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DelPhi Web Server: A Comprehensive Online Suite for Electrostatic Calculations of Biological Macromolecules and Their Complexes

DelPhi Web Server: A Comprehensive Online Suite for Electrostatic Calculations of Biological Macromolecules and Their Complexes
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Year:    2013

Communications in Computational Physics, Vol. 13 (2013), Iss. 1 : pp. 269–284

Abstract

Here we report a web server, the DelPhi web server, which utilizes DelPhi program to calculate electrostatic energies and the corresponding electrostatic potential and ionic distributions, and dielectric map. The server provides extra services to fix structural defects, as missing atoms in the structural file and allows for generation of missing hydrogen atoms. The hydrogen placement and the corresponding DelPhi calculations can be done with user selected force field parameters being either Charmm22, Amber98 or OPLS. Upon completion of the calculations, the user is given option to download fixed and protonated structural file, together with the parameter and Delphi output files for further analysis. Utilizing Jmol viewer, the user can see the corresponding structural file, to manipulate it and to change the presentation. In addition, if the potential map is requested to be calculated, the potential can be mapped onto the molecule surface. The DelPhi web server is available from http://compbio.clemson.edu/delphi webserver.

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Journal Article Details

Publisher Name:    Global Science Press

Language:    English

DOI:    https://doi.org/10.4208/cicp.300611.201011s

Communications in Computational Physics, Vol. 13 (2013), Iss. 1 : pp. 269–284

Published online:    2013-01

AMS Subject Headings:    Global Science Press

Copyright:    COPYRIGHT: © Global Science Press

Pages:    16

Keywords:   

  1. Protein Nano-Object Integrator (ProNOI) for generating atomic style objects for molecular modeling

    Smith, Nicholas | Campbell, Brandon | Li, Lin | Li, Chuan | Alexov, Emil

    BMC Structural Biology, Vol. 12 (2012), Iss. 1

    https://doi.org/10.1186/1472-6807-12-31 [Citations: 3]

  2. Fast iterative method for local steric Poisson–Boltzmann theories in biomolecular solvation

    Dou, Wei | Chen, Minhong | Zhou, Shenggao

    Computer Physics Communications, Vol. 291 (2023), Iss. P.108808

    https://doi.org/10.1016/j.cpc.2023.108808 [Citations: 1]

  3. Electrostatic Surface Potential of Macrophages Correlates with Their Functional Phenotype

    Chakraborty, Papiya | Dipankar, Pankaj | Dash, Shiba Prasad | Srivastava, Shreya | Dhyani, Rajat | Navani, Naveen Kumar | Sharma, Deepak | Sarangi, Pranita P.

    Inflammation, Vol. 43 (2020), Iss. 2 P.641

    https://doi.org/10.1007/s10753-019-01146-3 [Citations: 6]

  4. Accuracy Comparison of Generalized Born Models in the Calculation of Electrostatic Binding Free Energies

    Izadi, Saeed | Harris, Robert C. | Fenley, Marcia O. | Onufriev, Alexey V.

    Journal of Chemical Theory and Computation, Vol. 14 (2018), Iss. 3 P.1656

    https://doi.org/10.1021/acs.jctc.7b00886 [Citations: 25]

  5. Targeting the NS2B-NS3 protease of tick-borne encephalitis virus with pan-flaviviral protease inhibitors

    Akaberi, Dario | Båhlström, Amanda | Chinthakindi, Praveen K. | Nyman, Tomas | Sandström, Anja | Järhult, Josef D. | Palanisamy, Navaneethan | Lundkvist, Åke | Lennerstrand, Johan

    Antiviral Research, Vol. 190 (2021), Iss. P.105074

    https://doi.org/10.1016/j.antiviral.2021.105074 [Citations: 15]

  6. Low-molecular-weight chromium-binding substance (LMWCr) may bind and carry Cr(III) from the endosome

    Edwards, Kyle C. | Gannon, Michael W. | Frantom, Patrick A. | Vincent, John B.

