MOTIVATION: Interacting pairs of proteins should co-evolve to maintain functional and structural complementarity. Consequently, such a pair of protein families shows similarity between their phylogenetic trees. Although the tendency of co-evolution has been known for various ligand-receptor pairs, it has not been studied systematically in the widest possible scope. We investigated the degree of co-evolution for more than 900 family pairs in a global protein structural interactome map (PSIMAP--a map of all the structural domain-domain interactions in the PDB). RESULTS: There was significant correlation in 45% of the total SCOPs Family level pairs, rising to 78% in 454 reliable family interactions. Expectedly, the intra-molecular interactions between protein families showed stronger co-evolution than inter-molecular interactions. However, both types of interaction have a fundamentally similar pattern of co-evolution except for cases where different interfaces are involved. These results validate the use of co-evolution analysis with predictive methods such as PSIMAP to improve the accuracy of prediction based on "homologous interaction". The tendency of co-evolution enabled a nearly 5-fold enrichment in the identification of true interactions among the potential interlogues in PSIMAP. The estimated sensitivity was 79.2%, and the specificity was 78.6%. AVAILABILITY: The results of co-evolution analysis are available online at http://www.biointeraction.org

SUMMARY: We have developed a new program called InterViewer for drawing large-scale protein interaction networks in three-dimensional space. Unique features of InterViewer include (1) it is much faster than other recent implementations of drawing algorithms; (2) it can be used not only for visualizing protein interactions but also for analyzing them interactively; and (3) it provides an integrated framework for querying protein interaction databases and directly visualizes the query results. AVAILABILITY: http://wilab.inha.ac.kr/protein/

In the previous works, we have proposed new control schemes based on the sliding mode control and impedance control in order to cope with varying time delays. However, the previous controller needs local compliance to reduce contact forces between the slave and environment. In this paper, we modify the previous one to have a sliding surface for the slave include an impedance model. Since the nonlinear gain of the sliding controller is independent of the time delay as in the previous proposed controllers, it is not necessary to measure or estimate the time delay to implement the controller. The validity of the proposed control scheme is demonstrated by experiments with a 1-DOF master/slave system connected through the Internet.

The authors previously (1999) showed that a regular sliding-mode controller is difficult to be used in bilateral teleoperation systems with varying time delay in that its nonlinear gain should be set based on the worst time delay. As an alternative to the regular sliding-mode controller, a modified sliding-mode controller was proposed to compensate the varying time delay and to guarantee its nonlinear gain to be independent of the magnitude of the time delay. In this paper, the validity of the proposed control scheme is demonstrated by a series of experiments with a 1-DOF master/slave teleoperation system. In the experiments, it is shown that the proposed controller effectively compensates the effects of the varying time delay even when the magnitude of the delay, i.e., RTT (round-trip time) in the communication line becomes as large as 4.0 s, while the performance of the regular sliding-mode controller deteriorates, especially with a large value of the force scaling factor.

Proposes a hybrid control method of using the impedance control and the computed-torque control for biped robot locomotion. The computed-torque control is used for the supporting (constrained) leg. For the free leg, impedance control is used, where different values of impedance parameters are used depending on the gait phase of the biped robot. To reduce the magnitude of an impact and guarantee a stable footing when a foot contacts with the ground, the paper proposes to increase the damping of the leg drastically and to modify the reference trajectory of the leg. Computer simulations with a 3 DOF environment model for which a combination of a nonlinear and a linear compliant contact models is used, show that the proposed controller is superior to the computed-torque controllers in reducing impacts and stabilizing the footing.

This paper proposes a model called the gravity-compensated inverted pendulum mode (GCIPM) to generate a biped locomotion pattern that is similar to the one generated by the linear inverted pendulum mode, but accommodates the free leg dynamics based upon its predetermined trajectory. When the biped locomotion based upon the linear inverted pendulum mode is applied to real biped robots, the stability of the robot is disturbed due to the fact that the neglected dynamics of free legs is not actually negligible, moving the ZMP (zero moment point) away from the presumed fixed point. The GCIPM includes the effect of the dynamics of the free leg in a simple manner This paper also presents a control method for biped robots based upon the computed torque. Simulation results show that the biped robot is more stable with the walking pattern generated by the proposed method combined with the controller than with the one by the inverted pendulum mode.

Trunk motions are typically used to stabilize the locomotion of biped robots, which can be very large in some leg trajectories. This paper proposes a method to reduce the motion range of the trunk by generating a desired trajectory of the zero-moment point (ZMP). The trajectory is determined by a fuzzy logic based upon the leg trajectories that are arbitrary selected. The resulting ZMP trajectory is similar to human's one and the ZMP continuously moves forward. The proposed scheme is simulated on a 7-degree-of-freedom biped robot. Its results indicate that the proposed ZMP trajectory increases the stability of the locomotion and thus resulting in reduction of motion range of the trunk.