PROTDES: CHARMM toolbox for computational protein design

Abstract We present an open-source software able to automatically mutate any residue positions and find the best aminoacids in an arbitrary protein structure without requiring pairwise approximations. Our software, PROTDES, is based on CHARMM and it searches automatically for mutations optimizing a...
Ausführliche Beschreibung

Gespeichert in:

Autor*in:	Suárez, María [verfasserIn] Tortosa, Pablo [verfasserIn] Jaramillo, Alfonso [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2008

Schlagwörter:	Computational protein design Synthetic biology CHARMM Solvation models

Übergeordnetes Werk:	Enthalten in: Systems and synthetic biology - Dordrecht : Springer Netherlands, 2007, 2(2008), 3-4 vom: Dez., Seite 105-113
Übergeordnetes Werk:	volume:2 ; year:2008 ; number:3-4 ; month:12 ; pages:105-113

Links:	Volltext

DOI / URN:	10.1007/s11693-009-9026-7

Katalog-ID:	SPR021762902

Internformat


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520			\|a Abstract We present an open-source software able to automatically mutate any residue positions and find the best aminoacids in an arbitrary protein structure without requiring pairwise approximations. Our software, PROTDES, is based on CHARMM and it searches automatically for mutations optimizing a protein folding free energy. PROTDES allows the integration of molecular dynamics within the protein design. We have implemented an heuristic optimization algorithm that iteratively searches the best aminoacids and their conformations for an arbitrary set of positions within a structure. Our software allows CHARMM users to perform protein design calculations and to create their own procedures for protein design using their own energy functions. We show this by implementing three different energy functions based on different solvent treatments: surface area accessibility, generalized Born using molecular volume and an effective energy function. PROTDES, a tutorial, parameter sets, configuration tools and examples are freely available at http://soft.synth-bio.org/protdes.html.
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matchkey_str	article:18725333:2008----::rtecamtobxocmuainl
hierarchy_sort_str	2008
publishDate	2008
allfields	10.1007/s11693-009-9026-7 doi (DE-627)SPR021762902 (SPR)s11693-009-9026-7-e DE-627 ger DE-627 rakwb eng 570 ASE Suárez, María verfasserin aut PROTDES: CHARMM toolbox for computational protein design 2008 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract We present an open-source software able to automatically mutate any residue positions and find the best aminoacids in an arbitrary protein structure without requiring pairwise approximations. Our software, PROTDES, is based on CHARMM and it searches automatically for mutations optimizing a protein folding free energy. PROTDES allows the integration of molecular dynamics within the protein design. We have implemented an heuristic optimization algorithm that iteratively searches the best aminoacids and their conformations for an arbitrary set of positions within a structure. Our software allows CHARMM users to perform protein design calculations and to create their own procedures for protein design using their own energy functions. We show this by implementing three different energy functions based on different solvent treatments: surface area accessibility, generalized Born using molecular volume and an effective energy function. PROTDES, a tutorial, parameter sets, configuration tools and examples are freely available at http://soft.synth-bio.org/protdes.html. Computational protein design (dpeaa)DE-He213 Synthetic biology (dpeaa)DE-He213 CHARMM (dpeaa)DE-He213 Solvation models (dpeaa)DE-He213 Tortosa, Pablo verfasserin aut Jaramillo, Alfonso verfasserin aut Enthalten in Systems and synthetic biology Dordrecht : Springer Netherlands, 2007 2(2008), 3-4 vom: Dez., Seite 105-113 (DE-627)54601142X (DE-600)2390101-9 1872-5333 nnns volume:2 year:2008 number:3-4 month:12 pages:105-113 https://dx.doi.org/10.1007/s11693-009-9026-7 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2007 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2026 GBV_ILN_2031 GBV_ILN_2034 GBV_ILN_2037 GBV_ILN_2038 GBV_ILN_2039 GBV_ILN_2044 GBV_ILN_2055 GBV_ILN_2059 GBV_ILN_2064 GBV_ILN_2065 GBV_ILN_2068 GBV_ILN_2070 GBV_ILN_2086 GBV_ILN_2106 GBV_ILN_2108 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_4012 GBV_ILN_4035 GBV_ILN_4037 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_4328 GBV_ILN_4333 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 2 2008 3-4 12 105-113
