G. Song and N. M. Amato. Using motion planning to study protein folding pathways. Journal of Computational Biology, 26(2):282--304, 1978.  Home/Search   Document Details and Download   Summary   Related Articles   Check

.... biology, e.g. in structural databases and classification [10, 24] structure prediction [6, 7, 19, 26, 30, 31] analysis of trajectories through conformational space generated by molecular dynamics and Monte Carlo simulations [22, 29, 36] graph based methods for evaluating ensemble properties [2, 3, 33], etc. As opposed to sequence matching, structural matching requires a similarity measure that is based on spatial atom coordinates. Nevertheless, it is important whether the structures that are compared have the same amino acid sequence or not. For conformational samples from the same sequence ....

Guang Song and Nancy M. Amato. Using motion planning to study protein folding pathways. In RECOMB, pages 287--296, 2001.

....roadmap are weighted with transition probabilities, while the edges of a probabilistic roadmap are unweighted. Singh et al. introduced the PRM methods to the study of molecular motion in their work on ligand protein binding [27] Their approach has since been applied to protein folding as well [2,5,29]. Earlier work treats the roadmap as a deterministic graph, with heuristic edge weights based on the energy difference between molecule conformations. The heuristic edge weights measure the energetic difficulty of transitioning along the edges. Graph search techniques are used to extract ....

.... to , but the move must traverse at least one other node of the roadmap. Finally, a self transition probability ( is attached to each node , ensuring that the transition probabilities from any node sum up to 1. In contrast to the heuristic edge weights used in [5,27,29], the transition probabilities used in SRS allow us to establish a formal relationship between SRS and MC simulation [3] We now describe this important relationship. 3.2 Relationship with Monte Carlo simulation In MC simulation, we perform a random walk in the conformation space . We can ....

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G. Song and N.M. Amato. Using motion planning to study protein folding pathways. In Proc. ACM Int. Conf. on Computational Biology (RECOMB), pages 287--296, 2001.

....by constructing a graph of local paths connecting points randomly sampled from that space. Singh, et al. first introduced PRM methods to the study of molecular motion, more specifically ligand protein binding [SLB99] PRM methods have since been applied to protein folding as well [ADS02, ASBL01, SA01] These earlier works treat a roadmap as a deterministic graph with heuristic edge weights based on the energy difference between molecule conformations. The heuristic weight attached to an edge measures the energetic difficulty of transitioning along this edge. Classic search techniques are ....

....The conformation of a molecule determines its 3 D structure. Conformations can be specified in various ways. For example, for a protein molecule, one may specify the positions of constituent atoms in a lattice [KS96] In an off lattice model, the backbone torsional angles and are often used [SA01] A simpler representation is to associate 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 ....

[Article contains additional citation context not shown here]

G. Song and N.M. Amato. Using motion planning to study protein folding pathways. In Proc. ACM Int. Conf. on Computational Biology (RECOMB), pages 287--296, 2001.

....by constructing a graph of local paths connecting points randomly sampled from that space. Singh, et al. first introduced PRM methods to the study of molecular motion, more specifically ligand protein binding [SLB99] PRM methods have since been applied to protein folding as well [ADS02, ASBL01, SA01] These earlier works treat a roadmap as a deterministic graph with heuristic edge weights based on the energy difference between molecule conformations. The heuristic weight attached to an edge measures the energetic difficulty of transitioning along this edge. Classic search techniques are ....

....The conformation of a molecule determines its 3 D structure. Conformations can be specified in various ways. For example, for a protein molecule, one may specify the positions of constituent atoms in a lattice [KS96] In an off lattice model, the backbone torsional angles # and are often used [SA01] A simpler representation is to associate 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 ....

[Article contains additional citation context not shown here]

G. Song and N.M. Amato. Using motion planning to study protein folding pathways. In Proc. ACM Int. Conf. on Computational Biology (RECOMB), pages 287--296, 2001.

.... on planning schemes for modu lar and reconfigurable robots [8,41,42] planning for deformable robots [28,5] abstractions of random planning analysis to non parametric, non manifold spaces [27] approximate dimensionality reduction of configuration space [40] determining protein folding pathways [38], planning in the energy landscapes of molecules [4] and computing stationary distributions of Markov chains defined over roadmaps for analysis of Monte Carlo simulations of protein folding phenomena [3] Knots are artificial geometric objects. The space of all knots does not have a finite basis ....

