Search for approaches to improving the calculation accuracy of the protein—ligand binding energy by docking
Abstract The following reasons limiting the accuracy of calculations of the protein—ligand binding energy by the molecular docking programs are considered: the limited facilities of algorithms of finding a global minimum on a complicated multi-dimensional protein—ligand energy surface, restrictions...
Ausführliche Beschreibung
Gespeichert in:
| Autor*in: |
Sulimov, A. V. [verfasserIn] Kutov, D. C. [verfasserIn] Katkova, E. V. [verfasserIn] Kondakova, O. A. [verfasserIn] Sulimov, V. B. [verfasserIn] |
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| Format: |
E-Artikel |
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| Sprache: |
Englisch |
| Erschienen: |
2017 |
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| Schlagwörter: |
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| Übergeordnetes Werk: |
Enthalten in: Russian chemical bulletin - New York, NY [u.a.] : Consultants Bureau, 1952, 66(2017), 10 vom: Okt., Seite 1913-1924 |
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| Übergeordnetes Werk: |
volume:66 ; year:2017 ; number:10 ; month:10 ; pages:1913-1924 |
| Links: |
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| DOI / URN: |
10.1007/s11172-017-1966-6 |
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| Katalog-ID: |
SPR017338123 |
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| 024 | 7 | |a 10.1007/s11172-017-1966-6 |2 doi | |
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| 035 | |a (SPR)s11172-017-1966-6-e | ||
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| 084 | |a 35.00 |2 bkl | ||
| 100 | 1 | |a Sulimov, A. V. |e verfasserin |4 aut | |
| 245 | 1 | 0 | |a Search for approaches to improving the calculation accuracy of the protein—ligand binding energy by docking |
| 264 | 1 | |c 2017 | |
| 336 | |a Text |b txt |2 rdacontent | ||
| 337 | |a Computermedien |b c |2 rdamedia | ||
| 338 | |a Online-Ressource |b cr |2 rdacarrier | ||
| 520 | |a Abstract The following reasons limiting the accuracy of calculations of the protein—ligand binding energy by the molecular docking programs are considered: the limited facilities of algorithms of finding a global minimum on a complicated multi-dimensional protein—ligand energy surface, restrictions on the degrees of freedom of a protein—ligand system including docking into a rigid protein, inadequacy of the existing force fields, a lack of taking into account the solvent or too rough allowance for the solvent in the docking procedure, a lack of the local energy optimization in the docking process, an inaccuracy of the construction of models of a target protein and a ligand, simplification of the calculation method of the Gibbs free energy of a molecular system, and limited computer resources for docking of one ligand. A new approach to the development of the new generation of docking programs is proposed. The approach allows one to remove step-by-step the existing simplifications and to increase considerably the accuracy of the whole docking process, including the calculation accuracy of the protein—ligand binding energy. The results of the study are presented and demonstrate the computational feasibility of the assigned docking problem. | ||
| 650 | 4 | |a docking |7 (dpeaa)DE-He213 | |
| 650 | 4 | |a tensor train |7 (dpeaa)DE-He213 | |
| 650 | 4 | |a binding energy |7 (dpeaa)DE-He213 | |
| 650 | 4 | |a low-energy local minima spectrum |7 (dpeaa)DE-He213 | |
| 650 | 4 | |a flexible ligand |7 (dpeaa)DE-He213 | |
| 650 | 4 | |a drug design |7 (dpeaa)DE-He213 | |
| 700 | 1 | |a Kutov, D. C. |e verfasserin |4 aut | |
| 700 | 1 | |a Katkova, E. V. |e verfasserin |4 aut | |
| 700 | 1 | |a Kondakova, O. A. |e verfasserin |4 aut | |
| 700 | 1 | |a Sulimov, V. B. |e verfasserin |4 aut | |
| 773 | 0 | 8 | |i Enthalten in |t Russian chemical bulletin |d New York, NY [u.a.] : Consultants Bureau, 1952 |g 66(2017), 10 vom: Okt., Seite 1913-1924 |w (DE-627)325573417 |w (DE-600)2037677-7 |x 1573-9171 |7 nnns |
| 773 | 1 | 8 | |g volume:66 |g year:2017 |g number:10 |g month:10 |g pages:1913-1924 |
| 856 | 4 | 0 | |u https://dx.doi.org/10.1007/s11172-017-1966-6 |z lizenzpflichtig |3 Volltext |
