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      Publications (Jan 2012)
  • Velez-Vega,C., and Gilson,M.K. Calculation of standard binding free energies from reversible pulling calculations. J. Chem. Theo. Comp., submitted.
  • Velez-Vega,C., and Gilson,M.K. Force and stress along simulated dissociation pathways of cucurbituril-guest systems. J. Chem. Theo. Comp., in press.
  • Muddana,H.S., Varnado,D., Bielawski,C.W., Urbach,A.R., Isaacs,L., Geballe,M.T., and Gilson,M.K. Blind prediction of host-guest binding affinities: A new SAMPL3 challenge. J. Comput. Aided Mol. Des.,in press.
  • Muddana,H.S. and Gilson,M.K. Prediction of SAMPL3 host-guest binding affinities: evaluating the accuracy of generalized force fields. J. Comput. Aided Mol. Des., in press.
  • Moghaddam,S., Cheng,Y., Rekharsky,M., Ho Ko,Y., Kim,K., Inoue,Y., and Gilson,M.K. New ultrahigh affinity host|guest complexes of cucurbit[7]uril with bicyclo[2.2.2]octane and adamantane guests: Thermodynamic analysis and evaluation of M2 affinity calculations. JACS 133:3570-3581, 2011.
  • Somani,S. and Gilson,M.K. Accelerated convergence of molecular free energy via superposition approximation-based reference states. J. Chem. Phys. 134:134107, 2011.
  • Gilson MK, Radford SE. Protein folding and binding: from biology to physics and back again. Curr. Opin. Struct. Biol. 2011 211-3, 2011. (Editorial)
  • Gilson,M.K. and Irikura,K.K. Symmetry numbers for rigid, flexible and fluxional molecules: Theory and applications. J. Phys. Chem. B., 114:16304-16317, 2010.
  • Nalam,M.N.L, Ali,A., Altman,M.D., Reddy,G.S.K.K., Chellappan,S., Kairys,V., Ozen,A., Cao,H., Gilson,M.K., Tidor,B., Rana,T.M., and Schiffer,C.A. Evaluating the substrate-envelope hypothesis: structural analysis of novel HIV-1 protease inhibitors designed to be robust against drug resistance. J. Virol. 84:5386-5378, 2010.
  • Hnizdo,V. and Gilson,M.K. Thermodynamic and differential entropy under a change of variables. Entropy 12:578-590, 2010.
  • Gilson,M.K. Stress analysis at the molecular level: a forced cucurbituril-guest dissociation pathway. J. Chem. Theo. Comput. 6:637-646, 2010.
  • Zhou,H.-X. and Gilson,M.K. Theory of free energy and entropy in noncovalent binding, Chem. Rev., 109:4092-4107, 2009.
  • Kairys,V., Gilson,M.K., Lather,V., Schiffer,C.A., and Fernandes,M.X. Toward the design of mutation-resistant enzyme inhibitors: Further evaluation of the substrate envelope hypothesis. Chem. Biol. Drug Des. 74:234-245, 2009.
  • Killian,B.J., Yudenfreund Kravitz,J., Somani,S., Dasgupta,P., Pang,Y.-P., and Gilson,M.K. Configurational entropy in protein-peptide binding. Computational study of Tsg101 UEV domain with an HIV-derived PTAP nonapeptide. J. Molec. Biol., 389:315-335, 2009.
  • Somani,S., Killian,B.J., and Gilson,M.K. Sampling conformations in high dimensions using low-dimensional distribution functions J. Chem. Phys., 130:134102, 2009.
  • Moghaddam,S., Inoue,Y., and Gilson,M.K. Host-guest complexes with protein-ligand-like affinities: Computational analysis and design. J. Am. Chem. Soc. 131:4012-4021, 2009. [Includes cover art and ACS podcast.]
  • Jorissen,R.N., Reddy,G.S.K.K., Ali,A., Altman,M.D., Chellappan,S., Anjum,S.G., Tidor,B., Schiffer,C.A., Rana,T.M., and Gilson,M.K. Additivity in the analysis and design of HIV protease inhibitors. J. Med. Chem., 52:737-754, 2009.
