Automatic atom type and bond type perception in molecular mechanical calculations.

[1]  Peter Willett,et al.  A bibliometric analysis of the Journal of Molecular Graphics and Modelling. , 2007, Journal of molecular graphics & modelling.

[2]  Junmei Wang,et al.  Development and testing of a general amber force field , 2004, J. Comput. Chem..

[3]  Alessandro Pedretti,et al.  Atom-type description language: a universal language to recognize atom types implemented in the VEGA program , 2003 .

[4]  Christopher I. Bayly,et al.  Fast, efficient generation of high‐quality atomic charges. AM1‐BCC model: II. Parameterization and validation , 2002, J. Comput. Chem..

[5]  Junmei Wang,et al.  Automatic parameterization of force field by systematic search and genetic algorithms , 2001, J. Comput. Chem..

[6]  P. Kollman,et al.  Solvation Model Based on Weighted Solvent Accessible Surface Area , 2001 .

[7]  Junmei Wang,et al.  How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? , 2000, J. Comput. Chem..

[8]  Araz Jakalian,et al.  Fast, efficient generation of high‐quality atomic charges. AM1‐BCC model: I. Method , 2000 .

[9]  T. Halgren.  MMFF VII. Characterization of MMFF94, MMFF94s, and other widely available force fields for conformational energies and for intermolecular‐interaction energies and geometries , 1999, Journal of computational chemistry.

[10]  F. Müller-Plathe,et al.  Automatic parameterization of force fields for liquids by simplex optimization , 1999, J. Comput. Chem..

[11]  Peter A. Kollman,et al.  Application of the RESP Methodology in the Parametrization of Organic Solvents , 1998 .

[12]  Per-Ola Norrby,et al.  Automated molecular mechanics parameterization with simultaneous utilization of experimental and quantum mechanical data , 1998, J. Comput. Chem..

[13]  J. Phillip Bowen,et al.  Parameter analysis and refinement toolkit system and its application in MM3 parameterization for phosphine and its derivatives , 1996, J. Comput. Chem..

[14]  T. Halgren.  Merck molecular force field. II. MMFF94 van der Waals and electrostatic parameters for intermolecular interactions , 1996 .

[15]  Thomas A. Halgren,et al.  Merck molecular force field. III. Molecular geometries and vibrational frequencies for MMFF94 , 1996, J. Comput. Chem..

[16]  Thomas A. Halgren,et al.  Merck molecular force field. IV. conformational energies and geometries for MMFF94 , 1996, J. Comput. Chem..

[17]  T. Halgren.  Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94 , 1996, J. Comput. Chem..

[18]  Peter A. Kollman,et al.  Application of the multimolecule and multiconformational RESP methodology to biopolymers: Charge derivation for DNA, RNA, and proteins , 1995, J. Comput. Chem..

[19]  P. Kollman,et al.  A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules , 1995 .

[20]  Ming-Jing Hwang,et al.  Derivation of Class II Force Fields. 2. Derivation and Characterization of a Class II Force Field, CFF93, for the Alkyl Functional Group and Alkane Molecules , 1994 .

[21]  P. Kollman,et al.  A well-behaved electrostatic potential-based method using charge restraints for deriving atomic char , 1993 .

[22]  P. Kollman,et al.  Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of solvation , 1993 .

[23]  W. Goddard,et al.  UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations , 1992 .

[24]  F. Momany,et al.  Validation of the general purpose QUANTA ®3.2/CHARMm® force field , 1992 .

[25]  S. L. Mayo,et al.  DREIDING: A generic force field for molecular simulations , 1990 .

[26]  Norman L. Allinger,et al.  Molecular mechanics. The MM3 force field for hydrocarbons. 1 , 1989 .

[27]  R. Cramer,et al.  Validation of the general purpose tripos 5.2 force field , 1989 .

[28]  W. L. Jorgensen,et al.  The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin. , 1988, Journal of the American Chemical Society.

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

[30]  G. Grisetti,et al.  Further Reading , 1984, IEEE Spectrum.

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

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

[33]  S. Lifson,et al.  Consistent force field studies of intermolecular forces in hydrogen-bonded crystals. 1. Carboxylic acids, amides, and the C:O.cntdot..cntdot..cntdot.H- hydrogen bonds , 1979 .

[34]  Norman L. Allinger,et al.  Conformational analysis. 130. MM2. A hydrocarbon force field utilizing V1 and V2 torsional terms , 1977 .

[35]  MDL Information Systems, Inc. , 1995, Environmental science & technology.