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Items: 1 to 50 of 61

1.

The generalized Boltzmann distribution is the only distribution in which the Gibbs-Shannon entropy equals the thermodynamic entropy.

Gao X, Gallicchio E, Roitberg AE.

J Chem Phys. 2019 Jul 21;151(3):034113. doi: 10.1063/1.5111333.

PMID:
31325924
2.

Massive-Scale Binding Free Energy Simulations of HIV Integrase Complexes Using Asynchronous Replica Exchange Framework Implemented on the IBM WCG Distributed Network.

Xia J, Flynn W, Gallicchio E, Uplinger K, Armstrong JD, Forli S, Olson AJ, Levy RM.

J Chem Inf Model. 2019 Apr 22;59(4):1382-1397. doi: 10.1021/acs.jcim.8b00817. Epub 2019 Feb 22.

3.

A grid-based algorithm in conjunction with a gaussian-based model of atoms for describing molecular geometry.

Chakravorty A, Gallicchio E, Alexov E.

J Comput Chem. 2019 May 5;40(12):1290-1304. doi: 10.1002/jcc.25786. Epub 2019 Jan 30.

PMID:
30698861
4.

Analytical Model of the Free Energy of Alchemical Molecular Binding.

Kilburg D, Gallicchio E.

J Chem Theory Comput. 2018 Dec 11;14(12):6183-6196. doi: 10.1021/acs.jctc.8b00967. Epub 2018 Nov 16.

PMID:
30415541
5.

New Dopamine D3-Selective Receptor Ligands Containing a 6-Methoxy-1,2,3,4-tetrahydroisoquinolin-7-ol Motif.

Gadhiya S, Cordone P, Pal RK, Gallicchio E, Wickstrom L, Kurtzman T, Ramsey S, Harding WW.

ACS Med Chem Lett. 2018 Sep 10;9(10):990-995. doi: 10.1021/acsmedchemlett.8b00229. eCollection 2018 Oct 11.

PMID:
30344905
6.

Assessment of a Single Decoupling Alchemical Approach for the Calculation of the Absolute Binding Free Energies of Protein-Peptide Complexes.

Kilburg D, Gallicchio E.

Front Mol Biosci. 2018 Mar 8;5:22. doi: 10.3389/fmolb.2018.00022. eCollection 2018.

7.

Synthesis and biological assessment of 3,7-dihydroxytropolones.

Hirsch DR, Schiavone DV, Berkowitz AJ, Morrison LA, Masaoka T, Wilson JA, Lomonosova E, Zhao H, Patel BS, Datla SH, Hoft SG, Majidi SJ, Pal RK, Gallicchio E, Tang L, Tavis JE, Le Grice SFJ, Beutler JA, Murelli RP.

Org Biomol Chem. 2017 Dec 19;16(1):62-69. doi: 10.1039/c7ob02453c.

8.

Efficient gaussian density formulation of volume and surface areas of macromolecules on graphical processing units.

Zhang B, Kilburg D, Eastman P, Pande VS, Gallicchio E.

J Comput Chem. 2017 Apr 15;38(10):740-752. doi: 10.1002/jcc.24745. Epub 2017 Feb 4.

PMID:
28160511
9.

Synthetic α-Hydroxytropolones as Inhibitors of HIV Reverse Transcriptase Ribonuclease H Activity.

Murelli RP, D'Erasmo MP, Hirsch DR, Meck C, Masaoka T, Wilson JA, Zhang B, Pal RK, Gallicchio E, Beutler JA, Le Grice SF.

Medchemcomm. 2016 Sep 1;7(9):1783-1788. doi: 10.1039/C6MD00238B. Epub 2016 Jul 7.

10.

Erratum to: A combined treatment of hydration and dynamical effects for the modeling of host-guest binding thermodynamics: the SAMPL5 blinded challenge.

Pal RK, Haider K, Kaur D, Flynn W, Xia J, Levy RM, Taran T, Wickstrom L, Kurtzman T, Gallicchio E.

J Comput Aided Mol Des. 2017 Jan;31(1):45. doi: 10.1007/s10822-016-9987-z. No abstract available.

PMID:
27815770
11.

Large scale free energy calculations for blind predictions of protein-ligand binding: the D3R Grand Challenge 2015.

Deng N, Flynn WF, Xia J, Vijayan RS, Zhang B, He P, Mentes A, Gallicchio E, Levy RM.

J Comput Aided Mol Des. 2016 Sep;30(9):743-751. Epub 2016 Aug 25.