    Journal of Inorganic Biochemistry, Vol. 223 (2021), Iss. P.111555

    https://doi.org/10.1016/j.jinorgbio.2021.111555 [Citations: 9]

  7. Structure and Dynamics of the Acidosis-Resistant A162H Mutant of the Switch Region of Troponin I Bound to the Regulatory Domain of Troponin C

    Pineda-Sanabria, Sandra E. | Robertson, Ian M. | Sykes, Brian D.

    Biochemistry, Vol. 54 (2015), Iss. 23 P.3583

    https://doi.org/10.1021/acs.biochem.5b00178 [Citations: 2]

  8. Structure of the Streptococcus pyogenes NAD + Glycohydrolase Translocation Domain and Its Essential Role in Toxin Binding to Oropharyngeal Keratinocytes

    Velarde, Jorge J. | Piai, Alessandro | Lichtenstein, Ian J. | Lynskey, Nicola N. | Chou, James J. | Wessels, Michael R. | Federle, Michael J.

    Journal of Bacteriology, Vol. 204 (2022), Iss. 1

    https://doi.org/10.1128/JB.00366-21 [Citations: 5]

  9. Water models for biomolecular simulations

    Onufriev, Alexey V. | Izadi, Saeed

    WIREs Computational Molecular Science, Vol. 8 (2018), Iss. 2

    https://doi.org/10.1002/wcms.1347 [Citations: 144]
  10. Handbook of Research on Inventive Bioremediation Techniques

    Implications of Molecular Docking Assay for Bioremediation

    Basharat, Zarrin | Bibi, Monazza | Yasmin, Azra

    2017

    https://doi.org/10.4018/978-1-5225-2325-3.ch002 [Citations: 5]

  11. A conserved Neurite Outgrowth and Guidance motif with biomimetic potential in neuronal Cell Adhesion Molecules

    Scapin, Giorgia | Gasparotto, Matteo | Peterle, Daniele | Tescari, Simone | Porcellato, Elena | Piovesan, Alberto | Righetto, Irene | Acquasaliente, Laura | De Filippis, Vincenzo | Filippini, Francesco

    Computational and Structural Biotechnology Journal, Vol. 19 (2021), Iss. P.5622

    https://doi.org/10.1016/j.csbj.2021.10.005 [Citations: 3]

  12. Structural analysis of the TPI-Manchester, a thermolabile variant of human triosephosphate isomerase

    Romero, Jorge Miguel

    Archives of Biochemistry and Biophysics, Vol. 761 (2024), Iss. P.110156

    https://doi.org/10.1016/j.abb.2024.110156 [Citations: 0]

  13. FixBox: A General Algorithm to Fix Molecular Systems in Periodic Boxes

    Baptista, António M. | da Rocha, Lucie | Campos, Sara R. R.

    Journal of Chemical Information and Modeling, Vol. 62 (2022), Iss. 18 P.4435

    https://doi.org/10.1021/acs.jcim.2c00823 [Citations: 3]

  14. DelPhi Suite: New Developments and Review of Functionalities

    Li, Chuan | Jia, Zhe | Chakravorty, Arghya | Pahari, Swagata | Peng, Yunhui | Basu, Sankar | Koirala, Mahesh | Panday, Shailesh Kumar | Petukh, Marharyta | Li, Lin | Alexov, Emil

    Journal of Computational Chemistry, Vol. 40 (2019), Iss. 28 P.2502

    https://doi.org/10.1002/jcc.26006 [Citations: 42]

  15. SurfPB: A GPU-Accelerated Electrostatic Calculation and Visualization Tool for Biomolecules

    Liao, Jun | Shu, Zirui | Gao, Junyong | Wu, Mincong | Chen, Changjun

    Journal of Chemical Information and Modeling, Vol. 63 (2023), Iss. 15 P.4490

    https://doi.org/10.1021/acs.jcim.3c00745 [Citations: 1]