  • Boda,D., Valisko,M., Henderson,D., Gillespie,D., Eisenberg,R., and Gilson,M.K. Ions and inhibitors in the binding site of HIV protease: comparison of Monte Carlo simulations and the linearized Poisson-Boltzmann equation. Biophys. J. 96:1293-1306, 2009.
  • Hnizdo,V.*, Tan,J., Killian,B.J., and Gilson,M.K.*, Efficient calculation of configurational entropy from molecular simulations by combining the Mutual-Information Expansion and Nearest-Neighbor methods. J. Comput. Chem. 29:1605-1614, 2008.
  • Altman,M.K., Ali,A., Kiran Kumar Reddy G.S., Nalam,M.N.L., Anjum,S.G., Cao,H., Chellappan,S., Kairys,V., Fernandes,M.X., Gilson,M.K.*, Schiffer,C.A.*, Rana,T.M.* and Tidor,B.* HIV-1 protease inhibitors from inverse design in the substrate envelope exhibit subnanomolar binding to drug-resistant variants. J.Am.Chem.Soc., 130:6099-6113, 2008
  • Rekharsky,M.V., Mori,T., Yang,C., Ko,Y.H., Selvapalam,N., Kim,H., Sobrasingh,D., Kaifer,A.E., Liu,S., Isaacs,L.*, Chen,W., Moghaddam,S., Gilson,M.K.*, Kim,K.*, and Inoue,Y.*, A synthetic host-guest system achieves avidin-biotin affinity by overcoming enthalpy-entropy compensation. Proc. Nat. Acad. Sci. USA, 104:20737-20742, 2007.
  • Kerrien,S., Orchard,S., Montecchi-Palazzi,L., Aranda,B., Quinn,A.F., Vinod,N., Bader,G.D., Xenarios,I., Wojcik,J., Sherman,D., Tyers,M., Salama,J.J., Moore,S., Ceol,A., Chatraryamontri,A., Oesterheld,M. Stuempflen,V., Salwinski,L., Nerothin,J., Cusick,M.E. , Vidal,M., Gilson,M.K., Armstrong,J., Woollard,P., Hogue,C., Eisenberg,D., Cesareni,G., Apweiler,R., and Hermjakob,H. Broadening the horizon - Level 2.5 of the HUPO-PSI format for molecular interactions. BMC Biology, 5:44, 2007.
  • Killian,B.J., Kravitz,J.Y., and Gilson,M.K. Extraction of configurational entropy from molecular simulations via an expansion approximation. J. Chem. Phys., 127:024107, 2007.
  • Chellappan,S., Reddy,G.S.K.K., Ali,A., Nalam,M.N.L., Anjum,S.G., Cao,H., Kairys,V., Fernandes,M.X., Altman,M.D., Tidor,B., Rana, T.M., Schiffer,C.A. and Gilson,M.K. Design of mutation-resistant HIV protease inhibitors with the substrate envelope hypothesis. Chem. Biol. Drug. Des., 69:298-313, 2007.
  • Chellappan,S., Kairys,V., Fernandes,M.X., Schiffer,C. and Gilson,M.K. Evaluation of the substrate envelope hypothesis for inhibitors of HIV-1 protease. Proteins: Struct. Funct. Bioinf., 68:561-567, 2007.
  • Gilson,M.K. and Zhou,H-X Calculation of protein-ligand binding affinities.Ann. Rev. Biophys. Biomol. Struct. 2007, 36:21-42, 2007. (Invited review.)
  • Chang,CE, Chen, W., and Gilson, M.K. Ligand configurational entropy and protein binding. Proc. Nat. Acad. Sci. USA,1534-1539, 2007.
  • Chen,W. and Gilson,M.K ConCept: de novo design of synthetic receptors for targeted ligands. J. Chem. Inf. Mod. 47:425-434,2007.
  • Liu,T., Lin,Y., Wen,X., Jorissen,R.N. and Gilson,M.K. BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities. Nucl. Acids. Res. Database issue 2006.
