Literature DB >> 18250333

The kernel energy method of quantum mechanical approximation carried to fourth-order terms.

Lulu Huang1, Lou Massa, Jerome Karle.   

Abstract

It is now possible to calculate the ab initio quantum mechanics of very large biological molecules. Two things lead to this perspective, namely, (i) the advances of parallel supercomputers, and (ii) the discovery of a quantum formalism called quantum crystallography and the use of quantum kernels, a method that is well suited for parallel computation. The kernel energy method (KEM) carried to second order has been used to calculate the quantum mechanical ab initio molecular energy of peptides, protein (insulin and collagen), DNA, and RNA and the interaction of drugs with their biochemical molecular targets. The results were found to have good accuracy. In this article, the accuracy of the KEM is investigated up to an approximation including fourth-order interactions among kernels. Remarkable accuracy is achieved in the calculation of the energy of the ground state of the important biological molecule Leu1-zervamicin, whose crystal structure is known and used in the calculations.

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Year:  2008        PMID: 18250333      PMCID: PMC2538851          DOI: 10.1073/pnas.0711297105

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  6 in total

1.  Kernel Energy Method:  The Interaction Energy of the Collagen Triple Helix.

Authors:  Lulu Huang; Lou Massa; Jerome Karle
Journal:  J Chem Theory Comput       Date:  2007-07       Impact factor: 6.006

2.  Kernel energy method: application to insulin.

Authors:  Lulu Huang; Lou Massa; Jerome Karle
Journal:  Proc Natl Acad Sci U S A       Date:  2005-08-24       Impact factor: 11.205

3.  Kernel energy method: application to DNA.

Authors:  Lulu Huang; Lou Massa; Jerome Karle
Journal:  Biochemistry       Date:  2005-12-20       Impact factor: 3.162

4.  The Kernel Energy Method: application to a tRNA.

Authors:  Lulu Huang; Lou Massa; Jerome Karle
Journal:  Proc Natl Acad Sci U S A       Date:  2006-01-23       Impact factor: 11.205

5.  Drug target interaction energies by the kernel energy method in aminoglycoside drugs and ribosomal A site RNA targets.

Authors:  Lulu Huang; Lou Massa; Jerome Karle
Journal:  Proc Natl Acad Sci U S A       Date:  2007-03-01       Impact factor: 11.205

6.  Conformation of the flexible bent helix of Leu1-zervamicin in crystal C and a possible gating action for ion passage.

Authors:  I L Karle; J L Flippen-Anderson; S Agarwalla; P Balaram
Journal:  Biopolymers       Date:  1994-06       Impact factor: 2.505

  6 in total
  4 in total

1.  Calculation of strong and weak interactions in TDA1 and RangDP52 by the kernel energy method.

Authors:  Lulu Huang; Lou Massa; Isabella Karle; Jerome Karle
Journal:  Proc Natl Acad Sci U S A       Date:  2009-02-20       Impact factor: 11.205

2.  Protoribosome by quantum kernel energy method.

Authors:  Lulu Huang; Miri Krupkin; Anat Bashan; Ada Yonath; Lou Massa
Journal:  Proc Natl Acad Sci U S A       Date:  2013-08-26       Impact factor: 11.205

3.  The Kernel Energy Method: Construction of 3 & 4 tuple Kernels from a List of Double Kernel Interactions.

Authors:  Lulu Huang; Lou Massa
Journal:  Theochem       Date:  2010-12

4.  Fragmentation Method for Computing Quantum Mechanics and Molecular Mechanics Gradients for Force Matching: Validation with Hydration Free Energy Predictions Using Adaptive Force Matching.

Authors:  Dong Zheng; Ying Yuan; Feng Wang
Journal:  J Phys Chem A       Date:  2022-04-14       Impact factor: 2.944

  4 in total

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