  16. Structural journey of an insecticidal protein against western corn rootworm

    Marini, Guendalina | Poland, Brad | Leininger, Chris | Lukoyanova, Natalya | Spielbauer, Dan | Barry, Jennifer K. | Altier, Dan | Lum, Amy | Scolaro, Eric | Ortega, Claudia Pérez | Yalpani, Nasser | Sandahl, Gary | Mabry, Tim | Klever, Jeffrey | Nowatzki, Timothy | Zhao, Jian-Zhou | Sethi, Amit | Kassa, Adane | Crane, Virginia | Lu, Albert L. | Nelson, Mark E. | Eswar, Narayanan | Topf, Maya | Saibil, Helen R.

    Nature Communications, Vol. 14 (2023), Iss. 1

    https://doi.org/10.1038/s41467-023-39891-7 [Citations: 1]

  17. Ricin uses arginine 235 as an anchor residue to bind to P-proteins of the ribosomal stalk

    Zhou, Yijun | Li, Xiao-Ping | Chen, Brian Y. | Tumer, Nilgun E.

    Scientific Reports, Vol. 7 (2017), Iss. 1

    https://doi.org/10.1038/srep42912 [Citations: 14]

  18. SDPBS Web Server for Calculation of Electrostatics of Ionic Solvated Biomolecules

    Jiang, Yi | Xie, Yang | Ying, Jinyong | Xie, Dexuan | Yu, Zeyun

    Computational and Mathematical Biophysics, Vol. 3 (2015), Iss. 1

    https://doi.org/10.1515/mlbmb-2015-0011 [Citations: 3]

  19. Effect of the electrostatic surface potential on the oligomerization of full-length human recombinant prion protein at single-molecule level

    Wang, Bin | Lou, Zhichao | Zhang, Haiqian | Xu, Bingqian

    The Journal of Chemical Physics, Vol. 144 (2016), Iss. 11

    https://doi.org/10.1063/1.4943878 [Citations: 6]

  20. An Analysis of Inhibition of the Severe Acute Respiratory Syndrome Coronavirus 2 RNA-dependent Rna Polymerase By Zinc Ion: an in silico Approach

    Zoghi, Sina | Khamirani, Hossein Jafari | Dastgheib, Seyed Alireza | Dianatpour, Mehdi | Ghaffarieh, Alireza

    Future Virology, Vol. 16 (2021), Iss. 5 P.331

    https://doi.org/10.2217/fvl-2020-0369 [Citations: 9]
  21. Data Analytics in Medicine

    Implications of Molecular Docking Assay for Bioremediation

    Basharat, Zarrin | Bibi, Monazza | Yasmin, Azra

    2020

    https://doi.org/10.4018/978-1-7998-1204-3.ch078 [Citations: 2]

  22. Making the Case for Quantum Mechanics in Predictive Toxicology─Nearly 100 Years Too Late?

    Kostal, Jakub

    Chemical Research in Toxicology, Vol. 36 (2023), Iss. 9 P.1444

    https://doi.org/10.1021/acs.chemrestox.3c00171 [Citations: 8]

  23. Evidence of a putative glycosaminoglycan binding site on the glycosylated SARS-CoV-2 spike protein N-terminal domain

    Schuurs, Zachariah P. | Hammond, Edward | Elli, Stefano | Rudd, Timothy R. | Mycroft-West, Courtney J. | Lima, Marcelo A. | Skidmore, Mark A. | Karlsson, Richard | Chen, Yen-Hsi | Bagdonaite, Ieva | Yang, Zhang | Ahmed, Yassir A. | Richard, Derek J. | Turnbull, Jeremy | Ferro, Vito | Coombe, Deirdre R. | Gandhi, Neha S.

