Recent Advances in Molecular Distance Geometry

Distance geometry is geometric theory of molecular conformation, wherein one formulates conformational problems mathematically in terms of distance and chirality constraints. The most general method of generating a conformational ensemble is widely known as the EMBED algorithm. This algorithm actually puts several combinatorial and multivariate algorithms together in order to randomly generate coordinates that approximate satisfy the distance constraints. In this report we describe several recent improvements to the EMBED algorithm, as implemented by the DG-II program package, which substantially increase its efficiency and reliability in many important applications.

[1]  Timothy F. Havel,et al.  The theory and practice of distance geometry , 1983, Bulletin of Mathematical Biology.

[2]  Timothy F. Havel,et al.  A new method for building protein conformations from sequence alignments with homologues of known structure. , 1991, Journal of molecular biology.

[3]  Timothy F. Havel,et al.  NMR structure determination in solution: a critique and comparison with X-ray crystallography. , 1992, Annual review of biophysics and biomolecular structure.

[4]  Deepak Kapur,et al.  Geometric reasoning , 1989 .

[5]  Timothy F. Havel.  Predicting the Structure of the Flavodoxin from Eschericia coli by Homology Modeling, Distance Geometry and Molecular Dynamics , 1993 .

[6]  H. C. Longuet-Higgins.  The symmetry groups of non-rigid molecules , 1963 .

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

[8]  G. M. Crippen,et al.  Why energy embedding works , 1987 .

[9]  Timothy F. Havel,et al.  Derivatives of the Matrix Exponential and Their Computation , 1995 .

[10]  Gordon M. Crippen,et al.  Stable calculation of coordinates from distance information , 1978 .

[11]  Timothy F. Havel.  An evaluation of computational strategies for use in the determination of protein structure from distance constraints obtained by nuclear magnetic resonance. , 1991, Progress in biophysics and molecular biology.

[12]  H A Scheraga,et al.  An approach to the multiple-minima problem by relaxing dimensionality. , 1986, Proceedings of the National Academy of Sciences of the United States of America.

[13]  J. Deisenhofer,et al.  Crystallographic refinement of the structure of bovine pancreatic trypsin inhibitor at l.5 Å resolution , 1975 .

[14]  W F van Gunsteren,et al.  Molecular dynamics simulation techniques for determination of molecular structures from nuclear magnetic resonance data. , 1989, Methods in enzymology.

[15]  Gordon M. Crippen,et al.  Chemical distance geometry: Current realization and future projection , 1991 .

[16]  J. Bolin,et al.  Crystal structures of Escherichia coli and Lactobacillus casei dihydrofolate reductase refined at 1.7 A resolution. I. General features and binding of methotrexate. , 1982, The Journal of biological chemistry.

[17]  P. S. Kim,et al.  X-ray structure of the GCN4 leucine zipper, a two-stranded, parallel coiled coil. , 1991, Science.

[18]  I. Kuntz,et al.  [9] Distance geometry , 1989 .