The generalized Born/volume integral implicit solvent model: estimation of the free energy of hydration using London dispersion instead of atomic surface area

Journal of Computational Chemistry
Paul Labute


A new generalized Born model for estimating the free energy of hydration is presented. The new generalized Born/volume integral (GB/VI) estimates the free energy of hydration as a classical electrostatic energy plus a cavitation energy that is not based upon atomic surface area (SA) used in GB/SA hydration models but on a VI London dispersion energy estimated from quantities already calculated in the classical electrostatic energy. The (relatively few) GB/VI model parameters are fitted to experimental data, and parameterizations for two different atomic partial charge models are presented. Comparison of the calculated and experimental free energies of hydration for 560 small molecules (both neutral and charged) shows good agreement (r(2) = 0.94).


Oct 24, 2002·Journal of Computational Chemistry·Araz JakalianChristopher I Bayly
Jan 22, 2004·Journal of Computational Chemistry·Emilio Gallicchio, Ronald M Levy
May 20, 2006·Proceedings of the National Academy of Sciences of the United States of America·Jason A Wagoner, Nathan A Baker


Jan 10, 2012·European Biophysics Journal : EBJ·Yong-Xian ShaoHai-Bin Luo
Jan 23, 2013·Journal of Molecular Modeling·Li-Li ChenJian-Hua Zhang
May 9, 2012·Journal of Computer-aided Molecular Design·Christopher R CorbeilPaul Labute
Nov 14, 2012·Journal of Chemical Information and Modeling·Miklos Feher, Christopher I Williams
May 8, 2013·Journal of Chemical Information and Modeling·Shan CongJing-Fang Wang
Nov 5, 2013·Journal of Chemical Information and Modeling·Yi-You HuangHai-Bin Luo
Mar 29, 2014·PLoS Neglected Tropical Diseases·Martin HornJan Dvořák
May 3, 2011·The Journal of Chemical Physics·Alexey V Onufriev, Grigori Sigalov
Jun 15, 2011·The Journal of Chemical Physics·Jason A Wagoner, Vijay S Pande
Mar 27, 2012·Nature Chemical Biology·Lars RichterMargot Ernst
Nov 26, 2013·International Journal of Peptide Research and Therapeutics·Yi KongJi-Fu Wei
Nov 13, 2015·Journal of Computational Chemistry·Alexander CumberworthJörg Gsponer
Jan 29, 2016·Scientific Reports·Takashi TamuraFumitoshi Sato
Jan 29, 2013·Journal of Molecular Graphics & Modelling·Abdul Wadood, Zaheer-ulhaq Ulhaq
Mar 29, 2011·Biophysical Chemistry·Haibo LiuJun Xu
Feb 6, 2016·Journal of Chemical Information and Modeling·Karan KapoorJerome Baudry
Mar 19, 2014·Journal of Chemical Theory and Computation·Jean-François TruchonPaul Labute
Feb 6, 2016·The Plant Journal : for Cell and Molecular Biology·Li WangYan-Hua Su
Mar 8, 2016·Physical Chemistry Chemical Physics : PCCP·Chunxia GaoLeif A Eriksson
Jun 21, 2014·Scientific Reports·Chunxia GaoJames A L Brown
Jul 21, 2015·Bioorganic & Medicinal Chemistry·Mehr-un-NisaMisbahul A Khan
Jan 10, 2012·Proteins·Alessandra MozziEugenio Monti
Mar 12, 2010·Journal of Computational Chemistry·Li-Dong Gong, Zhong-Zhi Yang
Aug 5, 2014·ChemMedChem·Constantin VossBoris Schmidt
Jan 11, 2014·Protein Science : a Publication of the Protein Society·David J RosenmanChristopher Bystroff
Sep 16, 2014·Journal of Computational Chemistry·Junya YamagishiMakoto Taiji
Apr 2, 2014·Environmental Toxicology and Chemistry·Jason Brett HarrisJerome Baudry
Apr 14, 2016·General and Comparative Endocrinology·Ryohei YatsuTaisen Iguchi
Mar 11, 2015·Journal of Molecular Recognition : JMR·Miguel R Lugo, A Rod Merrill
Jan 1, 2013·International Journal of Medicinal Chemistry·Shinji AmariNoriaki Hirayama
Apr 30, 2015·Journal of Cardiovascular Pharmacology·Xing-li SuYi Kong
Jun 13, 2012·Journal of Proteomics·Satoko MatsunagaAkihide Ryo
Dec 1, 2009·Biochemical and Biophysical Research Communications·Renhua SunWenbing Yao
Jul 6, 2010·Bioorganic & Medicinal Chemistry Letters·Shinya NakamuraIsao Nakanishi
Jul 6, 2010·Journal of Molecular Biology·Kathryn L ChapmanJohn B C Findlay
Jun 20, 2015·Journal of Chemical Information and Modeling·Cen GaoMichal Vieth
Dec 3, 2014·European Journal of Pharmacology·Bassem SadekMurat Oz
Apr 29, 2015·The Journal of Experimental Medicine·Hyung W LimEric Verdin
May 25, 2010·Cancer Biology & Therapy·Keith R LaderoutePaula J Ehrlich
Oct 30, 2012·Bioorganic & Medicinal Chemistry Letters·Jérémie Fournier-Dit-ChabertKlaus Pors
May 27, 2014·European Journal of Medicinal Chemistry·Elena Diez-CeciliaIsabel Rozas
Dec 30, 2014·Journal of Chemical Information and Modeling·Christoph ScholzBoris Schmidt
May 12, 2015·PloS One·Valerie BerthelierJerome Baudry
Sep 29, 2011·The Journal of Physical Chemistry. B·Bo-Xue Tian, Leif A Eriksson
Jan 15, 2013·Journal of Chemical Theory and Computation·Peter EastmanVijay S Pande