    Computational and Structural Biotechnology Journal, Vol. 19 (2021), Iss. P.2806

    https://doi.org/10.1016/j.csbj.2021.05.002 [Citations: 36]

  24. Structure of the dimeric ATP synthase from bovine mitochondria

    Spikes, Tobias E. | Montgomery, Martin G. | Walker, John E.

    Proceedings of the National Academy of Sciences, Vol. 117 (2020), Iss. 38 P.23519

    https://doi.org/10.1073/pnas.2013998117 [Citations: 160]

  25. Unveiling the influence of factor VIII physicochemical properties on hemophilia A phenotype through an in silico methodology

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    Computer Methods and Programs in Biomedicine, Vol. 219 (2022), Iss. P.106768

    https://doi.org/10.1016/j.cmpb.2022.106768 [Citations: 4]

  26. Insights into the Molecular Inhibition of the Oncogenic Channel KV10.1 by Globular Toxins

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    Journal of Chemical Information and Modeling, Vol. 61 (2021), Iss. 5 P.2328

    https://doi.org/10.1021/acs.jcim.0c01353 [Citations: 1]

  27. The Photoactive Excited State of the B12-Based Photoreceptor CarH

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    The Journal of Physical Chemistry B, Vol. 124 (2020), Iss. 47 P.10732

    https://doi.org/10.1021/acs.jpcb.0c09428 [Citations: 27]

  28. Tofacitinib and peficitinib inhibitors of Janus kinase for autoimmune disease treatment: a quantum biochemistry approach

    Amaral, Jackson L. | Lucredi, Naiara C. | França, Victor L. B. | Santos, Samuel J. M. | Maia, Francisco F. | Morais, Pablo A. | Souza, Pedro F. N. | Comar, Jurandir F. | Freire, Valder N.

    Physical Chemistry Chemical Physics, Vol. 26 (2024), Iss. 17 P.13420

    https://doi.org/10.1039/D3CP06332A [Citations: 1]

  29. Cross‐linking mass spectrometry reveals the structural topology of peripheral NuRD subunits relative to the core complex

    Spruijt, Cornelia G. | Gräwe, Cathrin | Kleinendorst, Simone C. | Baltissen, Marijke P. A. | Vermeulen, Michiel

    The FEBS Journal, Vol. 288 (2021), Iss. 10 P.3231

    https://doi.org/10.1111/febs.15650 [Citations: 17]

  30. Y380Q novel mutation in receptor-binding domain of SARS-CoV-2 spike protein together with C379W interfere in the neutralizing antibodies interaction

    Sartor, Ivaine Tais Sauthier | Varela, Fernanda Hammes | Meireles, Mariana Rost | Kern, Luciane Beatriz | Azevedo, Thaís Raupp | Giannini, Gabriela Luchiari Tumioto | da Silva, Mariana Soares | Demoliner, Meriane | Gularte, Juliana Schons | de Almeida, Paula Rodrigues | Fleck, Juliane Deise | Zavaglia, Gabriela Oliveira | Fernandes, Ingrid Rodrigues | de David, Caroline Nespolo | Santos, Amanda Paz | de Almeida, Walquiria Aparecida Ferreira | Porto, Victor Bertollo Gomes | Scotta, Marcelo Comerlato | Vieira, Gustavo Fioravanti | Spilki, Fernando Rosado | Stein, Renato T. | Polese-Bonatto, Márcia

    Diagnostic Microbiology and Infectious Disease, Vol. 102 (2022), Iss. 4 P.115636

    https://doi.org/10.1016/j.diagmicrobio.2022.115636 [Citations: 2]

  31. Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2

    Thoms, Matthias | Buschauer, Robert | Ameismeier, Michael | Koepke, Lennart | Denk, Timo | Hirschenberger, Maximilian | Kratzat, Hanna | Hayn, Manuel | Mackens-Kiani, Timur | Cheng, Jingdong | Straub, Jan H. | Stürzel, Christina M. | Fröhlich, Thomas | Berninghausen, Otto | Becker, Thomas | Kirchhoff, Frank | Sparrer, Konstantin M. J. | Beckmann, Roland