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| 912 | |a GBV_ILN_73 | ||
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| 912 | |a GBV_ILN_90 | ||
| 912 | |a GBV_ILN_95 | ||
| 912 | |a GBV_ILN_100 | ||
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| 912 | |a GBV_ILN_110 | ||
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| 912 | |a GBV_ILN_138 | ||
| 912 | |a GBV_ILN_150 | ||
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| 912 | |a GBV_ILN_170 | ||
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| 912 | |a GBV_ILN_187 | ||
| 912 | |a GBV_ILN_213 | ||
| 912 | |a GBV_ILN_224 | ||
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| 912 | |a GBV_ILN_250 | ||
| 912 | |a GBV_ILN_281 | ||
| 912 | |a GBV_ILN_285 | ||
| 912 | |a GBV_ILN_293 | ||
| 912 | |a GBV_ILN_370 | ||
| 912 | |a GBV_ILN_602 | ||
| 912 | |a GBV_ILN_636 | ||
| 912 | |a GBV_ILN_702 | ||
| 912 | |a GBV_ILN_2001 | ||
| 912 | |a GBV_ILN_2003 | ||
| 912 | |a GBV_ILN_2004 | ||
| 912 | |a GBV_ILN_2005 | ||
| 912 | |a GBV_ILN_2006 | ||
| 912 | |a GBV_ILN_2007 | ||
| 912 | |a GBV_ILN_2008 | ||
| 912 | |a GBV_ILN_2009 | ||
| 912 | |a GBV_ILN_2010 | ||
| 912 | |a GBV_ILN_2011 | ||
| 912 | |a GBV_ILN_2014 | ||
| 912 | |a GBV_ILN_2015 | ||
| 912 | |a GBV_ILN_2020 | ||
| 912 | |a GBV_ILN_2021 | ||
| 912 | |a GBV_ILN_2025 | ||
| 912 | |a GBV_ILN_2026 | ||
| 912 | |a GBV_ILN_2027 | ||
| 912 | |a GBV_ILN_2031 | ||
| 912 | |a GBV_ILN_2034 | ||
| 912 | |a GBV_ILN_2037 | ||
| 912 | |a GBV_ILN_2038 | ||
| 912 | |a GBV_ILN_2039 | ||
| 912 | |a GBV_ILN_2044 | ||
| 912 | |a GBV_ILN_2048 | ||
| 912 | |a GBV_ILN_2049 | ||
| 912 | |a GBV_ILN_2050 | ||
| 912 | |a GBV_ILN_2055 | ||
| 912 | |a GBV_ILN_2057 | ||
| 912 | |a GBV_ILN_2059 | ||
| 912 | |a GBV_ILN_2061 | ||
| 912 | |a GBV_ILN_2064 | ||
| 912 | |a GBV_ILN_2065 | ||
| 912 | |a GBV_ILN_2068 | ||
| 912 | |a GBV_ILN_2070 | ||
| 912 | |a GBV_ILN_2086 | ||
| 912 | |a GBV_ILN_2088 | ||
| 912 | |a GBV_ILN_2093 | ||
| 912 | |a GBV_ILN_2106 | ||
| 912 | |a GBV_ILN_2107 | ||
| 912 | |a GBV_ILN_2108 | ||
| 912 | |a GBV_ILN_2110 | ||
| 912 | |a GBV_ILN_2111 | ||
| 912 | |a GBV_ILN_2112 | ||
| 912 | |a GBV_ILN_2113 | ||
| 912 | |a GBV_ILN_2116 | ||
| 912 | |a GBV_ILN_2118 | ||
| 912 | |a GBV_ILN_2119 | ||
| 912 | |a GBV_ILN_2122 | ||
| 912 | |a GBV_ILN_2129 | ||
| 912 | |a GBV_ILN_2143 | ||
| 912 | |a GBV_ILN_2144 | ||
| 912 | |a GBV_ILN_2147 | ||
| 912 | |a GBV_ILN_2148 | ||
| 912 | |a GBV_ILN_2152 | ||
| 912 | |a GBV_ILN_2153 | ||
| 912 | |a GBV_ILN_2188 | ||
| 912 | |a GBV_ILN_2190 | ||
| 912 | |a GBV_ILN_2232 | ||
| 912 | |a GBV_ILN_2336 | ||
| 912 | |a GBV_ILN_2446 | ||
| 912 | |a GBV_ILN_2470 | ||
| 912 | |a GBV_ILN_2472 | ||
| 912 | |a GBV_ILN_2507 | ||
| 912 | |a GBV_ILN_2522 | ||
| 912 | |a GBV_ILN_2548 | ||
| 912 | |a GBV_ILN_4012 | ||
| 912 | |a GBV_ILN_4035 | ||
| 912 | |a GBV_ILN_4037 | ||
| 912 | |a GBV_ILN_4046 | ||
| 912 | |a GBV_ILN_4112 | ||
| 912 | |a GBV_ILN_4125 | ||
| 912 | |a GBV_ILN_4126 | ||
| 912 | |a GBV_ILN_4242 | ||
| 912 | |a GBV_ILN_4246 | ||
| 912 | |a GBV_ILN_4249 | ||
| 912 | |a GBV_ILN_4251 | ||
| 912 | |a GBV_ILN_4305 | ||
| 912 | |a GBV_ILN_4306 | ||
| 912 | |a GBV_ILN_4307 | ||
| 912 | |a GBV_ILN_4313 | ||
| 912 | |a GBV_ILN_4322 | ||
| 912 | |a GBV_ILN_4323 | ||
| 912 | |a GBV_ILN_4324 | ||
| 912 | |a GBV_ILN_4325 | ||
| 912 | |a GBV_ILN_4326 | ||
| 912 | |a GBV_ILN_4333 | ||
| 912 | |a GBV_ILN_4334 | ||
| 912 | |a GBV_ILN_4335 | ||
| 912 | |a GBV_ILN_4336 | ||
| 912 | |a GBV_ILN_4338 | ||
| 912 | |a GBV_ILN_4393 | ||
| 912 | |a GBV_ILN_4700 | ||
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| 952 | |d 66 |j 2017 |e 10 |c 10 |h 1913-1924 | ||
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2017 |
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10.1007/s11172-017-1966-6 doi (DE-627)SPR017338123 (SPR)s11172-017-1966-6-e DE-627 ger DE-627 rakwb eng 540 ASE 35.00 bkl Sulimov, A. V. verfasserin aut Search for approaches to improving the calculation accuracy of the protein—ligand binding energy by docking 2017 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract The following reasons limiting the accuracy of calculations of the protein—ligand binding energy by the molecular docking programs are considered: the limited facilities of algorithms of finding a global minimum on a complicated multi-dimensional protein—ligand energy surface, restrictions on the degrees of freedom of a protein—ligand system including docking into a rigid protein, inadequacy of the existing force fields, a lack of taking into account the solvent or too rough allowance for the solvent in the docking procedure, a lack of the local energy optimization in the docking process, an inaccuracy of the construction of models of a target protein and a ligand, simplification of the calculation method of the Gibbs free energy of a molecular system, and limited computer resources for docking of one ligand. A new approach to the development of the new generation of docking programs is proposed. The approach allows one to remove step-by-step the existing simplifications and to increase considerably the accuracy of the whole docking process, including the calculation accuracy of the protein—ligand binding energy. The results of the study are presented and demonstrate the computational feasibility of the assigned docking problem. docking (dpeaa)DE-He213 tensor train (dpeaa)DE-He213 binding energy (dpeaa)DE-He213 low-energy local minima spectrum (dpeaa)DE-He213 flexible ligand (dpeaa)DE-He213 drug design (dpeaa)DE-He213 Kutov, D. C. verfasserin aut Katkova, E. V. verfasserin aut Kondakova, O. A. verfasserin aut Sulimov, V. B. verfasserin aut Enthalten in Russian chemical bulletin New York, NY [u.a.] : Consultants Bureau, 1952 66(2017), 10 vom: Okt., Seite 1913-1924 (DE-627)325573417 (DE-600)2037677-7 1573-9171 nnns volume:66 year:2017 number:10 month:10 pages:1913-1924 https://dx.doi.org/10.1007/s11172-017-1966-6 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_32 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_101 GBV_ILN_105 GBV_ILN_110 GBV_ILN_120 GBV_ILN_138 GBV_ILN_150 GBV_ILN_151 GBV_ILN_152 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_187 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_250 GBV_ILN_281 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_636 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2031 GBV_ILN_2034 GBV_ILN_2037 GBV_ILN_2038 GBV_ILN_2039 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2057 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2065 GBV_ILN_2068 GBV_ILN_2070 GBV_ILN_2086 GBV_ILN_2088 GBV_ILN_2093 GBV_ILN_2106 GBV_ILN_2107 GBV_ILN_2108 GBV_ILN_2110 GBV_ILN_2111 GBV_ILN_2112 GBV_ILN_2113 GBV_ILN_2116 GBV_ILN_2118 GBV_ILN_2119 GBV_ILN_2122 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2144 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2188 GBV_ILN_2190 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2446 GBV_ILN_2470 GBV_ILN_2472 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_2548 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4046 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4246 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4336 GBV_ILN_4338 GBV_ILN_4393 GBV_ILN_4700 35.00 ASE AR 66 2017 10 10 1913-1924 |
| spelling |
10.1007/s11172-017-1966-6 doi (DE-627)SPR017338123 (SPR)s11172-017-1966-6-e DE-627 ger DE-627 rakwb eng 540 ASE 35.00 bkl Sulimov, A. V. verfasserin aut Search for approaches to improving the calculation accuracy of the protein—ligand binding energy by docking 2017 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract The following reasons limiting the accuracy of calculations of the protein—ligand binding energy by the molecular docking programs are considered: the limited facilities of algorithms of finding a global minimum on a complicated multi-dimensional protein—ligand energy surface, restrictions on the degrees of freedom of a protein—ligand system including docking into a rigid protein, inadequacy of the existing force fields, a lack of taking into account the solvent or too rough allowance for the solvent in the docking procedure, a lack of the local energy optimization in the docking process, an inaccuracy of the construction of models of a target protein and a ligand, simplification of the calculation method of the Gibbs free energy of a molecular system, and limited computer resources for docking of one ligand. A new