SATIS: Atom Typing from Chemical Connectivity

SATIS (simple atom type information system) is a protocol for the definition and automatic assignment of atom types and the classification of atoms according to their covalent connectivity. Its distinctive feature is that no bond type information is involved. Rather, the classification of each atom is based on a connectivity code describing the atom and its covalent partners. It is particularly useful when handling coordinate-based molecular representations with no bond order information, such as the PDB format. We survey the occurrence of the various connectivity codes in the 20 common amino acid residues in a sample of 304 different moieties from PDB protein−ligand complexes and also in a pseudo-random sample of 309 organic molecules from the CSD. We illustrate how connectivity codes can be grouped together to define atom types. We expect SATIS to be applicable to the derivation of atom types for statistical potentials, to the analysis of atomic interactions in structural databases, to studies of molecu...

[1]  P. Kollman,et al.  An all atom force field for simulations of proteins and nucleic acids , 1986, Journal of computational chemistry.

[2]  Robin Taylor,et al.  IsoStar: A library of information about nonbonded interactions , 1997, J. Comput. Aided Mol. Des..

[3]  P K Warme,et al.  A survey of atomic interactions in 21 proteins. , 1978, Journal of molecular biology.

[4]  J M Thornton,et al.  LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. , 1995, Protein engineering.

[5]  F. Melo,et al.  Novel knowledge-based mean force potential at atomic level. , 1997, Journal of molecular biology.

[6]  Friedrich Rippmann,et al.  BALI: Automatic Assignment of Bond and Atom Types for Protein Ligands in the Brookhaven Protein Databank , 1997, J. Chem. Inf. Comput. Sci..

[7]  H. Scheraga,et al.  Local structure in ribonuclease A. Effect of amino acid substitutions on the preferential formation of the native disulfide loop in synthetic peptides corresponding to residues Cys58-Cys72 of bovine pancreatic ribonuclease A , 1990 .

[8]  Michael F. Lynch,et al.  Analysis of structural characteristics of chemical compounds in a large computer-based file. Part II. Atom-centred fragments , 1970 .

[9]  R. Venkatesan.  The phase problem and its relation to the spin-glass problem , 1991 .

[10]  J M Thornton,et al.  X-SITE: use of empirically derived atomic packing preferences to identify favourable interaction regions in the binding sites of proteins. , 1996, Journal of molecular biology.

[11]  H. Mitchell,et al.  A Stable Methyl Phosphane Oxide/Lithium Amide Complex: a Structural and MO Calculational Investigation of the Mechanism of Proton Abstraction by Alkali Metal Reagents† , 1996 .

[12]  U. Singh,et al.  A NEW FORCE FIELD FOR MOLECULAR MECHANICAL SIMULATION OF NUCLEIC ACIDS AND PROTEINS , 1984 .

[13]  Janet M. Thornton,et al.  BLEEP—potential of mean force describing protein–ligand interactions: I. Generating potential , 1999 .

[14]  Janet M. Thornton,et al.  BLEEP - potential of mean force describing protein-ligand interactions: II. Calculation of binding energies and comparison with experimental data , 1999, J. Comput. Chem..

[15]  David E. Cane,et al.  Biosynthetic origin of the carbon skeleton and oxygen atoms of nargenicin A1 , 1984 .

[16]  R. Huber,et al.  Accurate Bond and Angle Parameters for X-ray Protein Structure Refinement , 1991 .

[17]  G J Williams,et al.  The Protein Data Bank: a computer-based archival file for macromolecular structures. , 1978, Archives of biochemistry and biophysics.

[18]  Sarah L. Price,et al.  A TRANSFERABLE DISTRIBUTED MULTIPOLE MODEL FOR THE ELECTROSTATIC INTERACTIONS OF PEPTIDES AND AMIDES , 1990 .

[19]  David Weininger,et al.  SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules , 1988, J. Chem. Inf. Comput. Sci..

[20]  M. Karplus,et al.  CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .