Deterministic global optimization and torsion angle dynamics for molecular structure prediction
The problem of protein folding has become the subject of intense theoretical and experimental study over the past few decades. This work presents a new method for protein structure prediction using distance and dihedral angle restraints derived from NMR data. Both the formulation and solution approa...
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| Published in | Computers & chemical engineering Vol. 24; no. 2; pp. 1761 - 1766 |
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| Main Authors | , |
| Format | Journal Article |
| Language | English |
| Published |
Elsevier Ltd
15.07.2000
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| Subjects | |
| Online Access | Get full text |
| ISSN | 0098-1354 1873-4375 |
| DOI | 10.1016/S0098-1354(00)00461-0 |
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| Abstract | The problem of protein folding has become the subject of intense theoretical and experimental study over the past few decades. This work presents a new method for protein structure prediction using distance and dihedral angle restraints derived from NMR data. Both the formulation and solution approach differ substantially from traditional molecular structure prediction techniques. The traditional formulation is recast as a constrained global optimization problem whose solution is obtained through the use of the αBB algorithm, a deterministic global optimizationa approach suitable for nonconvex constrained problems. To enhance the efficiency of this method, torsion angle dynamics is introduced as an integral part of the solution approach. The proposed algorithm is tested on the Compstatin structure prediction problem. |
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| AbstractList | The problem of protein folding has become the subject of intense theoretical and experimental study over the past few decades. This work presents a new method for protein structure prediction using distance and dihedral angle restraints derived from NMR data. Both the formulation and solution approach differ substantially from traditional molecular structure prediction techniques. The traditional formulation is recast as a constrained global optimization problem whose solution is obtained through the use of the αBB algorithm, a deterministic global optimizationa approach suitable for nonconvex constrained problems. To enhance the efficiency of this method, torsion angle dynamics is introduced as an integral part of the solution approach. The proposed algorithm is tested on the Compstatin structure prediction problem. |
| Author | Klepeis, J.L. Floudas, C.A. |
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| Cites_doi | 10.1016/S0098-1354(98)00027-1 10.4049/jimmunol.157.2.884 10.1006/jmbi.1998.2372 10.1007/BF01099647 10.1126/science.282.5389.740 10.1002/(SICI)1096-987X(199910)20:13<1354::AID-JCC3>3.0.CO;2-N 10.1002/(SICI)1096-987X(19990430)20:6<636::AID-JCC10>3.0.CO;2-D 10.1002/pro.5560070311 10.1002/prot.340190403 10.1023/A:1008224308626 10.1002/pro.5560070314 10.1016/S0021-9991(83)71106-X 10.1016/S0098-1354(97)00258-5 10.1063/1.448118 10.1016/S0098-1354(98)00218-X 10.1006/jmbi.1997.1284 |
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| Keywords | Global optimization Torsion angle dynamics Molecular structure prediction |
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| References | Adjiman, Dallwig, Floudas, Neumaier (BIB2) 1998; 22 Duan, Kollman (BIB8) 1998; 282 Rice, Brünger (BIB18) 1994; 19 Morikis, Assa-Munt, Sahu, Lambris (BIB16) 1998; 7 Standley, Eyrich, Felts, Friesner, McDermott (BIB20) 1999; 285 Klepeis, Floudas, Morikis, Lambris (BIB14) 1999; 20 Berendsen, Postina, van Gunsteren, DiNola, Haak (BIB5) 1984; 81 Maranas, Androulakis, Floudas (BIB15) 1996; 23 Adjiman, Androulakis, Floudas (BIB1) 1998; 22 Caves, Evanseck, Karplus (BIB7) 1998; 7 Némethy, Gibson, Palmer, Yoon, Paterlini, Zagari, Rumsey, Scheraga (BIB17) 1992; 96 Klepeis, Floudas (BIB12) 1999 Sahu, Kay, Lambris (BIB19) 1996; 157 Brünger (BIB6) 1992 Floudas (BIB9) 2000 Klepeis, Androulakis, Ierapetritou, Floudas (BIB13) 1998; 22 Güntert, Mumenthaler, Wüthrich (BIB10) 1997; 273 Jain, Vaidehi, Rodriguez (BIB11) 1993; 106 Androulakis, Maranas, Floudas (BIB3) 1995; 7 Androulakis, Maranas, Floudas (BIB4) 1997; 11 Androulakis (10.1016/S0098-1354(00)00461-0_BIB4) 1997; 11 Duan (10.1016/S0098-1354(00)00461-0_BIB8) 1998; 282 Floudas (10.1016/S0098-1354(00)00461-0_BIB9) 2000 Jain (10.1016/S0098-1354(00)00461-0_BIB11) 1993; 106 Rice (10.1016/S0098-1354(00)00461-0_BIB18) 1994; 19 Klepeis (10.1016/S0098-1354(00)00461-0_BIB13) 1998; 22 Sahu (10.1016/S0098-1354(00)00461-0_BIB19) 1996; 157 Némethy (10.1016/S0098-1354(00)00461-0_BIB17) 1992; 96 Adjiman (10.1016/S0098-1354(00)00461-0_BIB1) 1998; 22 Androulakis (10.1016/S0098-1354(00)00461-0_BIB3) 1995; 7 Klepeis (10.1016/S0098-1354(00)00461-0_BIB12) 1999 Güntert (10.1016/S0098-1354(00)00461-0_BIB10) 1997; 273 Berendsen (10.1016/S0098-1354(00)00461-0_BIB5) 1984; 81 Brünger (10.1016/S0098-1354(00)00461-0_BIB6) 1992 Adjiman (10.1016/S0098-1354(00)00461-0_BIB2) 1998; 22 Klepeis (10.1016/S0098-1354(00)00461-0_BIB14) 1999; 20 Morikis (10.1016/S0098-1354(00)00461-0_BIB16) 1998; 7 Caves (10.1016/S0098-1354(00)00461-0_BIB7) 1998; 7 Standley (10.1016/S0098-1354(00)00461-0_BIB20) 1999; 285 Maranas (10.1016/S0098-1354(00)00461-0_BIB15) 1996; 23 |
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10.1063/1.448118 – volume: 22 start-page: 1159 year: 1998 ident: 10.1016/S0098-1354(00)00461-0_BIB1 article-title: A global optimization method, αBB, for general twice-differentiable NLPs — II.: implementation and computational results publication-title: Computers and Chemical Engineering doi: 10.1016/S0098-1354(98)00218-X – volume: 96 start-page: 6472 year: 1992 ident: 10.1016/S0098-1354(00)00461-0_BIB17 article-title: Energy parameters in polypeptides publication-title: Journal of Physical Chemistry – volume: 273 start-page: 283 year: 1997 ident: 10.1016/S0098-1354(00)00461-0_BIB10 article-title: Torsion angle dynamics for NMR structure calculation with the new program dyana publication-title: Journal of Molecular Biology doi: 10.1006/jmbi.1997.1284 |
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| Title | Deterministic global optimization and torsion angle dynamics for molecular structure prediction |
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