spelling	10.1007/s11693-009-9026-7 doi (DE-627)SPR021762902 (SPR)s11693-009-9026-7-e DE-627 ger DE-627 rakwb eng 570 ASE Suárez, María verfasserin aut PROTDES: CHARMM toolbox for computational protein design 2008 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract We present an open-source software able to automatically mutate any residue positions and find the best aminoacids in an arbitrary protein structure without requiring pairwise approximations. Our software, PROTDES, is based on CHARMM and it searches automatically for mutations optimizing a protein folding free energy. PROTDES allows the integration of molecular dynamics within the protein design. We have implemented an heuristic optimization algorithm that iteratively searches the best aminoacids and their conformations for an arbitrary set of positions within a structure. Our software allows CHARMM users to perform protein design calculations and to create their own procedures for protein design using their own energy functions. We show this by implementing three different energy functions based on different solvent treatments: surface area accessibility, generalized Born using molecular volume and an effective energy function. PROTDES, a tutorial, parameter sets, configuration tools and examples are freely available at http://soft.synth-bio.org/protdes.html. Computational protein design (dpeaa)DE-He213 Synthetic biology (dpeaa)DE-He213 CHARMM (dpeaa)DE-He213 Solvation models (dpeaa)DE-He213 Tortosa, Pablo verfasserin aut Jaramillo, Alfonso verfasserin aut Enthalten in Systems and synthetic biology Dordrecht : Springer Netherlands, 2007 2(2008), 3-4 vom: Dez., Seite 105-113 (DE-627)54601142X (DE-600)2390101-9 1872-5333 nnns volume:2 year:2008 number:3-4 month:12 pages:105-113 https://dx.doi.org/10.1007/s11693-009-9026-7 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2007 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2026 GBV_ILN_2031 GBV_ILN_2034 GBV_ILN_2037 GBV_ILN_2038 GBV_ILN_2039 GBV_ILN_2044 GBV_ILN_2055 GBV_ILN_2059 GBV_ILN_2064 GBV_ILN_2065 GBV_ILN_2068 GBV_ILN_2070 GBV_ILN_2086 GBV_ILN_2106 GBV_ILN_2108 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_4012 GBV_ILN_4035 GBV_ILN_4037 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_4328 GBV_ILN_4333 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 2 2008 3-4 12 105-113
allfields_unstemmed	10.1007/s11693-009-9026-7 doi (DE-627)SPR021762902 (SPR)s11693-009-9026-7-e DE-627 ger DE-627 rakwb eng 570 ASE Suárez, María verfasserin aut PROTDES: CHARMM toolbox for computational protein design 2008 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract We present an open-source software able to automatically mutate any residue positions and find the best aminoacids in an arbitrary protein structure without requiring pairwise approximations. Our software, PROTDES, is based on CHARMM and it searches automatically for mutations optimizing a protein folding free energy. PROTDES allows the integration of molecular dynamics within the protein design. We have implemented an heuristic optimization algorithm that iteratively searches the best aminoacids and their conformations for an arbitrary set of positions within a structure. Our software allows CHARMM users to perform protein design calculations and to create their own procedures for protein design using their own energy functions. We show this by implementing three different energy functions based on different solvent treatments: surface area accessibility, generalized Born using molecular volume and an effective energy function. PROTDES, a tutorial, parameter sets, configuration tools and examples are freely available at http://soft.synth-bio.org/protdes.html. Computational protein design (dpeaa)DE-He213 Synthetic biology (dpeaa)DE-He213 CHARMM (dpeaa)DE-He213 Solvation models (dpeaa)DE-He213 Tortosa, Pablo verfasserin aut Jaramillo, Alfonso verfasserin aut Enthalten in Systems and synthetic biology Dordrecht : Springer Netherlands, 2007 2(2008), 3-4 vom: Dez., Seite 105-113 (DE-627)54601142X (DE-600)2390101-9 1872-5333 nnns volume:2 year:2008 number:3-4 month:12 pages:105-113 https://dx.doi.org/10.1007/s11693-009-9026-7 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2007 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2026 GBV_ILN_2031 GBV_ILN_2034 GBV_ILN_2037 GBV_ILN_2038 GBV_ILN_2039 GBV_ILN_2044 GBV_ILN_2055 GBV_ILN_2059 GBV_ILN_2064 GBV_ILN_2065 GBV_ILN_2068 GBV_ILN_2070 GBV_ILN_2086 GBV_ILN_2106 GBV_ILN_2108 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_4012 GBV_ILN_4035 GBV_ILN_4037 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_4328 GBV_ILN_4333 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 2 2008 3-4 12 105-113