approach to the development of the new generation of docking programs is proposed. The approach allows one to remove step-by-step the existing simplifications and to increase considerably the accuracy of the whole docking process, including the calculation accuracy of the protein—ligand binding energy. The results of the study are presented and demonstrate the computational feasibility of the assigned docking problem. docking (dpeaa)DE-He213 tensor train (dpeaa)DE-He213 binding energy (dpeaa)DE-He213 low-energy local minima spectrum (dpeaa)DE-He213 flexible ligand (dpeaa)DE-He213 drug design (dpeaa)DE-He213 Kutov, D. C. verfasserin aut Katkova, E. V. verfasserin aut Kondakova, O. A. verfasserin aut Sulimov, V. B. verfasserin aut Enthalten in Russian chemical bulletin New York, NY [u.a.] : Consultants Bureau, 1952 66(2017), 10 vom: Okt., Seite 1913-1924 (DE-627)325573417 (DE-600)2037677-7 1573-9171 nnns volume:66 year:2017 number:10 month:10 pages:1913-1924 https://dx.doi.org/10.1007/s11172-017-1966-6 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_32 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_101 GBV_ILN_105 GBV_ILN_110 GBV_ILN_120 GBV_ILN_138 GBV_ILN_150 GBV_ILN_151 GBV_ILN_152 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_187 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_250 GBV_ILN_281 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_636 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2031 GBV_ILN_2034 GBV_ILN_2037 GBV_ILN_2038 GBV_ILN_2039 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2057 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2065 GBV_ILN_2068 GBV_ILN_2070 GBV_ILN_2086 GBV_ILN_2088 GBV_ILN_2093 GBV_ILN_2106 GBV_ILN_2107 GBV_ILN_2108 GBV_ILN_2110 GBV_ILN_2111 GBV_ILN_2112 GBV_ILN_2113 GBV_ILN_2116 GBV_ILN_2118 GBV_ILN_2119 GBV_ILN_2122 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2144 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2188 GBV_ILN_2190 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2446 GBV_ILN_2470 GBV_ILN_2472 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_2548 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4046 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4246 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4336 GBV_ILN_4338 GBV_ILN_4393 GBV_ILN_4700 35.00 ASE AR 66 2017 10 10 1913-1924 |
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10.1007/s11172-017-1966-6 doi (DE-627)SPR017338123 (SPR)s11172-017-1966-6-e DE-627 ger DE-627 rakwb eng 540 ASE 35.00 bkl Sulimov, A. V. verfasserin aut Search for approaches to improving the calculation accuracy of the protein—ligand binding energy by docking 2017 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract The following reasons limiting the accuracy of calculations of the protein—ligand binding energy by the molecular docking programs are considered: the limited facilities of algorithms of finding a global minimum on a complicated multi-dimensional protein—ligand energy surface, restrictions on the degrees of freedom of a protein—ligand system including docking into a rigid protein, inadequacy of the existing force fields, a lack of taking into account the solvent or too rough allowance for the solvent in the docking procedure, a lack of the local energy optimization in the docking process, an inaccuracy of the construction of models of a target protein and a ligand, simplification of the calculation method of the Gibbs free energy of a molecular system, and limited computer resources for docking of one ligand. A new approach to the development of the new generation of docking programs is proposed. The approach allows one to remove step-by-step the existing simplifications and to increase considerably the accuracy of the whole docking process, including the calculation accuracy of the protein—ligand binding energy. The results of the study are presented and demonstrate the computational feasibility of the assigned docking problem. docking (dpeaa)DE-He213 tensor train (dpeaa)DE-He213 binding energy (dpeaa)DE-He213 low-energy local minima spectrum (dpeaa)DE-He213 flexible ligand (dpeaa)DE-He213 drug design (dpeaa)DE-He213 Kutov, D. C. verfasserin aut Katkova, E. V. verfasserin aut