, J.C. and Vajda, S., Protein docking along smooth association pathways, PNAS, 98:10636--10641, 2001.

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