    Science, Vol. 369 (2020), Iss. 6508 P.1249

    https://doi.org/10.1126/science.abc8665 [Citations: 658]

  32. Energy landscape of a GSTP1 polymorph linked with cytological function decay in response to chemical stressors

    Basharat, Zarrin | Yasmin, Azra

    Gene, Vol. 609 (2017), Iss. P.19

    https://doi.org/10.1016/j.gene.2017.01.034 [Citations: 7]

  33. Integration of molecular modelling and in vitro studies to inhibit LexA proteolysis

    Schuurs, Zachariah P. | McDonald, John P. | Croft, Laura V. | Richard, Derek J. | Woodgate, Roger | Gandhi, Neha S.

    Frontiers in Cellular and Infection Microbiology, Vol. 13 (2023), Iss.

    https://doi.org/10.3389/fcimb.2023.1051602 [Citations: 3]

  34. Two distinct nucleic acid binding surfaces of Cdc5 regulate development

    Wang, Chao | Li, Mu | Li, Guorui | Liu, Xinsen | Zhao, Wensheng | Yu, Bin | Liu, Junfeng | Yang, Jun | Peng, You-Liang

    Biochemical Journal, Vol. 476 (2019), Iss. 21 P.3355

    https://doi.org/10.1042/BCJ20190502 [Citations: 4]

  35. On the electrostatic properties of homodimeric proteins

    Campbell, Brandon | Petukh, Marharyta | Alexov, Emil | Li, Chuan

    Journal of Theoretical and Computational Chemistry, Vol. 13 (2014), Iss. 03 P.1440007

    https://doi.org/10.1142/S0219633614400070 [Citations: 11]

  36. The role of the Aspergillus nidulans high mobility group B protein HmbA, the orthologue of Saccharomyces cerevisiae Nhp6p

    Ámon, Judit | Varga, Gabriella | Pfeiffer, Ilona | Farkas, Zoltán | Karácsony, Zoltán | Hegedűs, Zsófia | Vágvölgyi, Csaba | Hamari, Zsuzsanna

    Scientific Reports, Vol. 12 (2022), Iss. 1

    https://doi.org/10.1038/s41598-022-22202-3 [Citations: 2]

  37. Mutations in the KDM5C ARID Domain and Their Plausible Association with Syndromic Claes-Jensen-Type Disease

    Peng, Yunhui | Suryadi, Jimmy | Yang, Ye | Kucukkal, Tugba | Cao, Weiguo | Alexov, Emil

    International Journal of Molecular Sciences, Vol. 16 (2015), Iss. 11 P.27270

    https://doi.org/10.3390/ijms161126022 [Citations: 21]

  38. Predicting Protein–Protein Interfaces that Bind Intrinsically Disordered Protein Regions

    Wong, Eric T.C. | Gsponer, Jörg

    Journal of Molecular Biology, Vol. 431 (2019), Iss. 17 P.3157

    https://doi.org/10.1016/j.jmb.2019.06.010 [Citations: 6]

  39. Molecular determinants of drug-specific sensitivity for epidermal growth factor receptor (EGFR) exon 19 and 20 mutants in non-small cell lung cancer

    Tsigelny, Igor F. | Wheler, Jennifer J. | Greenberg, Jerry P. | Kouznetsova, Valentina L. | Stewart, David J. | Bazhenova, Lyudmila | Kurzrock, Razelle

    Oncotarget, Vol. 6 (2015), Iss. 8 P.6029

    https://doi.org/10.18632/oncotarget.3472 [Citations: 24]

  40. Inclusion of Water Multipoles into the Implicit Solvation Framework Leads to Accuracy Gains

    Tolokh, Igor S. | Folescu, Dan E. | Onufriev, Alexey V.