....a major improvement to the speed of the planner. Use of energy There are several planning applications with natural energy functions such as protein folding, molecular docking and realistic deformable robots. Also, there has been some investigation in using energy when planning for such systems [38,4]. Our planner is a potential field planner which uses tree expanding planning to escape minima. In particular, we have demonstrated that both planning and energy hints are necessary for the untangler s efficiency. Furthermore, we observed that for the knot untangling planner, low energy ....

G. Song and N. Amato. Using motion planning to study protein folding pathways. In International Conference on Computational Molecular Biology (RECOMB) , pages 287-296, April 2001.

....energy minimization and conformational search. 1 1 Introduction During the last two decades a lot of emphasis has been placed in studying problems that involve reasoning about three dimensional (3D) molecular conformations in simulation (e.g. docking, protein folding, molecular dynamics, etc. [3, 4, 6, 7, 8, 9, 10, 11, 12]. Little research has been done, however, to understand how to eciently represent, derive and update molecular conformations from molecular data. The ecient derivation of molecular conformations can greatly impact the performance of conformational search procedures, energy minimization procedures, ....

Song, G.; Amato, N. M. Using Motion Planning to Study Protein Folding Pathways. Proceedings of the Fifth Annual International Conference on Computational Biology, 2001, 287-296. 19

....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 ....

....sampled milestones. For 1hdd, Figure 7 shows that there are milestones of lower energy than the folded state. This may be due to the various approximations made in the energy model. In (b) the energy profile shows a barrier just before reaching the folded state, similar to the profiles in [SA00]. But several runs led different plots, and (c) shows another profile, for a different PCR of the same size and for another random starting configuration. No barrier is observed before reaching the folded state and no node is visited extensively in the 200 best paths. For 1le2, our PCR found a ....

G. Song and N.M. Amato. Using Motion Planning to Study Protein Folding Pathways. TR00-026, Dept. of Comp. Sci., Texas A&M U., Oct. 2000.

.... was used in conjunction with forward and inverse kinematics for problems involving closed chain systems, 12] uses energy minimization techniques in a prm based approach for exible objects, and biased sampling around the (known) goal con guration was used to compute protein folding pathways in [25, 26]. Our approach to the disassembly problem involves biasing the sampling based on the geometric characteristics of con gurations known to be reachable from the assembled con guration (the start) In particular, information based on the relative positions of the parts in one con guration will be ....

G. Song and N. M. Amato. Using motion planning to study protein folding pathways. In Proc. Int. Conf. Comput. Molecular Biology (RECOMB), pages 278-287, 2001.

.... 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, we apply the prm ....

G. Song and N. M. Amato. Using motion planning to study protein folding pathways. In Proc. Int. Conf. Comput. Molecular Biology (RECOMB), pages 278-287, 2001.

....fashion within the PRM framework. Our preliminary experimental results with traditional paper crafts and small proteins of approximately 60 residues, or 120 degrees of freedom, are quite promising. See Figures 1 and 2 for some path snapshots. Further results on protein folding can be found in [27]. 2 Related work Paper Folding. Many problems related to the folding and unfolding of polyhedral objects have recently attracted the attention of the computational geometry community [25] For example, 8] shows that every polyhedron can be wrapped by folding a strip of paper around it, which ....

G. Song and N. M. Amato. Using motion planning to study protein folding pathways. In Proc. Int. Conf. Comput. Molecular Biology (RECOMB), pages 278--287, 2001.

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G. Song and N. M. Amato. Using motion planning to study protein folding pathways. Journal of Computational Biology, 26(2):282--304, 1978.

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N. M. Amato and G. Song. Using motion planning to study protein folding pathways. Journal of Computational Biology, 9(2):149--168, 2002.

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G. Song and N.M. Amato. Using Motion Planning to Study Protein Folding Pathways. Proc. 5th Int.l Conf. on Computational Molecular Biology (RECOMB'01), April 2001, pp. 287-296.

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G. Song and N.M. Amato. Using motion planning to study protein folding pathways. Journal of Computational Biology, 9(2):149--168, 2002.

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G. Song and N. Amato, "Using motion planning to study protein folding pathways," Journal of Computational Biology, vol. 9.

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G. Song and N.M. Amato. Using motion planning to study protein folding pathways. In Proc. ACM Int. Conf. on Computational Biology (RECOMB), pages 287--296, 2001.

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G. Song and N. Amato. Using motion planning to study protein folding pathways. In Proceedings the 5th International Conference on Computational Molecular Biology (RECOMB), pages 287-- 296, Montreal, April 2001.

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