Aug 16, 2013·The Journal of Physical Chemistry. B·Eric A Mills, Steven S Plotkin
Sep 15, 2016·Scientific Reports·Dalia AlansaryBarbara A Niemeyer
Sep 7, 2016·Journal of Medicinal Chemistry·Cecilia EngdahlAnna Linusson
May 10, 2017·Journal of Chemical Information and Modeling·Benjamin D SellersAlberto Gobbi
Aug 23, 2016·Organic & Biomolecular Chemistry·Kozo YonedaHideo Kigoshi
May 27, 2015·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Francesco GentileJack A Tuszynski
Aug 17, 2017·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Marco Gaetano LepreJack A Tuszynski
Apr 24, 2018·PloS One·Min PiLeigh Darryl Quarles
Mar 23, 2010·The Journal of Biological Chemistry·Zac YatesBoxu Yan
Feb 7, 2018·Biotechnology and Applied Biochemistry·U KalathiyaMaciej Baginski
Oct 12, 2018·Organic & Biomolecular Chemistry·Rei WatanabeMasaki Kita
Oct 26, 2018·ChemMedChem·Simone SchierleDaniel Merk
Oct 19, 2018·Journal of Biomolecular Structure & Dynamics·Yueqi WangDong-Qing Wei
May 28, 2009·Physiologia Plantarum·Maja LebskaGrazyna Muszyńska
Apr 2, 2019·Nature Communications·Swechha M PokharelSantanu Bose
Dec 12, 2012·Quarterly Reviews of Biophysics·Pengyu RenNathan A Baker
Jun 13, 2019·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Chang WenJun Xu
Jul 12, 2014·Virus Genes·Mushtaq HussainJoanna B Wilson
Nov 19, 2019·PLoS Neglected Tropical Diseases·Hideaki ShimizuTatsuo Shioda
Mar 24, 2016·Endocrinology·Min PiLeigh Darryl Quarles
Oct 7, 2015·Molecular Endocrinology·Min PiLeigh Darryl Quarles
Dec 25, 2012·The Journal of Biological Chemistry·Derek HoA Rod Merrill
Dec 25, 2016·The Journal of Biological Chemistry·Hui-Min QinMasaru Tanokura
Jan 5, 2019·In Silico Pharmacology·Raju DashS M Zahid Hosen
Mar 13, 2019·Annual Review of Biophysics·Alexey V Onufriev, David A Case
Jul 5, 2019·Scientific Reports·Ammad FahimRehan Zafar Paracha
Aug 7, 2019·BMC Chemistry·Syed Lal BadshahYahia N Mabkhot
Jan 1, 2020·Chemical Biology & Drug Design·Francesco GentileJack A Tuszynski
Mar 22, 2020·Scientific Reports·Hirofumi KashiwagiYoshie Kametani
Apr 24, 2020·Journal of Biomolecular Structure & Dynamics·Nasir AhmadKhalid Khan
Apr 4, 2017·Molecular Biology and Evolution·Yoshinori FukasawaKenichiro Imai
Jan 10, 2017·Frontiers in Endocrinology·Muhammad ZafarMuhammad Arif Lodhi
Aug 14, 2019·Journal of Enzyme Inhibition and Medicinal Chemistry·Giulia RotondiClaudiu T Supuran
Apr 26, 2020·International Journal of Molecular Sciences·Özlen Güzel-AkdemirAtilla Akdemir
Jul 8, 2011·Molecular and Cellular Biochemistry·Takayoshi KinoshitaGozoh Tsujimoto
May 1, 2014·Journal of Theoretical & Computational Chemistry·Alexey V Onufriev, Boris Aguilar
Sep 11, 2018·Frontiers in Chemistry·Luca PalazzoloIvano Eberini
May 15, 2019·International Journal of Molecular Sciences·Kübra Demir-YazıcıÖzlen Güzel-Akdemir
May 6, 2020·International Journal of Molecular Sciences·Kübra Demir-YazıcıAtilla Akdemir
Jul 1, 2020·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Maggie C DuncanIan Tietjen
Aug 14, 2020·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Hemat S KhalafAhmed H Bakheit
Jun 14, 2008·Journal of Virology·David BhellaIan G Goodfellow
Aug 16, 2012·Physical Chemistry Chemical Physics : PCCP·Emma S E Eriksson, Leif A Eriksson
Feb 16, 2020·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Genaro Rocha-GarduñoGabriel Navarrete-Vázquez
Feb 6, 2017·Journal of Computational Chemistry·Baofeng ZhangEmilio Gallicchio
Jan 6, 2021·Cancer Chemotherapy and Pharmacology·Gloria CinieroLars Petter Jordheim
Nov 1, 2018·Journal of Colloid and Interface Science·Jingda HuangFeng Fu
Dec 20, 2020·Biochimica Et Biophysica Acta. General Subjects·Karan KapoorJeremy C Smith
Aug 3, 2020·Computational Biology and Chemistry·Shafiq Ur RahmanJamshed Iqbal
Nov 13, 2019·Biochemical and Biophysical Research Communications·Hiroshi IshiiTetsuro Matano
Jan 10, 2021·The Science of the Total Environment·Hiroshi IshibashiKoji Arizono
Mar 22, 2020·Biochemical and Biophysical Research Communications·Yan LiuLiying Hao
Nov 14, 2015·Bioscience, Biotechnology, and Biochemistry·Takahiro FukuharaTakashi Tamura
Dec 23, 2018·Biochimica Et Biophysica Acta. Proteins and Proteomics·Shinya SutohTakashi Tamura
Aug 17, 2019·Bioorganic & Medicinal Chemistry Letters·Xavier FraderaJason D Katz
Apr 27, 2010·Journal of Chemical Theory and Computation·Emilio GallicchioRonald M Levy
Sep 8, 2009·Journal of Chemical Theory and Computation·Aleksandr V MarenichDonald G Truhlar
Apr 27, 2021·Journal of Biomolecular Structure & Dynamics·Zaira RehmanPeter John
Apr 19, 2021·Frontiers in Bioengineering and Biotechnology·Gamal Nasser Abdel-HadyRyuichi Hirota

