New Method for Direct Linear-Scaling Calculation of Electron Density of Proteins
A new scheme for direct linear-scaling quantum mechanical calculation of electron density of protein systems is developed. The new scheme gives much improved accuracy of electron density for proteins than the original MFCC (molecular fractionation with conjugate caps) approach in efficient linear-sc...
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| Veröffentlicht in: | The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory Molecules, spectroscopy, kinetics, environment, & general theory, 2005-01, Vol.109 (1), p.2-5 |
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| container_title | The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory |
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| creator | Mei, Ye Zhang, Da W. Zhang, J. Z. H. |
| description | A new scheme for direct linear-scaling quantum mechanical calculation of electron density of protein systems is developed. The new scheme gives much improved accuracy of electron density for proteins than the original MFCC (molecular fractionation with conjugate caps) approach in efficient linear-scaling calculation for protein systems. In this new approach, the error associated with each cut in the MFCC approach is estimated by computing the two neighboring amino acids in both cut and uncut calculations and is corrected. Numerical tests are performed on six oligopeptide taken from PDB (protein data bank), and the results show that the new scheme is efficient and accurate. |
| doi_str_mv | 10.1021/jp045109y |
| format | Article |
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Z. H.</creatorcontrib><title>New Method for Direct Linear-Scaling Calculation of Electron Density of Proteins</title><title>The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory</title><addtitle>J. Phys. Chem. A</addtitle><description>A new scheme for direct linear-scaling quantum mechanical calculation of electron density of protein systems is developed. The new scheme gives much improved accuracy of electron density for proteins than the original MFCC (molecular fractionation with conjugate caps) approach in efficient linear-scaling calculation for protein systems. In this new approach, the error associated with each cut in the MFCC approach is estimated by computing the two neighboring amino acids in both cut and uncut calculations and is corrected. Numerical tests are performed on six oligopeptide taken from PDB (protein data bank), and the results show that the new scheme is efficient and accurate.</description><subject>Computer Simulation</subject><subject>Crystallography, X-Ray</subject><subject>Electrons</subject><subject>Molecular Structure</subject><subject>Peptides - chemistry</subject><subject>Proteins - chemistry</subject><subject>Static Electricity</subject><issn>1089-5639</issn><issn>1520-5215</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2005</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNpt0E1LAzEQBuAgiq3Vg39A9qLgYTUfm2xylLZaoWqhFaGXkKaJpm43NdlF--_d0lIvnmaYeZiBF4BzBG8QxOh2sYIZRVCsD0AbUQxTihE9bHrIRUoZES1wEuMCQogIzo5BCzFOBOS4DUbP5jt5MtWHnyfWh6TngtFVMnSlUSEda1W48j3pqkLXhaqcLxNvk37RmND0PVNGV603s1HwlXFlPAVHVhXRnO1qB7ze9yfdQTp8eXjs3g1TRSiqUsRyjZGiLJsZwy3SlFluM8FZbilndiasIkxwy5lGuSIcZ5zkAs4wh3Nh56QDrrZ3V8F_1SZWcumiNkWhSuPrKHOIckwz3MDrLdTBxxiMlavgliqsJYJyE5_cx9fYi93RerY08z-5y6sB6Ra4WJmf_V6FT8lyklM5GY0ln46mjL9xOWj85dYrHeXC16FsMvnn8S99NITN</recordid><startdate>20050113</startdate><enddate>20050113</enddate><creator>Mei, Ye</creator><creator>Zhang, Da W.</creator><creator>Zhang, J. 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A</addtitle><date>2005-01-13</date><risdate>2005</risdate><volume>109</volume><issue>1</issue><spage>2</spage><epage>5</epage><pages>2-5</pages><issn>1089-5639</issn><eissn>1520-5215</eissn><abstract>A new scheme for direct linear-scaling quantum mechanical calculation of electron density of protein systems is developed. The new scheme gives much improved accuracy of electron density for proteins than the original MFCC (molecular fractionation with conjugate caps) approach in efficient linear-scaling calculation for protein systems. In this new approach, the error associated with each cut in the MFCC approach is estimated by computing the two neighboring amino acids in both cut and uncut calculations and is corrected. 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| ispartof | The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory, 2005-01, Vol.109 (1), p.2-5 |
| issn | 1089-5639 1520-5215 |
| language | eng |
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| source | MEDLINE; American Chemical Society Journals |
| subjects | Computer Simulation Crystallography, X-Ray Electrons Molecular Structure Peptides - chemistry Proteins - chemistry Static Electricity |
| title | New Method for Direct Linear-Scaling Calculation of Electron Density of Proteins |
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