allfieldsGer	10.1007/s11693-009-9026-7 doi (DE-627)SPR021762902 (SPR)s11693-009-9026-7-e DE-627 ger DE-627 rakwb eng 570 ASE Suárez, María verfasserin aut PROTDES: CHARMM toolbox for computational protein design 2008 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract We present an open-source software able to automatically mutate any residue positions and find the best aminoacids in an arbitrary protein structure without requiring pairwise approximations. Our software, PROTDES, is based on CHARMM and it searches automatically for mutations optimizing a protein folding free energy. PROTDES allows the integration of molecular dynamics within the protein design. We have implemented an heuristic optimization algorithm that iteratively searches the best aminoacids and their conformations for an arbitrary set of positions within a structure. Our software allows CHARMM users to perform protein design calculations and to create their own procedures for protein design using their own energy functions. We show this by implementing three different energy functions based on different solvent treatments: surface area accessibility, generalized Born using molecular volume and an effective energy function. PROTDES, a tutorial, parameter sets, configuration tools and examples are freely available at http://soft.synth-bio.org/protdes.html. Computational protein design (dpeaa)DE-He213 Synthetic biology (dpeaa)DE-He213 CHARMM (dpeaa)DE-He213 Solvation models (dpeaa)DE-He213 Tortosa, Pablo verfasserin aut Jaramillo, Alfonso verfasserin aut Enthalten in Systems and synthetic biology Dordrecht : Springer Netherlands, 2007 2(2008), 3-4 vom: Dez., Seite 105-113 (DE-627)54601142X (DE-600)2390101-9 1872-5333 nnns volume:2 year:2008 number:3-4 month:12 pages:105-113 https://dx.doi.org/10.1007/s11693-009-9026-7 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2007 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2026 GBV_ILN_2031 GBV_ILN_2034 GBV_ILN_2037 GBV_ILN_2038 GBV_ILN_2039 GBV_ILN_2044 GBV_ILN_2055 GBV_ILN_2059 GBV_ILN_2064 GBV_ILN_2065 GBV_ILN_2068 GBV_ILN_2070 GBV_ILN_2086 GBV_ILN_2106 GBV_ILN_2108 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_4012 GBV_ILN_4035 GBV_ILN_4037 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_4328 GBV_ILN_4333 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 2 2008 3-4 12 105-113
allfieldsSound	10.1007/s11693-009-9026-7 doi (DE-627)SPR021762902 (SPR)s11693-009-9026-7-e DE-627 ger DE-627 rakwb eng 570 ASE Suárez, María verfasserin aut PROTDES: CHARMM toolbox for computational protein design 2008 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract We present an open-source software able to automatically mutate any residue positions and find the best aminoacids in an arbitrary protein structure without requiring pairwise approximations. Our software, PROTDES, is based on CHARMM and it searches automatically for mutations optimizing a protein folding free energy. PROTDES allows the integration of molecular dynamics within the protein design. We have implemented an heuristic optimization algorithm that iteratively searches the best aminoacids and their conformations for an arbitrary set of positions within a structure. Our software allows CHARMM users to perform protein design calculations and to create their own procedures for protein design using their own energy functions. We show this by implementing three different energy functions based on different solvent treatments: surface area accessibility, generalized Born using molecular volume and an effective energy function. PROTDES, a tutorial, parameter sets, configuration tools and examples are freely available at http://soft.synth-bio.org/protdes.html. Computational protein design (dpeaa)DE-He213 Synthetic biology (dpeaa)DE-He213 CHARMM (dpeaa)DE-He213 Solvation models (dpeaa)DE-He213 Tortosa, Pablo verfasserin aut Jaramillo, Alfonso verfasserin aut Enthalten in Systems and synthetic biology Dordrecht : Springer Netherlands, 2007 2(2008), 3-4 vom: Dez., Seite 105-113 (DE-627)54601142X (DE-600)2390101-9 1872-5333 nnns volume:2 year:2008 number:3-4 month:12 pages:105-113 https://dx.doi.org/10.1007/s11693-009-9026-7 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2007 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2026 GBV_ILN_2031 GBV_ILN_2034 GBV_ILN_2037 GBV_ILN_2038 GBV_ILN_2039 GBV_ILN_2044 GBV_ILN_2055 GBV_ILN_2059 GBV_ILN_2064 GBV_ILN_2065 GBV_ILN_2068 GBV_ILN_2070 GBV_ILN_2086 GBV_ILN_2106 GBV_ILN_2108 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_4012 GBV_ILN_4035 GBV_ILN_4037 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_4328 GBV_ILN_4333 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 2 2008 3-4 12 105-113
language	English
source	Enthalten in Systems and synthetic biology 2(2008), 3-4 vom: Dez., Seite 105-113 volume:2 year:2008 number:3-4 month:12 pages:105-113
sourceStr	Enthalten in Systems and synthetic biology 2(2008), 3-4 vom: Dez., Seite 105-113 volume:2 year:2008 number:3-4 month:12 pages:105-113
format_phy_str_mv	Article
institution	findex.gbv.de
topic_facet	Computational protein design Synthetic biology CHARMM Solvation models
dewey-raw	570
isfreeaccess_bool	true
container_title	Systems and synthetic biology
authorswithroles_txt_mv	Suárez, María @@aut@@ Tortosa, Pablo @@aut@@ Jaramillo, Alfonso @@aut@@
publishDateDaySort_date	2008-12-01T00:00:00Z
hierarchy_top_id	54601142X
dewey-sort	3570
id	SPR021762902
language_de	englisch
