MOTIVATION: This paper investigates the sequence-structure specificity of a representative knowledge based energy function by applying it to threading at the level of secondary structures of proteins. Assessing the strengths and weaknesses of an energy function at this fundamental level provides more detailed and insightful information than at the tertiary structure level and the results obtained can be useful in tertiary level threading. RESULTS: We threaded each of the 293 non-redundant proteins onto the secondary structures contained in its respective native protein (host template). We also used 68 pairs of proteins with similar folds and low sequence identity. For each pair, we threaded the sequence of one protein onto the secondary structures of the other protein. The discerning power of the total energy function and its one-body, pairwise, and mutation components is studied. We then applied our energy function to a recent study which demonstrated how a designed 11-amino acid sequence can replace distinct segments (one segment is an alpha-helix, the other is a beta-sheet) of a protein without changing its fold. We conducted random mutations of the designed sequence to determine the patterns for favorable mutations. We also studied the sequence-structure specificity at the boundaries of a secondary structure. Finally, we demonstrated how to speed up tertiary level threading by filtering out alignments found to be energetically unfavorable during the secondary structure threading. AVAILABILITY: The program is available on request from the authors. CONTACT: [email protected]

Since a vehicle with two or more steerable drive wheels is always traveling in a circle about an instantaneous center of rotation, the motion of the wheels is constrained. The wheel translational velocity divided by the radius to the center of rotation must be the same for all wheels. When the drive wheels are controlled independently using position control, the motion of the wheels may violate the constraints and the wheels may slip. Consequently, substantial errors can occur in the position and orientation of the vehicle. A vehicle with N steerable drive wheels has N holonomic constraints on the steering angles, (N-1) nonholonomic constraints on the wheel velocities, and one degree of freedom. The authors have developed a new approach to the control of a vehicle with N steerable drive wheels. The novel aspect of their approach is the introduction of variables to control the constraint forces. To control the vehicle, the authors have one variable to control motion and (N-1) variables that can control the constraint forces to reduce errors. Kankaanranta and Koivo (1988) developed a control architecture that allows the control variables for force and position to be decoupled. In the work of Kankaaranta and Koivo the control variables for force are an exogenous input. The authors have made the central variables for force endogenous by defining them in terms of the errors in satisfying the nonholonomic constraints. The authors have applied the control architecture to the HERMIES-III robot and have measured a dramatic reduction in error (more than a factor of 20) compared to motions without constraint force control.>

A dynamical model and a control architecture are developed for the closed-chain motion of two N-joint manipulators holding a rigid object in a three-dimensional workspace. Dynamic and kinematic constraints are determined and combined with the equations of motion of the manipulators to obtain a dynamical model of the entire system in the joint space. Reduced-order equations of motion and a functional relation for the generalized contact forces are developed. The problem of solving the reduced-order model for the forward and inverse dynamics is discussed. Control laws are determined so as to decouple the force-controlled and position-controlled degrees of freedom during motion of the system.>