Related Concepts

Atom (substance)
Hydration Status
Small Molecule

Trending Feeds


Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Lipidomics & Rhinovirus Infection

Lipidomics can be used to examine the lipid species involved with pathogenic conditions, such as viral associated inflammation. Discovered the latest research on Lipidomics & Rhinovirus Infection.

Alzheimer's Disease: MS4A

Variants within the membrane-spanning 4-domains subfamily A (MS4A) gene cluster have recently been implicated in Alzheimer's disease in genome-wide association studies. Here is the latest research on Alzheimer's disease and MS4A.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Torsion Dystonia

Torsion dystonia is a movement disorder characterized by loss of control of voluntary movements appearing as sustained muscle contractions and/or abnormal postures. Here is the latest research.

Generating Insulin-Secreting Cells

Reprogramming cells or using induced pluripotent stem cells to generate insulin-secreting cells has significant therapeutic implications for diabetics. Here is the latest research on generation of insulin-secreting cells.

Central Pontine Myelinolysis

Central Pontine Myelinolysis is a neurologic disorder caused most frequently by rapid correction of hyponatremia and is characterized by demyelination that affects the central portion of the base of the pons. Here is the latest research on this disease.

Epigenome Editing

Epigenome editing is the directed modification of epigenetic marks on chromatin at specified loci. This tool has many applications in research as well as in the clinic. Find the latest research on epigenome editing here.