Kondakova, O. A. verfasserin aut Sulimov, V. B. verfasserin aut Enthalten in Russian chemical bulletin New York, NY [u.a.] : Consultants Bureau, 1952 66(2017), 10 vom: Okt., Seite 1913-1924 (DE-627)325573417 (DE-600)2037677-7 1573-9171 nnns volume:66 year:2017 number:10 month:10 pages:1913-1924 https://dx.doi.org/10.1007/s11172-017-1966-6 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_32 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_101 GBV_ILN_105 GBV_ILN_110 GBV_ILN_120 GBV_ILN_138 GBV_ILN_150 GBV_ILN_151 GBV_ILN_152 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_187 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_250 GBV_ILN_281 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_636 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2031 GBV_ILN_2034 GBV_ILN_2037 GBV_ILN_2038 GBV_ILN_2039 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2057 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2065 GBV_ILN_2068 GBV_ILN_2070 GBV_ILN_2086 GBV_ILN_2088 GBV_ILN_2093 GBV_ILN_2106 GBV_ILN_2107 GBV_ILN_2108 GBV_ILN_2110 GBV_ILN_2111 GBV_ILN_2112 GBV_ILN_2113 GBV_ILN_2116 GBV_ILN_2118 GBV_ILN_2119 GBV_ILN_2122 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2144 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2188 GBV_ILN_2190 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2446 GBV_ILN_2470 GBV_ILN_2472 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_2548 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4046 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4246 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4336 GBV_ILN_4338 GBV_ILN_4393 GBV_ILN_4700 35.00 ASE AR 66 2017 10 10 1913-1924 |
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10.1007/s11172-017-1966-6 doi (DE-627)SPR017338123 (SPR)s11172-017-1966-6-e DE-627 ger DE-627 rakwb eng 540 ASE 35.00 bkl Sulimov, A. V. verfasserin aut Search for approaches to improving the calculation accuracy of the protein—ligand binding energy by docking 2017 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract The following reasons limiting the accuracy of calculations of the protein—ligand binding energy by the molecular docking programs are considered: the limited facilities of algorithms of finding a global minimum on a complicated multi-dimensional protein—ligand energy surface, restrictions on the degrees of freedom of a protein—ligand system including docking into a rigid protein, inadequacy of the existing force fields, a lack of taking into account the solvent or too rough allowance for the solvent in the docking procedure, a lack of the local energy optimization in the docking process, an inaccuracy of the construction of models of a target protein and a ligand, simplification of the calculation method of the Gibbs free energy of a molecular system, and limited computer resources for docking of one ligand. A new approach to the development of the new generation of docking programs is proposed. The approach allows one to remove step-by-step the existing simplifications and to increase considerably the accuracy of the whole docking process, including the calculation accuracy of the protein—ligand binding energy. The results of the study are presented and demonstrate the computational feasibility of the assigned docking problem. docking (dpeaa)DE-He213 tensor train (dpeaa)DE-He213 binding energy (dpeaa)DE-He213 low-energy local minima spectrum (dpeaa)DE-He213 flexible ligand (dpeaa)DE-He213 drug design (dpeaa)DE-He213 Kutov, D. C. verfasserin aut Katkova, E. V. verfasserin aut Kondakova, O. A. verfasserin aut Sulimov, V. B. verfasserin aut Enthalten in Russian chemical bulletin New York, NY [u.a.] : Consultants Bureau, 1952 66(2017), 10 vom: Okt., Seite 1913-1924 (DE-627)325573417 (DE-600)2037677-7 1573-9171 nnns volume:66 year:2017 number:10 month:10 pages:1913-1924 https://dx.doi.org/10.1007/s11172-017-1966-6 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_32 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_101 GBV_ILN_105 GBV_ILN_110 GBV_ILN_120 GBV_ILN_138 GBV_ILN_150 GBV_ILN_151 GBV_ILN_152 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_187 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_250 GBV_ILN_281 