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author	Suárez, María
spellingShingle	Suárez, María ddc 570 misc Computational protein design misc Synthetic biology misc CHARMM misc Solvation models PROTDES: CHARMM toolbox for computational protein design
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topic_title	570 ASE PROTDES: CHARMM toolbox for computational protein design Computational protein design (dpeaa)DE-He213 Synthetic biology (dpeaa)DE-He213 CHARMM (dpeaa)DE-He213 Solvation models (dpeaa)DE-He213
topic	ddc 570 misc Computational protein design misc Synthetic biology misc CHARMM misc Solvation models
topic_unstemmed	ddc 570 misc Computational protein design misc Synthetic biology misc CHARMM misc Solvation models
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title	PROTDES: CHARMM toolbox for computational protein design
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title_full	PROTDES: CHARMM toolbox for computational protein design
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author_browse	Suárez, María Tortosa, Pablo Jaramillo, Alfonso
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title_sort	protdes: charmm toolbox for computational protein design
title_auth	PROTDES: CHARMM toolbox for computational protein design
abstract	Abstract We present an open-source software able to automatically mutate any residue positions and find the best aminoacids in an arbitrary protein structure without requiring pairwise approximations. Our software, PROTDES, is based on CHARMM and it searches automatically for mutations optimizing a protein folding free energy. PROTDES allows the integration of molecular dynamics within the protein design. We have implemented an heuristic optimization algorithm that iteratively searches the best aminoacids and their conformations for an arbitrary set of positions within a structure. Our software allows CHARMM users to perform protein design calculations and to create their own procedures for protein design using their own energy functions. We show this by implementing three different energy functions based on different solvent treatments: surface area accessibility, generalized Born using molecular volume and an effective energy function. PROTDES, a tutorial, parameter sets, configuration tools and examples are freely available at http://soft.synth-bio.org/protdes.html.
abstractGer	Abstract We present an open-source software able to automatically mutate any residue positions and find the best aminoacids in an arbitrary protein structure without requiring pairwise approximations. Our software, PROTDES, is based on CHARMM and it searches automatically for mutations optimizing a protein folding free energy. PROTDES allows the integration of molecular dynamics within the protein design. We have implemented an heuristic optimization algorithm that iteratively searches the best aminoacids and their conformations for an arbitrary set of positions within a structure. Our software allows CHARMM users to perform protein design calculations and to create their own procedures for protein design using their own energy functions. We show this by implementing three different energy functions based on different solvent treatments: surface area accessibility, generalized Born using molecular volume and an effective energy function. PROTDES, a tutorial, parameter sets, configuration tools and examples are freely available at http://soft.synth-bio.org/protdes.html.
abstract_unstemmed	Abstract We present an open-source software able to automatically mutate any residue positions and find the best aminoacids in an arbitrary protein structure without requiring pairwise approximations. Our software, PROTDES, is based on CHARMM and it searches automatically for mutations optimizing a protein folding free energy. PROTDES allows the integration of molecular dynamics within the protein design. We have implemented an heuristic optimization algorithm that iteratively searches the best aminoacids and their conformations for an arbitrary set of positions within a structure. Our software allows CHARMM users to perform protein design calculations and to create their own procedures for protein design using their own energy functions. We show this by implementing three different energy functions based on different solvent treatments: surface area accessibility, generalized Born using molecular volume and an effective energy function. PROTDES, a tutorial, parameter sets, configuration tools and examples are freely available at http://soft.synth-bio.org/protdes.html.
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title_short	PROTDES: CHARMM toolbox for computational protein design
url	https://dx.doi.org/10.1007/s11693-009-9026-7
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author2	Tortosa, Pablo Jaramillo, Alfonso
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up_date	2024-07-04T00:16:31.786Z
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