  • Reiner,J.E., Crawford,A.M., Kishore,R.B., Goldner,L.S., Helmerson,K., and Gilson,M.K. Optically trapped aqueous droplets for single molecule studies. Appl. Phys. Lett. 89, 013904.
  • Chen,W., Chang,CE and Gilson, M.K. Concepts in receptor optimization: Targeting the RGD peptide J.Am.Chem.Soc. 128:4675-4684, 2006.
  • Gilson,M.K. Sensitivity analysis and charge-optimization for flexible ligands: Applicability to lead optimizationJ. Chem. Theo. Comput. 2:259-270, 2006.
  • Kairys, V., Fernandes, M. and Gilson,M.K Screening drug-like compounds by docking to homology models: a systematic study. J. Chem. Inf. Model. 46:365-379, 2006.
  • Chang,C., Chen,W. and Gilson,M.K. Evaluating the accuracy of the quasiharmonic approximation. J. Chem. Theory Comput. 1:1017-1028, 2005.
  • Jorissen,R.N. and Gilson,M.K. Virtual screening of molecular databases using a Support Vector Machine. J. Chem. Inf. Model. 45:549-561, 2005.
  • Fernandes,M.X., Kairys,V., and Gilson,M.K. Comparing ligand interactions with multiple receptors via serial docking. J.Chem.Inf. Comput. Sci. 44:1961-1970, 2004
  • Chen,W., Chang,C. and Gilson,M.K. Calculation of cyclodextrin binding affinities: Energy, entropy and implications for drug design. Biophys. J., 87:3035-3049, 2004.
  • Chang,C. and Gilson,M.K. Free energy, entropy, and induced fit in host-guest recognition. J.Am.Chem.Soc. 126:13156-13164, 2004.
  • Chen,W., Huang,J., and Gilson, M.K. Identification of symmetries in molecules and complexes. J. Chem. Inf. Comput. Sci. 44:1301-1313, 2004.
  • Kairys,V., Gilson,M.K.* and Luy,B*. Structural model for an AxxxG-mediated dimer of surfactant-associated Protein C. Eur. J. Bioch., 271:2086-2092, 2004.
  • Mihailescu,M. and Gilson,M.K. On the theory of noncovalent association, Biophys.J., 87:23-36, 2004.
  • Gilson,M.K., Gilson,H.S.R. and Potter,M.J. Fast assignment of accurate partial atomic charges: An electronegativity equalization method that accounts for alternate resonance forms. J. Chem. Inf. Comput. Sci., 43:1982-1997, 2003.
  • Parsons,L., Bonander,N., Eisenstein,E., Gilson,M., Kairys,V., and Orban,J. Solution structure and functional ligand screening of HI0719, a highly conserved protein from bacteria to humans in the YjgF/YER057c/UK114 family. Biochem. 42:80-89, 2003.
  • DeJong,E.S., Chang,C-E.,Gilson,M.K. and Marino,J.P. Proflavine acts as a Rev inhibitor by targeting the high-affinity Rev binding site of the Rev responsive element of HIV-1. Biochemistry 42:8035-8046, 2003.
  • Chang,C. and Gilson,M.K. Tork: Conformational analysis method for molecules and complexes. J. Comput. Chem. 24:1987-1998, 2003.
  • Chang,C., Potter,M. and Gilson,M.K. Calculation of molecular configuration integrals, J. Phys. Chem. B, 107:1048-1055, 2003.
  • Kairys,V. and Gilson,M.K. Enhanced docking with the mining minima optimizer: Acceleration and side-chain flexibility. J. Comput. Chem. 23:1656-1670, 2002.
  • Luo,R., David,L. and Gilson,M.K. Accelerated Poisson-Boltzmann calculations for static and dynamic systems. J. Comput. Chem. 23:1244-1253, 2002.
  • Potter,M.J. and Gilson,M.K. Coordinate systems and the calculation of molecular properties. J. Phys. Chem. A 106: 563-566, 2002.
