RECONSTRUCTION OF SAXS PROFILES FROM PROTEIN STRUCTURES
Small angle X-ray scattering (SAXS) is used for low resolution structural characterization of proteins often in combination with other experimental techniques. After briefly reviewing the theory of SAXS we discuss computational methods based on 1) the Debye equation and 2) Spherical Harmonics to com...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2013-08-01
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| Series: | Computational and Structural Biotechnology Journal |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2001037014600180 |
| _version_ | 1819084922859552768 |
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| author | Daniel K. Putnam Edward W. Lowe Jr. Jens Meiler |
| author_facet | Daniel K. Putnam Edward W. Lowe Jr. Jens Meiler |
| author_sort | Daniel K. Putnam |
| collection | DOAJ |
| description | Small angle X-ray scattering (SAXS) is used for low resolution structural characterization of proteins often in combination with other experimental techniques. After briefly reviewing the theory of SAXS we discuss computational methods based on 1) the Debye equation and 2) Spherical Harmonics to compute intensity profiles from a particular macromolecular structure. Further, we review how these formulas are parameterized for solvent density and hydration shell adjustment. Finally we introduce our solution to compute SAXS profiles utilizing GPU acceleration. |
| first_indexed | 2024-12-21T20:56:10Z |
| format | Article |
| id | doaj.art-8348fb4c0d294042a3c69867f8738a42 |
| institution | Directory Open Access Journal |
| issn | 2001-0370 |
| language | English |
| last_indexed | 2024-12-21T20:56:10Z |
| publishDate | 2013-08-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Computational and Structural Biotechnology Journal |
| spelling | doaj.art-8348fb4c0d294042a3c69867f8738a422022-12-21T18:50:35ZengElsevierComputational and Structural Biotechnology Journal2001-03702013-08-0181110.5936/csbj.201308006RECONSTRUCTION OF SAXS PROFILES FROM PROTEIN STRUCTURESDaniel K. Putnam0Edward W. Lowe Jr.1Jens Meiler2Center for Structural Biology, Vanderbilt University, Nashville, TN 37212, USACenter for Structural Biology, Vanderbilt University, Nashville, TN 37212, USACenter for Structural Biology, Vanderbilt University, Nashville, TN 37212, USASmall angle X-ray scattering (SAXS) is used for low resolution structural characterization of proteins often in combination with other experimental techniques. After briefly reviewing the theory of SAXS we discuss computational methods based on 1) the Debye equation and 2) Spherical Harmonics to compute intensity profiles from a particular macromolecular structure. Further, we review how these formulas are parameterized for solvent density and hydration shell adjustment. Finally we introduce our solution to compute SAXS profiles utilizing GPU acceleration.http://www.sciencedirect.com/science/article/pii/S2001037014600180AXESCRYSOLDALAIDebye formulaFOXSPHAISTOSSASTBXSAXSTERsmall angle X-ray scatteringspherical harmonics |
| spellingShingle | Daniel K. Putnam Edward W. Lowe Jr. Jens Meiler RECONSTRUCTION OF SAXS PROFILES FROM PROTEIN STRUCTURES Computational and Structural Biotechnology Journal AXES CRYSOL DALAI Debye formula FOXS PHAISTOS SASTBX SAXSTER small angle X-ray scattering spherical harmonics |
| title | RECONSTRUCTION OF SAXS PROFILES FROM PROTEIN STRUCTURES |
| title_full | RECONSTRUCTION OF SAXS PROFILES FROM PROTEIN STRUCTURES |
| title_fullStr | RECONSTRUCTION OF SAXS PROFILES FROM PROTEIN STRUCTURES |
| title_full_unstemmed | RECONSTRUCTION OF SAXS PROFILES FROM PROTEIN STRUCTURES |
| title_short | RECONSTRUCTION OF SAXS PROFILES FROM PROTEIN STRUCTURES |
| title_sort | reconstruction of saxs profiles from protein structures |
| topic | AXES CRYSOL DALAI Debye formula FOXS PHAISTOS SASTBX SAXSTER small angle X-ray scattering spherical harmonics |
| url | http://www.sciencedirect.com/science/article/pii/S2001037014600180 |
| work_keys_str_mv | AT danielkputnam reconstructionofsaxsprofilesfromproteinstructures AT edwardwlowejr reconstructionofsaxsprofilesfromproteinstructures AT jensmeiler reconstructionofsaxsprofilesfromproteinstructures |