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9744242275
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PDB code: 1A4G
-
PDB code: 1A4G.
-
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10
-
-
9744249703
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-
PDB code: 1A4Q
-
PDB code: 1A4Q.
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11
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0032510373
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Dihydropyrancarboxamides related to zanamivir: A new series of inhibitors of influenza virus sialidases. 2. Crystallographic and molecular modeling study of complexes of 4-Amino-4H-pyran-6-carboxamides and sialidase from influenza virus types A and B
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12
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9744233175
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PDB code: 1ERE
-
PDB code: 1ERE.
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13
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9744269509
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PDB code: 1ERR
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PDB code: 1ERR.
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14
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0030667676
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9744233927
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note
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In structure-based design, calculating free energies of binding based on a static X-ray structure, e.g. using docking in combination with scoring, typically does not yield accurate predictions. Therefore, free-energy perturbation, linear-interaction energy methods, etc. sample many possible configurations throughout a Monte Carlo or molecular-dynamics simulation, resulting in a more reliable estimation of binding affinities. On the basis of this principle, we make use of MD simulations in combination with the modified FIRF approach to obtain a more accurate observation of the strength of the physicochemical fields the ligands experience by the receptor.
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-
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17
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9744231645
-
-
note
-
To monitor the physicochemical fields a substance is exposed to during a simulation, a grid is constructed around the starting configuration of the ligand. Since the conformation of a nonrigid molecule is changing throughout the simulation, the surrounding grid is deformed as well. Within the floating independent reference frames (FIRF), each grid point is linked to its nearest ligand's heavy atom and a coordinate system is defined for each grid point based on that heavy atom, its bond partner, and the atacedent bonded partner. Each grid-point vector undergoes translation and rotation along with the atom it is coupled to. In this way, the reference frame for two adjacent grid points can differ, and an appropriate grid can be produced even when parts of the ligand are flexible.
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18
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0004195760
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University of California: San Francisco
-
Each compound was docked into the structure of the estrogen receptor (PDB code: 1ERE). A solvation cap of 30 Å around the geometric center of the binding pocket was created, and the whole system was minimized using AMBER 7.0 (Case, D. A.; Pearlman, D. A.; Caldwell, J. W.; Cheatham, T. E., III; Wang, J.; Ross, W. S.; Simmerling, C. L.; Darden, T. A.; Merz, K. M.; Stanton, R. V.; Cheng, A. L.; Vincent, J. J.; Crowley, M.; Tsui, V.; Gohlke, H.; Radmer, R. J.; Duan, Y.; Pitera, J.; Massova, I.; Seibel, G. L.; Singh, U. C.; Weiner, P. K.; Kollman, P. A. AMBER 7; University of California: San Francisco, 2002). During the MD simulation (100 ps equilibration, slowly heating from 100 to 300 K, followed by 400 ps of data collection) all atoms more than 25 Å away from the center were constrained.
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Case, D.A.1
Pearlman, D.A.2
Caldwell, J.W.3
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Massova, I.19
Seibel, G.L.20
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Weiner, P.K.22
Kollman, P.A.23
more..
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19
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0141547411
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Field functions for implicit surfaces
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max is the solvent-accessible radius plus an additional 0.5 Å for smearing purposes. Next, a triangulated surface is created on an isocontour level using the marching cubes algorithm [Lorensen, W. E.; Cline, H. E. Marching Cubes: A High Resolution 3D Surface Construction Algorithm. Comput. Graphics (Proc.SIGGRAPH '87) 1987, 21, 163-169]. For the inner shell, only the experimentally most affine ligand is taken into account, while for the outer layer, all ligands from the training set are included. This way, a smoothed solvent-accessible surface results for for the inner envelope.
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At this stage, the values can have up to eight discrete values. To accelerate the optimization the fields of the ligands are precomputed for the domains. Tabu search (TS) is a heuristic global optimization technique, which is an iterative procedure for exploring the search space by a sequence of moves, making use of an adaptive form of memory. In each tabu step, the properties of 25-50% of the domains are changed. Within one step, the properties can change their value only to their discrete neighboring level. To avoid being trapped in a local optimum, each step is taken as starting point for the next move. To improve the efficiency of the exploration process, the information from previous steps is taken into account in addition to the actual move. This is done by introducing a tabu list, which prevents a domain from assuming the same value as at the starting point of the previous step. By rejecting these moves (=tabu) the algorithm is forced to find new solutions and avoids cycling in the neighborhood of suboptimal solutions. An aspiration criterion is defined which allows one to overcome any tabu, if this move leads to an unprecedented best solution. Besides the short-time memory of a tabu list, a long-time memory is used storing a few best local minima encountered so far. The tabu search is stopped after a given number of moves or, alternatively, when no better solution is found for some time. Then, the long-time memory is used as restart point for local search which thoroughly examines promising areas. The tabu search is repeated several times from different starting points in the search space, avoiding any configuration stored in the long-time memory.
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