  • Chen,X., Lin,Y. and Gilson,M.K. The Binding Database: Overview and User's Guide. Biopolymers Nucleic Acid Sci. 61:127-141, 2002.
  • Gilson, MK. Molecular Recognition Databases. Biopolymers Nucleic Acid Sci. 61:97-98, 2002. (Editorial)
  • Chen,X. Lin,Y. Liu,M. and Gilson,M.K. The Binding Database: Data Management and Interface Design. Bioinformatics, 18:130-139, 2002.
  • Chen,X., Liu,M., and Gilson,M.K. BindingDB: A web-accessible molecular recognition database. Combinatorial Chemistry and High-Throughput Screening, 4:719-725, 2001.
  • Mardis,K.L., Luo,R. and Gilson,M.K. Interpreting trends in the binding of cyclic ureas to HIV-1 protease. J. Molec. Biol. 309:507-517, 2001.
  • David,L., Luo,R., and Gilson,M.K. Ligand-receptor docking with the Mining Minima optimizer. J. Comput. Aid. Molec.Design. 15:157-171, 2001.
  • 50. Luo,R., Gilson,H.S.R., Potter,M.J., and Gilson,M.K. The physical basis of nucleic acid base stacking in water. Biophys. J., 80:140-148, 2001.
  • Mardis,K.L., Brune,B.J., Vishwanath,P., Giorgis,B., Payne,G.F, and Gilson,M.K. Intramolecular versus intermolecular hydrogen bonding in the adsorption of aromatic alcohols onto an acrylic ester sorbent. J. Phys. Chem. B 104:4735-4744, 2000.
  • Luo,R. and Gilson,M.K. Synthetic adenine receptors: Direct calculation of binding affinities. J. Amer. Chem. Soc.122:2934-2937, 2000.
  • Mardis,K.L., Glemza,A.J., Brune,B.J., Payne,G.F. and Gilson,M.K. Differential adsorption of phenol derivatives onto a polymeric sorbent: A combined molecular modeling and experimental study. J. Phys. Chem. B 103:9879-9887, 1999.
  • Glemza,A.J., Mardis,K.L., Chaudhry,A.A., Gilson,M.K. and Payne,G.F. Competition between intra- and inter-molecular hydrogen bonding: effect on para/ortho adsorptive selectivity for substituted phenols. Indust. & Eng. Chem. Res., 39:463-472, 2000.
  • David,L., Luo,R. and Gilson,M.K. Comparison of the generalized Born and Poisson models of electrostatics: Energetics and dynamics of the HIV-1 protease. J. Comput. Chem., 21:295-309, 2000.
  • Luo,R., David,L., Head,M.S., Given,J.A. and Gilson,M.K. Nucleic acid base-pairing and N-methylacetamide self-association in chloroform: Affinity and conformation. Biophys. Chem. 78: 183-193, 1999.
  • David,L., Luo,R., Head,M.S. and Gilson,M.K. Computational study of KNI-272, a potent inhibitor of HIV-1 protease. On the mechanism of preorganization. J. Phys. Chem. 103:1031-1044, 1999.
  • Luo,R., David,L., Hung,H., Devaney,J., and Gilson,M.K. The strength of solvent-exposed salt bridges. J. Phys. Chem. 103: 727-736, 1999.
  • Trylska,J. Antosiewicz,J., Geller,M., Hodge,C.N., Klabe,R.M., Head,M.S., and Gilson,M.K. Thermodynamic linkage between protonation and binding of inhibitors to HIV protease. Protein Science 8:180-195, 1999.
  • Given,J.A. and Gilson,M.K. A hierarchical method for the generation of low-energy conformers of a protein-ligand complex. Proteins: Structure, Function and Genetics 33:475-495, 1998.
  • Luo,R., Head,M.S., Moult,J., and Gilson,M.K. (1998) pKa shifts in small molecules and HIV protease: Electrostatics and conformation. J. Amer. Chem. Soc. 120:6138-6146.