    The Journal of Physical Chemistry B, Vol. 128 (2024), Iss. 24 P.5855

    https://doi.org/10.1021/acs.jpcb.4c00254 [Citations: 0]

  41. Structural and mechanistic basis of substrate transport by the multidrug transporter MRP4

    Bloch, Magnus | Raj, Isha | Pape, Tillmann | Taylor, Nicholas M.I.

    Structure, Vol. 31 (2023), Iss. 11 P.1407

    https://doi.org/10.1016/j.str.2023.08.014 [Citations: 8]

  42. Glycosaminoglycan Concentration and Sulfation Patterns of Biohybrid Polymer Matrices Direct Microvascular Network Formation and Stability

    Limasale, Yanuar Dwi Putra | Fusenig, Maximilian | Samulowitz, Marten | Atallah, Passant | Sievers, Jana | Dennison, Nicholas | Freudenberg, Uwe | Friedrichs, Jens | Werner, Carsten

    Advanced Functional Materials, Vol. (2024), Iss.

    https://doi.org/10.1002/adfm.202411475 [Citations: 0]

  43. Electrostatics of Prokaryotic Ribosome and Its Biological Implication

    Wang, Jun | Karki, Chitra | Xiao, Yi | Li, Lin

    Biophysical Journal, Vol. 118 (2020), Iss. 5 P.1205

    https://doi.org/10.1016/j.bpj.2020.01.014 [Citations: 16]

  44. Charge Shielding Prevents Aggregation of Supercharged GFP Variants at High Protein Concentration

    Laber, Joshua R. | Dear, Barton J. | Martins, Matheus L. | Jackson, Devin E. | DiVenere, Andrea | Gollihar, Jimmy D. | Ellington, Andrew D. | Truskett, Thomas M. | Johnston, Keith P. | Maynard, Jennifer A.

    Molecular Pharmaceutics, Vol. 14 (2017), Iss. 10 P.3269

    https://doi.org/10.1021/acs.molpharmaceut.7b00322 [Citations: 29]

  45. NKNK: a New Essential Motif in the C-Terminal Domain of HIV-1 Group M Integrases

    Kanja, Marine | Cappy, Pierre | Levy, Nicolas | Oladosu, Oyndamola | Schmidt, Sylvie | Rossolillo, Paola | Winter, Flore | Gasser, Romain | Moog, Christiane | Ruff, Marc | Negroni, Matteo | Lener, Daniela | Simon, Viviana

    Journal of Virology, Vol. 94 (2020), Iss. 20

    https://doi.org/10.1128/JVI.01035-20 [Citations: 7]

  46. Electrostatics in Computational Biophysics and Its Implications for Disease Effects

    Sun, Shengjie | Poudel, Pitambar | Alexov, Emil | Li, Lin

    International Journal of Molecular Sciences, Vol. 23 (2022), Iss. 18 P.10347

    https://doi.org/10.3390/ijms231810347 [Citations: 7]

  47. Light Boosts the Activity of Novel LPMO from Aspergillus fumigatus Leading to Oxidative Cleavage of Cellulose and Hemicellulose

    Velasco, Josman | Sepulchro, Ana Gabriela V. | Higasi, Paula M. R. | Pellegrini, Vanessa O. A. | Cannella, David | de Oliveira, Leandro Cristante | Polikarpov, Igor | Segato, Fernando

    ACS Sustainable Chemistry & Engineering, Vol. 10 (2022), Iss. 50 P.16969

    https://doi.org/10.1021/acssuschemeng.2c06281 [Citations: 11]

  48. Quantum Mechanical Modeling: A Tool for the Understanding of Enzyme Reactions

    Náray-Szabó, Gábor | Oláh, Julianna | Krámos, Balázs

    Biomolecules, Vol. 3 (2013), Iss. 3 P.662

    https://doi.org/10.3390/biom3030662 [Citations: 20]