The electrostatic profile of consecutive Cβ atoms applied to protein structure quality assessment [v3; ref status: indexed, http://f1000r.es/4dq]
The structure of a protein provides insight into its physiological interactions with other components of the cellular soup. Methods that predict putative structures from sequences typically yield multiple, closely-ranked possibilities. A critical component in the process is the model quality assessi...
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| Format: | Article |
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F1000 Research Ltd
2014-09-01
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| Online Access: | http://f1000research.com/articles/2-243/v3 |
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| author | Sandeep Chakraborty Ravindra Venkatramani Basuthkar J. Rao Bjarni Asgeirsson Abhaya M. Dandekar |
| author_facet | Sandeep Chakraborty Ravindra Venkatramani Basuthkar J. Rao Bjarni Asgeirsson Abhaya M. Dandekar |
| author_sort | Sandeep Chakraborty |
| collection | DOAJ |
| description | The structure of a protein provides insight into its physiological interactions with other components of the cellular soup. Methods that predict putative structures from sequences typically yield multiple, closely-ranked possibilities. A critical component in the process is the model quality assessing program (MQAP), which selects the best candidate from this pool of structures. Here, we present a novel MQAP based on the physical properties of sidechain atoms. We propose a method for assessing the quality of protein structures based on the electrostatic potential difference (EPD) of Cβ atoms in consecutive residues. We demonstrate that the EPDs of Cβ atoms on consecutive residues provide unique signatures of the amino acid types. The EPD of Cβ atoms are learnt from a set of 1000 non-homologous protein structures with a resolution cuto of 1.6 Å obtained from the PISCES database. Based on the Boltzmann hypothesis that lower energy conformations are proportionately sampled more, and on Annsen's thermodynamic hypothesis that the native structure of a protein is the minimum free energy state, we hypothesize that the deviation of observed EPD values from the mean values obtained in the learning phase is minimized in the native structure. We achieved an average specificity of 0.91, 0.94 and 0.93 on hg_structal, 4state_reduced and ig_structal decoy sets, respectively, taken from the Decoys `R' Us database. The source code and manual is made available at https://github.com/sanchak/mqap and permanently available on 10.5281/zenodo.7134. |
| first_indexed | 2024-04-13T16:19:14Z |
| format | Article |
| id | doaj.art-bd033d47cf1e4bbfba551bf26135c8dc |
| institution | Directory Open Access Journal |
| issn | 2046-1402 |
| language | English |
| last_indexed | 2024-04-13T16:19:14Z |
| publishDate | 2014-09-01 |
| publisher | F1000 Research Ltd |
| record_format | Article |
| series | F1000Research |
| spelling | doaj.art-bd033d47cf1e4bbfba551bf26135c8dc2022-12-22T02:39:58ZengF1000 Research LtdF1000Research2046-14022014-09-01210.12688/f1000research.2-243.v35678The electrostatic profile of consecutive Cβ atoms applied to protein structure quality assessment [v3; ref status: indexed, http://f1000r.es/4dq]Sandeep Chakraborty0Ravindra Venkatramani1Basuthkar J. Rao2Bjarni Asgeirsson3Abhaya M. Dandekar4Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, 400 005, IndiaDepartment of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, 400 005, IndiaDepartment of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, 400 005, IndiaScience Institute, Department of Biochemistry, University of Iceland, IS-107 Reykjavik, IcelandPlant Sciences Department, University of California,, Davis, CA, 95616, USAThe structure of a protein provides insight into its physiological interactions with other components of the cellular soup. Methods that predict putative structures from sequences typically yield multiple, closely-ranked possibilities. A critical component in the process is the model quality assessing program (MQAP), which selects the best candidate from this pool of structures. Here, we present a novel MQAP based on the physical properties of sidechain atoms. We propose a method for assessing the quality of protein structures based on the electrostatic potential difference (EPD) of Cβ atoms in consecutive residues. We demonstrate that the EPDs of Cβ atoms on consecutive residues provide unique signatures of the amino acid types. The EPD of Cβ atoms are learnt from a set of 1000 non-homologous protein structures with a resolution cuto of 1.6 Å obtained from the PISCES database. Based on the Boltzmann hypothesis that lower energy conformations are proportionately sampled more, and on Annsen's thermodynamic hypothesis that the native structure of a protein is the minimum free energy state, we hypothesize that the deviation of observed EPD values from the mean values obtained in the learning phase is minimized in the native structure. We achieved an average specificity of 0.91, 0.94 and 0.93 on hg_structal, 4state_reduced and ig_structal decoy sets, respectively, taken from the Decoys `R' Us database. The source code and manual is made available at https://github.com/sanchak/mqap and permanently available on 10.5281/zenodo.7134.http://f1000research.com/articles/2-243/v3Protein FoldingStructural GenomicsTheory & Simulation |
| spellingShingle | Sandeep Chakraborty Ravindra Venkatramani Basuthkar J. Rao Bjarni Asgeirsson Abhaya M. Dandekar The electrostatic profile of consecutive Cβ atoms applied to protein structure quality assessment [v3; ref status: indexed, http://f1000r.es/4dq] F1000Research Protein Folding Structural Genomics Theory & Simulation |
| title | The electrostatic profile of consecutive Cβ atoms applied to protein structure quality assessment [v3; ref status: indexed, http://f1000r.es/4dq] |
| title_full | The electrostatic profile of consecutive Cβ atoms applied to protein structure quality assessment [v3; ref status: indexed, http://f1000r.es/4dq] |
| title_fullStr | The electrostatic profile of consecutive Cβ atoms applied to protein structure quality assessment [v3; ref status: indexed, http://f1000r.es/4dq] |
| title_full_unstemmed | The electrostatic profile of consecutive Cβ atoms applied to protein structure quality assessment [v3; ref status: indexed, http://f1000r.es/4dq] |
| title_short | The electrostatic profile of consecutive Cβ atoms applied to protein structure quality assessment [v3; ref status: indexed, http://f1000r.es/4dq] |
| title_sort | electrostatic profile of consecutive cβ atoms applied to protein structure quality assessment v3 ref status indexed http f1000r es 4dq |
| topic | Protein Folding Structural Genomics Theory & Simulation |
| url | http://f1000research.com/articles/2-243/v3 |
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