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_636 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2031 GBV_ILN_2034 GBV_ILN_2037 GBV_ILN_2038 GBV_ILN_2039 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2057 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2065 GBV_ILN_2068 GBV_ILN_2070 GBV_ILN_2086 GBV_ILN_2088 GBV_ILN_2093 GBV_ILN_2106 GBV_ILN_2107 GBV_ILN_2108 GBV_ILN_2110 GBV_ILN_2111 GBV_ILN_2112 GBV_ILN_2113 GBV_ILN_2116 GBV_ILN_2118 GBV_ILN_2119 GBV_ILN_2122 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2144 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2188 GBV_ILN_2190 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2446 GBV_ILN_2470 GBV_ILN_2472 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_2548 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4046 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4246 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4336 GBV_ILN_4338 GBV_ILN_4393 GBV_ILN_4700 35.00 ASE AR 66 2017 10 10 1913-1924 |
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10.1007/s11172-017-1966-6 doi (DE-627)SPR017338123 (SPR)s11172-017-1966-6-e DE-627 ger DE-627 rakwb eng 540 ASE 35.00 bkl Sulimov, A. V. verfasserin aut Search for approaches to improving the calculation accuracy of the protein—ligand binding energy by docking 2017 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract The following reasons limiting the accuracy of calculations of the protein—ligand binding energy by the molecular docking programs are considered: the limited facilities of algorithms of finding a global minimum on a complicated multi-dimensional protein—ligand energy surface, restrictions on the degrees of freedom of a protein—ligand system including docking into a rigid protein, inadequacy of the existing force fields, a lack of taking into account the solvent or too rough allowance for the solvent in the docking procedure, a lack of the local energy optimization in the docking process, an inaccuracy of the construction of models of a target protein and a ligand, simplification of the calculation method of the Gibbs free energy of a molecular system, and limited computer resources for docking of one ligand. A new approach to the development of the new generation of docking programs is proposed. The approach allows one to remove step-by-step the existing simplifications and to increase considerably the accuracy of the whole docking process, including the calculation accuracy of the protein—ligand binding energy. The results of the study are presented and demonstrate the computational feasibility of the assigned docking problem. docking (dpeaa)DE-He213 tensor train (dpeaa)DE-He213 binding energy (dpeaa)DE-He213 low-energy local minima spectrum (dpeaa)DE-He213 flexible ligand (dpeaa)DE-He213 drug design (dpeaa)DE-He213 Kutov, D. C. verfasserin aut Katkova, E. V. verfasserin aut Kondakova, O. A. verfasserin aut Sulimov, V. B. verfasserin aut Enthalten in Russian chemical bulletin New York, NY [u.a.] : Consultants Bureau, 1952 66(2017), 10 vom: Okt., Seite 1913-1924 (DE-627)325573417 (DE-600)2037677-7 1573-9171 nnns volume:66 year:2017 number:10 month:10 pages:1913-1924 https://dx.doi.org/10.1007/s11172-017-1966-6 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_32 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_101 GBV_ILN_105 GBV_ILN_110 GBV_ILN_120 GBV_ILN_138 GBV_ILN_150 GBV_ILN_151 GBV_ILN_152 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_187 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_250 GBV_ILN_281 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_636 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2031 GBV_ILN_2034 GBV_ILN_2037 GBV_ILN_2038 GBV_ILN_2039 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2057 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2065 GBV_ILN_2068 GBV_ILN_2070 GBV_ILN_2086 GBV_ILN_2088 GBV_ILN_2093 GBV_ILN_2106 GBV_ILN_2107 GBV_ILN_2108 GBV_ILN_2110 GBV_ILN_2111 GBV_ILN_2112 GBV_ILN_2113 GBV_ILN_2116 GBV_ILN_2118 GBV_ILN_2119 GBV_ILN_2122 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2144 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2188 GBV_ILN_2190 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2446 GBV_ILN_2470 GBV_ILN_2472 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_2548 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4046 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4246 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4336 GBV_ILN_4338 GBV_ILN_4393 GBV_ILN_4700 35.00 ASE AR 66 2017 10 10 1913-1924 |
