Kinematic manipulation of molecular chains subject to rigid constraints

We present algorithms for kinematic manipulation of molecular chains subject to fixed bond lengths and bond angles. They are useful for calculating conformations of a molecule subject to geometric constraints, such as those derived from two-dimensional NMR experiments. Other applications include searching out the full range of conformations available to a molecule such as cyclic configurations. We make use of results from robot kinematics and recently developed algorithms for solving polynomial systems. In particular, we model the molecule as a serial chain using the Denavit-Hartenberg formulation and reduce these problems to inverse kinematics of a serial chain. We also highlight the relationship between molecular embedding problems and inverse kinematics. As compared to earlier methods, the main advantages of the kinematic formulation are its generality to all molecular chains without any restrictions on the geometry and efficiency in terms of performance. The algorithms give us real time performance (order of tens of milliseconds) on smaller chains and are applicable to all chains.