O. Burchan Bayazit, Guang Song, and Nancy M. Amato. Ligand binding with obprm and haptic user input. In Proc. IEEE Int. Conf. on Robotics & Automation, 2001.  Home/Search   Document Details and Download   Summary   Related Articles   Check

.... vectors to secondary structural elements and treat the angles between these vectors as the conformation parameters [ASBL01] For ligand protein binding, one often assumes that the protein is rigid and model the ligand with a root atom and a torsional angle for each non terminal atom [SLB99, BSA01] Representing the protein as non rigid can be done, for example by identifying its main degrees of freedom [TPK02] and including them as additional dimensions of the conformation space of the ligand protein complex. SRS is applicable to many different representations, provided that the ....

O. Burchan Bayazit, Guang Song, and Nancy M. Amato. Ligand binding with obprm and haptic user input. In Proc. IEEE Int. Conf. on Robotics & Automation, 2001.

.... vectors to secondary structural elements and treat the angles between these vectors as the conformation parameters [ASBL01] For ligand protein binding, one often assumes that the protein is rigid and model the ligand with a root atom and a torsional angle for each non terminal atom [SLB99, BSA01] Representing the protein as non rigid can be done, for example by identifying its main degrees of freedom [TPK02] and including them as additional dimensions of the conformation space of the ligand protein complex. SRS is applicable to many different representations, provided that the ....

O. Burchan Bayazit, Guang Song, and Nancy M. Amato. Ligand binding with obprm and haptic user input. In Proc. IEEE Int. Conf. on Robotics & Automation, 2001.

....the greedy algorithm propagates errors resulting from initial bad choices that lead to missing final conformations of lower energy. In order to solve the docking problem conformation methods using standard robotics techniques such as probabilistic roadmap planning have been recently described [8,9] . In addition to being successful in finding the correct docking conformation these methods are Figure 2 A drug molecule. Spheres represent atoms and bonds connecting them are represented by sticks. Curved arrows represent the rotatable degrees of freedom around bonds. useful in ....

Bayazit, O.B., Song, G. & Amato, N.M. Ligand Binding with OBPRM and Haptic User Input. in 2001 IEEE International Conference on Robotics and Automation (ICRA'01) (Seoul, Korea, 2001).

....its application to ligand protein binding. The present paper extends this concept, provides new results for ligand protein binding, and explores the application of PCRs to protein folding. Other ongoing research aimed at applying PCRs to ligand protein binding and protein folding is reported in [BSA00, SA00]. The problem of capturing functional landscapes over complex spaces is one of general interest. For example, outdoor mobile robots must compute motion plans that take the navigability of the local terrain into account (e.g. muddy and steep areas are more difficult to traverse than flat hard ....

O.B. Bayazit, G. Song and N.M. Amato. Ligand Binding with OBPRM and Haptic User Input: Enhancing Automatic Motion Planning with Virtual Touch. TR00-025, Dept. of Comp. Sci., Texas A&M U., Oct. 2000.

.... techniques were applied to a number of challenging problems arising in a variety of elds including robotics (e.g. closed chain systems [9, 15] CAD (e.g. assembly [23] maintainability [3, 7] deformable objects [2, 10] and even computational Biology and Chemistry (e.g. ligand docking [4, 18], protein folding [20, 21] Indeed, it can be argued that the prm framework was instrumental in this broadening of the range of applicability of motion planning, as many of these problems had never before been considered candidates for automatic methods. Customizable PRM (C PRM) In this work, ....

O. B. Bayazit, G. Song, and N. M. Amato. Ligand binding with obprm and haptic user input: Enhancing automatic motion planning with virtual touch. In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), 2001. To appear. This work will be presented as a poster at RECOMB'01.

....this paper, we present an alternative approach that finds approximations to the folding pathways while avoiding detailed simulations. Our motion planning approach is based on the successful probabilistic roadmap (PRM) method [17] which has been used to study the related problem of ligand binding [3, 16, 26], which is of interest in drug design. The results were quite promising. Advantages of the PRM approach are that it efficiently covers a large portion of the planning space, in this case, the conformation space, and that it also provides an effective way to incorporate and study various initial ....

O. B. Bayazit, G. Song, and N. M. Amato. Ligand binding with obprm and haptic user input: Enhancing automatic motion planning with virtual touch. In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), 2001. To appear. This work will be presented as a poster at RECOMB'01.

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