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Enthalten in Russian chemical bulletin 66(2017), 10 vom: Okt., Seite 1913-1924 volume:66 year:2017 number:10 month:10 pages:1913-1924 |
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Sulimov, A. V. @@aut@@ Kutov, D. C. @@aut@@ Katkova, E. V. @@aut@@ Kondakova, O. A. @@aut@@ Sulimov, V. B. @@aut@@ |
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V.</subfield><subfield code="e">verfasserin</subfield><subfield code="4">aut</subfield></datafield><datafield tag="245" ind1="1" ind2="0"><subfield code="a">Search for approaches to improving the calculation accuracy of the protein—ligand binding energy by docking</subfield></datafield><datafield tag="264" ind1=" " ind2="1"><subfield code="c">2017</subfield></datafield><datafield tag="336" ind1=" " ind2=" "><subfield code="a">Text</subfield><subfield code="b">txt</subfield><subfield code="2">rdacontent</subfield></datafield><datafield tag="337" ind1=" " ind2=" "><subfield code="a">Computermedien</subfield><subfield code="b">c</subfield><subfield code="2">rdamedia</subfield></datafield><datafield tag="338" ind1=" " ind2=" "><subfield code="a">Online-Ressource</subfield><subfield code="b">cr</subfield><subfield code="2">rdacarrier</subfield></datafield><datafield tag="520" ind1=" " ind2=" "><subfield code="a">Abstract The following reasons limiting the accuracy of calculations of the protein—ligand binding energy by the molecular docking programs are considered: the limited facilities of algorithms of finding a global minimum on a complicated multi-dimensional protein—ligand energy surface, restrictions on the degrees of freedom of a protein—ligand system including docking into a rigid protein, inadequacy of the existing force fields, a lack of taking into account the solvent or too rough allowance for the solvent in the docking procedure, a lack of the local energy optimization in the docking process, an inaccuracy of the construction of models of a target protein and a ligand, simplification of the calculation method of the Gibbs free energy of a molecular system, and limited computer resources for docking of one ligand. A new approach to the development of the new generation of docking programs is proposed. The approach allows one to remove step-by-step the existing simplifications and to increase considerably the accuracy of the whole docking process, including the calculation accuracy of the protein—ligand binding energy. 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Sulimov, A. V. |
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Sulimov, A. V. ddc 540 bkl 35.00 misc docking misc tensor train misc binding energy misc low-energy local minima spectrum misc flexible ligand misc drug design Search for approaches to improving the calculation accuracy of the protein—ligand binding energy by docking |
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540 ASE 35.00 bkl Search for approaches to improving the calculation accuracy of the protein—ligand binding energy by docking docking (dpeaa)DE-He213 tensor train (dpeaa)DE-He213 binding energy (dpeaa)DE-He213 low-energy local minima spectrum (dpeaa)DE-He213 flexible ligand (dpeaa)DE-He213 drug design (dpeaa)DE-He213 |
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search for approaches to improving the calculation accuracy of the protein—ligand binding energy by docking |
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Search for approaches to improving the calculation accuracy of the protein—ligand binding energy by docking |
| abstract |