  • Forsyth,W.R., Gilson,M.K., Antosiewicz,J., Jaren,O.R. and Robertson,A.D. (1998) Theoretical and experimental analysis of ionization equilibria in turkey ovomucoid third domain. Biochemistry 37: 8643-8652.
  • Luo,R., Moult,J., and Gilson,M.K. (1997) A dielectric screening treatment of electrostatic solvation. J. Phys. Chem. B 101:11226-11236.
  • Gilson,M.K. Modeling protonation equilibria in biomolecules. In Computer Simulations of Biomolecular Systems, W.F. van Gunsteren, P.K. Weiner and A.J. Wilkinson, Eds. Kluwer/Escom, Dordrecht, 1997, pp. 199-222.
  • Orban,J., Alexander,P., Antosiewicz,J., Gilson,M.K., and Khare,D. (1997) pKa measurements for the B1 and B2 IgG-binding domains of protein G from NMR: Comparison with calculated values for NMR and X-ray structures. Biochemistry 36: 3580-3589.
  • Gilson,M.K., Given,J.A. and Head,M.S. (1997) A new class of models for computing receptor-ligand binding affinities. Chem.& Biol. 4:87-92.
  • Head,M.S., Given,J.A., and Gilson,M.K. (1997) "Mining minima": Direct computation of conformational free energy. J. Phys. Chem. 101:1609-1618.
  • Gilson,M.K., Given,J.A., Bush,B., and McCammon,J.A. (1997) The statistical-thermodynamic basis for computation of binding affinities. A critical review. Biophys. J. 72:1047-1069.
  • Antosiewicz,J., McCammon,J.A. and Gilson,M.K. (1996) The determinants of pKas in proteins. Biochemistry 35:7819-7833.
  • Gilson,M.K. Theory of electrostatic interactions in macromolecules. (1995) Curr. Opin. Struct. Biol. 5: 216-223.
  • Antosiewicz,J., Wlodek,S.T., McCammon,J.A., and Gilson,M.K. (1995) Simulation of charge-mutant acetylcholinesterases. Biochemistry 34: 4211-4219.

      Selected Prior Publications
  • Antosiewicz,J., McCammon,J.A. and Gilson,M.K. Prediction of pH-dependent properties of proteins. (1994) J. Molec. Biol. 238: 415-436.
  • Gilson,M.K., Straatsma,T.P., McCammon,J.A., Ripoll,D.R., Faerman,C.H., Axelsen,P.H., Silman,I. and Sussman,J.L. (1994) Open "back door" in a molecular dynamics simulation of Acetylcholinesterase. Science 253:1276-1278.
  • Gilson,M.K., Davis,M.E., Luty,B.A. and McCammon,J.A. (1993) Computation of electrostatic forces on solvated molecules using the Poisson-Boltzmann equation. J. Phys. Chem. 97:3591-3600.
  • Gilson,M.K. (1993) Multiple-site titration and molecular modeling: Two rapid methods for computing energies and forces for ionizable groups in proteins. Proteins: Structure, Function and Genetics 15:266-282.
  • Gilson,M.K. and Honig,B. (1991) The inclusion of electrostatic hydration energies in molecular mechanics calculations. J. Computer-Aided Drug Design 5:5-20.
  • Gilson,M.K. and Honig,B. (1988) Calculation of the total electrostatic energy of a macromolecular system: Solvation energies, binding energies, and conformational analysis. Proteins: Structure, Function, and Genetics 4:7-18.
  • Gilson,M.K. and Honig,B. (1987) Energetics of charge-charge interactions in proteins. Proteins: Structure, Function and Genetics 3:32-52.
  • Gilson,M.K. and Honig,B. (1987) Calculation of electrostatic potentials in an enzyme active site. Nature 330: 84-86.
  • Gilson,M.K., Sharp,K.A. and Honig,B. (1987) Calculating electrostatic interactions in biomolecules: Method and error assessment. J. Comput. Chem. 9:327-335.
  • Gilson,M.K. and Honig,B. (1986) The dielectric constant of a folded protein. Biopolymers 25:2907-2119.

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