Bluues_cplx: Electrostatics at Protein–Protein and Protein–Ligand Interfaces
(1) Background: Electrostatics plays a capital role in protein–protein and protein–ligand interactions. Implicit solvent models are widely used to describe electrostatics and complementarity at interfaces. Electrostatic complementarity at the interface is not trivial, involving surface potentials ra...
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MDPI AG
2025-01-01
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| Series: | Molecules |
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| author | Miguel Angel Soler Rayyan Bassem Adel Yakout Ozge Ozkilinc Gennaro Esposito Walter Rocchia Christian Klein Federico Fogolari |
| author_facet | Miguel Angel Soler Rayyan Bassem Adel Yakout Ozge Ozkilinc Gennaro Esposito Walter Rocchia Christian Klein Federico Fogolari |
| author_sort | Miguel Angel Soler |
| collection | DOAJ |
| description | (1) Background: Electrostatics plays a capital role in protein–protein and protein–ligand interactions. Implicit solvent models are widely used to describe electrostatics and complementarity at interfaces. Electrostatic complementarity at the interface is not trivial, involving surface potentials rather than the charges of surfacial contacting atoms. (2) Results: The program bluues_cplx, here used in conjunction with the software NanoShaper to compute molecular surfaces, has been used to compute the electrostatic properties of 756 protein–protein and 189 protein–ligand complexes along with the corresponding isolated molecules. (3) Methods: The software we make available here uses Generalized Born (GB) radii, computed by a molecular surface integral, to output several descriptors of electrostatics at protein (and in general, molecular) interfaces. We illustrate the usage of the software by analyzing a dataset of protein–protein and protein–ligand complexes, thus extending and refining previous analyses of electrostatic complementarity at protein interfaces. (4) Conclusions: The complete analysis of a molecular complex is performed in tens of seconds on a PC, and the results include the list of surfacial contacting atoms, their charges and Pearson correlation coefficient, the list of contacting surface points with the electrostatic potential (computed for the isolated molecules) and Pearson correlation coefficient, the electrostatic and hydrophobic free energy with different contributions for the isolated molecules, their complex and the difference for all terms. The software is readily usable for any molecular complex in solution. |
| format | Article |
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| institution | Kabale University |
| issn | 1420-3049 |
| language | English |
| publishDate | 2025-01-01 |
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| series | Molecules |
| spelling | doaj-art-9c450c281f5643d1b8ee0c140ff8b4722025-01-10T13:19:04ZengMDPI AGMolecules1420-30492025-01-0130115910.3390/molecules30010159Bluues_cplx: Electrostatics at Protein–Protein and Protein–Ligand InterfacesMiguel Angel Soler0Rayyan Bassem Adel Yakout1Ozge Ozkilinc2Gennaro Esposito3Walter Rocchia4Christian Klein5Federico Fogolari6Dipartimento di Scienze Matematiche, Informatiche e Fisiche (DMIF), University of Udine, 33100 Udine, ItalyInstitute of Biotechnology, IMC Krems University of Applied Sciences, 3500 Krems an der Donau, AustriaDipartimento di Scienze Matematiche, Informatiche e Fisiche (DMIF), University of Udine, 33100 Udine, ItalyScience and Math Division, New York University at Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab EmiratesComputational MOdelling of NanosCalE and BioPhysical SysTems CONCEPT Lab, Istituto Italiano di Tecnologia (IIT), 16152 Genoa, ItalyInstitute of Biotechnology, IMC Krems University of Applied Sciences, 3500 Krems an der Donau, AustriaDipartimento di Scienze Matematiche, Informatiche e Fisiche (DMIF), University of Udine, 33100 Udine, Italy(1) Background: Electrostatics plays a capital role in protein–protein and protein–ligand interactions. Implicit solvent models are widely used to describe electrostatics and complementarity at interfaces. Electrostatic complementarity at the interface is not trivial, involving surface potentials rather than the charges of surfacial contacting atoms. (2) Results: The program bluues_cplx, here used in conjunction with the software NanoShaper to compute molecular surfaces, has been used to compute the electrostatic properties of 756 protein–protein and 189 protein–ligand complexes along with the corresponding isolated molecules. (3) Methods: The software we make available here uses Generalized Born (GB) radii, computed by a molecular surface integral, to output several descriptors of electrostatics at protein (and in general, molecular) interfaces. We illustrate the usage of the software by analyzing a dataset of protein–protein and protein–ligand complexes, thus extending and refining previous analyses of electrostatic complementarity at protein interfaces. (4) Conclusions: The complete analysis of a molecular complex is performed in tens of seconds on a PC, and the results include the list of surfacial contacting atoms, their charges and Pearson correlation coefficient, the list of contacting surface points with the electrostatic potential (computed for the isolated molecules) and Pearson correlation coefficient, the electrostatic and hydrophobic free energy with different contributions for the isolated molecules, their complex and the difference for all terms. The software is readily usable for any molecular complex in solution.https://www.mdpi.com/1420-3049/30/1/159bluueselectrostaticsproteinfree energysoftwareligand |
| spellingShingle | Miguel Angel Soler Rayyan Bassem Adel Yakout Ozge Ozkilinc Gennaro Esposito Walter Rocchia Christian Klein Federico Fogolari Bluues_cplx: Electrostatics at Protein–Protein and Protein–Ligand Interfaces Molecules bluues electrostatics protein free energy software ligand |
| title | Bluues_cplx: Electrostatics at Protein–Protein and Protein–Ligand Interfaces |
| title_full | Bluues_cplx: Electrostatics at Protein–Protein and Protein–Ligand Interfaces |
| title_fullStr | Bluues_cplx: Electrostatics at Protein–Protein and Protein–Ligand Interfaces |
| title_full_unstemmed | Bluues_cplx: Electrostatics at Protein–Protein and Protein–Ligand Interfaces |
| title_short | Bluues_cplx: Electrostatics at Protein–Protein and Protein–Ligand Interfaces |
| title_sort | bluues cplx electrostatics at protein protein and protein ligand interfaces |
| topic | bluues electrostatics protein free energy software ligand |
| url | https://www.mdpi.com/1420-3049/30/1/159 |
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