Geometric Problems in Molecular Biology and Robotics

Some of the geometric problems of interest to molecular biologists have macroscopic analogues in the field of robotics. Two examples of such analogies are those between protein docking and model-based perception, and between ring closure and inverse kinematics. Molecular dynamics simulation, too, has much in common with the study of robot dynamics. In this paper we give a brief survey of recent work on these and related problems.

[1]  H. Dyson,et al.  Peptide conformation and protein folding , 1993 .

[2]  W. Grimson,et al.  Model-Based Recognition and Localization from Sparse Range or Tactile Data , 1984 .

[3]  Ed Anderson,et al.  LAPACK users' guide - [release 1.0] , 1992 .

[4]  K. Dill.  Folding proteins: finding a needle in a haystack , 1993 .

[5]  Donald Lee Pieper.  The kinematics of manipulators under computer control , 1968 .

[6]  Gordon M. Crippen,et al.  Distance Geometry and Molecular Conformation , 1988 .

[7]  Mark A. Murcko,et al.  Use of structural information in drug design , 1992, Current Biology.

[8]  Kenneth J. Waldron,et al.  A study of a kinematically redundant manipulator structure , 1986, Proceedings. 1986 IEEE International Conference on Robotics and Automation.

[9]  M. Murcko,et al.  Use of structural information in drug design , 1992, Current Biology.

[10]  J. Janin,et al.  Protein docking algorithms: simulating molecular recognition , 1993 .

[11]  Abhinandan Jain,et al.  Spatial Operator Algebra for multibody system dynamics , 1992 .

[12]  J. Moult,et al.  An algorithm for determining the conformation of polypeptide segments in proteins by systematic search , 1986, Proteins.

[13]  Olivier Faugeras,et al.  Three-Dimensional Computer Vision , 1993 .

[14]  A. Morgan,et al.  SOLVING THE 6R INVERSE POSITION PROBLEM USING A GENERIC-CASE SOLUTION METHODOLOGY , 1991 .

[15]  N. Go,et al.  Ring Closure and Local Conformational Deformations of Chain Molecules , 1970 .

[16]  C. Chothia,et al.  The structure of protein-protein recognition sites. , 1990, The Journal of biological chemistry.

[17]  Ioannis Z. Emiris.  An Efficient Computation Of Mixed Volume , 1993 .

[18]  H. Scheraga,et al.  Revised algorithms for the build‐up procedure for predicting protein conformations by energy minimization , 1987 .

[19]  Richard M. Murray,et al.  A Mathematical Introduction to Robotic Manipulation , 1994 .

[20]  D. K. Friesen,et al.  A combinatorial algorithm for calculating ligand binding , 1984 .

[21]  E. Primrose.  On the input-output equation of the general 7R-mechanism , 1986 .

[22]  Dinesh Manocha,et al.  Real time inverse kinematics for general 6R manipulators , 1992, Proceedings 1992 IEEE International Conference on Robotics and Automation.

[23]  D Fischer,et al.  Molecular surface representations by sparse critical points , 1994, Proteins.

[24]  A. Morgan,et al.  Solving the Kinematics of the Most General Six- and Five-Degree-of-Freedom Manipulators by Continuation Methods , 1985 .

[25]  Ferdinand Freudenstein.  Kinematics: Past, present and future , 1973 .

[26]  I. Kuntz,et al.  Protein docking and complementarity. , 1991, Journal of molecular biology.

[27]  A. Cooper.  Dynamics of Proteins and Nucleic Acids , 1988 .

[28]  John J. Craig Zhu,et al.  Introduction to robotics mechanics and control , 1991 .

[29]  Joseph James Duffy,et al.  A displacement analysis of the general spatial 7-link, mechanism , 1980 .

[30]  Yehezkel Lamdan,et al.  Geometric Hashing: A General And Efficient Model-based Recognition Scheme , 1988, [1988 Proceedings] Second International Conference on Computer Vision.

[31]  I. Kuntz.  Structure-Based Strategies for Drug Design and Discovery , 1992, Science.

[32]  Bernard Roth,et al.  Kinematic analysis of the 6R manipulator of general geometry , 1991 .

[33]  Abhinandan Jain,et al.  A fast recursive algorithm for molecular dynamics simulation , 1993 .

[34]  S. Kim,et al.  "Soft docking": matching of molecular surface cubes. , 1991, Journal of molecular biology.

[35]  Dinesh Manocha,et al.  Object localization using crossbeam sensing , 1993, [1993] Proceedings IEEE International Conference on Robotics and Automation.

[36]  John F. Canny,et al.  A practical method for the sparse resultant , 1993, ISSAC '93.

[37]  W R Taylor,et al.  Protein structure alignment. , 1989, Journal of molecular biology.

[38]  K. Tasaki,et al.  Observations concerning the treatment of long‐range interactions in molecular dynamics simulations , 1993, J. Comput. Chem..

[39]  K. Dill.  Theory for the folding and stability of globular proteins. , 1985, Biochemistry.

[40]  W. C. Still,et al.  The multiple minimum problem in molecular modeling. Tree searching internal coordinate conformational space , 1988 .

[41]  J. Mccammon,et al.  Dynamics of Proteins and Nucleic Acids , 2018 .

[42]  H. Wolfson,et al.  Molecular surface recognition by a computer vision-based technique. , 1994, Protein engineering.

[43]  G. Ciccotti,et al.  Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes , 1977 .

[44]  Shoshana J. Wodak,et al.  Generating and testing protein folds , 1993 .

[45]  Bernard Roth,et al.  On the Design of Computer Controlled Manipulators , 1974 .

[46]  A E Howard,et al.  An analysis of current methodologies for conformational searching of complex molecules. , 1988, Journal of medicinal chemistry.

[47]  Mark H. Overmars,et al.  Point Location in Fat Subdivisions , 1992, Inf. Process. Lett..

[48]  David S. Johnson,et al.  Computers and Intractability: A Guide to the Theory of NP-Completeness , 1978 .

[49]  J M Blaney,et al.  A geometric approach to macromolecule-ligand interactions. , 1982, Journal of molecular biology.

[50]  Hong Y. Lee,et al.  Displacement analysis of the general spatial 7-link 7R mechanism , 1988 .

[51]  H. Wolfson,et al.  Efficient detection of three-dimensional structural motifs in biological macromolecules by computer vision techniques. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[52]  Keith L. Doty,et al.  A Robot Manipulator With 16 Real Inverse Kinematic Solution Sets , 1989, Int. J. Robotics Res..