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TINKER is a complete package for performing empirical force field molecular mechanics and dynamics calculations. It is intended to serve as a platform for algorithm development and parameterization, while still being efficient enough for most production work. The available potentials include Amber and our AMOEBA polarizable atomic multipole-based potential.(More)
We assume that each class of protein has a core structure that is defined by internal residues, and that the external, solvent-contacting residues contribute to the stability of the structure, are of primary importance to function, but do not determine the architecture of the core portions of the polypeptide chain. An algorithm has been developed to supply(More)
A large superfamily of transmembrane receptors control cellular responses to diverse extracellular signals by catalyzing activation of specific types of heterotrimeric GTP-binding proteins. How these receptors recognize and promote nucleotide exchange on G protein alpha subunits to initiate signal amplification is unknown. The three-dimensional structure of(More)
  • E S Huang, R Samudrala, J W Ponder
  • 1999
The problem of protein tertiary structure prediction from primary sequence can be separated into two subproblems: generation of a library of possible folds and specification of a best fold given the library. A distance geometry procedure based on random pairwise metrization with good sampling properties was used to generate a library of 500 possible(More)
A protocol is described for the treatment of molecular polarization in force field calculations. The resulting model is consistent in that both inter- and intramolecular polarization are handled within a single scheme. An analytical formula for removing intramolecular polarization from a set of atomic multipoles for an arbitrary static structure or(More)
Molecular force fields have been approaching a generational transition over the past several years, moving away from well-established and well-tuned, but intrinsically limited, fixed point charge models toward more intricate and expensive polarizable models that should allow more accurate description of molecular properties. The recently introduced AMOEBA(More)
Inositol polyphosphate 1-phosphatase, inositol monophosphate phosphatase, and fructose 1,6-bisphosphatase share a sequence motif, Asp-Pro-(Ile or Leu)-Asp-(Gly or Ser)-(Thr or Ser), that has been shown by crystallographic and mutagenesis studies to bind metal ions and participate in catalysis. We compared the six alpha-carbon coordinates of this motif from(More)
Potential smoothing, a deterministic analog of stochastic simulated annealing, is a powerful paradigm for the solution of conformational search problems that require extensive sampling, and should be a useful tool in computational approaches to structure prediction and refinement. A novel potential smoothing and search (PSS) algorithm has been developed and(More)
Global energy optimization of a molecular system is difficult due to the well-known " multiple minimum " problem. The rugged potential energy surface (PES) characteristic of multidimensional systems can be transformed reversibly using potential smoothing to generate a new surface that is easier to search for favorable configurations. The diffusion equation(More)