Abstract The following reasons limiting the accuracy of calculations of the protein—ligand binding energy by the molecular docking programs are considered: the limited facilities of algorithms of finding a global minimum on a complicated multi-dimensional protein—ligand energy surface, restrictions on the degrees of freedom of a protein—ligand system including docking into a rigid protein, inadequacy of the existing force fields, a lack of taking into account the solvent or too rough allowance for the solvent in the docking procedure, a lack of the local energy optimization in the docking process, an inaccuracy of the construction of models of a target protein and a ligand, simplification of the calculation method of the Gibbs free energy of a molecular system, and limited computer resources for docking of one ligand. A new approach to the development of the new generation of docking programs is proposed. The approach allows one to remove step-by-step the existing simplifications and to increase considerably the accuracy of the whole docking process, including the calculation accuracy of the protein—ligand binding energy. The results of the study are presented and demonstrate the computational feasibility of the assigned docking problem. |
| abstractGer |
Abstract The following reasons limiting the accuracy of calculations of the protein—ligand binding energy by the molecular docking programs are considered: the limited facilities of algorithms of finding a global minimum on a complicated multi-dimensional protein—ligand energy surface, restrictions on the degrees of freedom of a protein—ligand system including docking into a rigid protein, inadequacy of the existing force fields, a lack of taking into account the solvent or too rough allowance for the solvent in the docking procedure, a lack of the local energy optimization in the docking process, an inaccuracy of the construction of models of a target protein and a ligand, simplification of the calculation method of the Gibbs free energy of a molecular system, and limited computer resources for docking of one ligand. A new approach to the development of the new generation of docking programs is proposed. The approach allows one to remove step-by-step the existing simplifications and to increase considerably the accuracy of the whole docking process, including the calculation accuracy of the protein—ligand binding energy. The results of the study are presented and demonstrate the computational feasibility of the assigned docking problem. |
| abstract_unstemmed |
Abstract The following reasons limiting the accuracy of calculations of the protein—ligand binding energy by the molecular docking programs are considered: the limited facilities of algorithms of finding a global minimum on a complicated multi-dimensional protein—ligand energy surface, restrictions on the degrees of freedom of a protein—ligand system including docking into a rigid protein, inadequacy of the existing force fields, a lack of taking into account the solvent or too rough allowance for the solvent in the docking procedure, a lack of the local energy optimization in the docking process, an inaccuracy of the construction of models of a target protein and a ligand, simplification of the calculation method of the Gibbs free energy of a molecular system, and limited computer resources for docking of one ligand. A new approach to the development of the new generation of docking programs is proposed. The approach allows one to remove step-by-step the existing simplifications and to increase considerably the accuracy of the whole docking process, including the calculation accuracy of the protein—ligand binding energy. The results of the study are presented and demonstrate the computational feasibility of the assigned docking problem. |
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| container_issue |
10 |
| title_short |
Search for approaches to improving the calculation accuracy of the protein—ligand binding energy by docking |
| url |
https://dx.doi.org/10.1007/s11172-017-1966-6 |
| remote_bool |
true |
| author2 |
Kutov, D. C. Katkova, E. V. Kondakova, O. A. Sulimov, V. B. |
| author2Str |
Kutov, D. C. Katkova, E. V. Kondakova, O. A. Sulimov, V. B. |
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325573417 |
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c |
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| doi_str |
10.1007/s11172-017-1966-6 |
| up_date |
2024-07-04T03:02:04.721Z |
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| score |
7.401758 |