12.

Free Energy-Based Virtual Screening and Optimization of RNase H Inhibitors of HIV-1 Reverse Transcriptase.

Zhang B, D'Erasmo MP, Murelli RP, Gallicchio E.

ACS Omega. 2016 Sep 30;1(3):435-447. Epub 2016 Sep 21.

13.

A combined treatment of hydration and dynamical effects for the modeling of host-guest binding thermodynamics: the SAMPL5 blinded challenge.

Pal RK, Haider K, Kaur D, Flynn W, Xia J, Levy RM, Taran T, Wickstrom L, Kurtzman T, Gallicchio E.

J Comput Aided Mol Des. 2017 Jan;31(1):29-44. doi: 10.1007/s10822-016-9956-6. Epub 2016 Sep 30. Erratum in: J Comput Aided Mol Des. 2017 Jan;31(1):45.

14.

Recent Advances in Computational Models for the Study of Protein-Peptide Interactions.

Kilburg D, Gallicchio E.

Adv Protein Chem Struct Biol. 2016;105:27-57. doi: 10.1016/bs.apcsb.2016.06.002. Epub 2016 Aug 3. Review.

PMID:
27567483
15.

Asynchronous Replica Exchange Software for Grid and Heterogeneous Computing.

Gallicchio E, Xia J, Flynn WF, Zhang B, Samlalsingh S, Mentes A, Levy RM.

Comput Phys Commun. 2015 Nov;196:236-246.

16.

Simulating Replica Exchange: Markov State Models, Proposal Schemes, and the Infinite Swapping Limit.

Zhang BW, Dai W, Gallicchio E, He P, Xia J, Tan Z, Levy RM.

J Phys Chem B. 2016 Aug 25;120(33):8289-301. doi: 10.1021/acs.jpcb.6b02015. Epub 2016 Apr 29.

17.

Binding Energy Distribution Analysis Method: Hamiltonian Replica Exchange with Torsional Flattening for Binding Mode Prediction and Binding Free Energy Estimation.

Mentes A, Deng NJ, Vijayan RS, Xia J, Gallicchio E, Levy RM.

J Chem Theory Comput. 2016 May 10;12(5):2459-70. doi: 10.1021/acs.jctc.6b00134. Epub 2016 Apr 26.

18.

Parameterization of an effective potential for protein-ligand binding from host-guest affinity data.

Wickstrom L, Deng N, He P, Mentes A, Nguyen C, Gilson MK, Kurtzman T, Gallicchio E, Levy RM.

J Mol Recognit. 2016 Jan;29(1):10-21. doi: 10.1002/jmr.2489. Epub 2015 Aug 10.

19.

Large-scale asynchronous and distributed multidimensional replica exchange molecular simulations and efficiency analysis.

Xia J, Flynn WF, Gallicchio E, Zhang BW, He P, Tan Z, Levy RM.

J Comput Chem. 2015 Sep 5;36(23):1772-85. doi: 10.1002/jcc.23996. Epub 2015 Jul 7.

20.

A unique binding mode of the eukaryotic translation initiation factor 4E for guiding the design of novel peptide inhibitors.

Di Marino D, D'Annessa I, Tancredi H, Bagni C, Gallicchio E.

Protein Sci. 2015 Sep;24(9):1370-82. doi: 10.1002/pro.2708.

21.

BEDAM binding free energy predictions for the SAMPL4 octa-acid host challenge.

Gallicchio E, Chen H, Chen H, Fitzgerald M, Gao Y, He P, Kalyanikar M, Kao C, Lu B, Niu Y, Pethe M, Zhu J, Levy RM.

J Comput Aided Mol Des. 2015 Apr;29(4):315-25. doi: 10.1007/s10822-014-9795-2. Epub 2015 Mar 1.

22.

Distinguishing binders from false positives by free energy calculations: fragment screening against the flap site of HIV protease.

Deng N, Forli S, He P, Perryman A, Wickstrom L, Vijayan RS, Tiefenbrunn T, Stout D, Gallicchio E, Olson AJ, Levy RM.

J Phys Chem B. 2015 Jan 22;119(3):976-88. doi: 10.1021/jp506376z. Epub 2014 Sep 17.

23.
24.

Virtual screening of integrase inhibitors by large scale binding free energy calculations: the SAMPL4 challenge.

Gallicchio E, Deng N, He P, Wickstrom L, Perryman AL, Santiago DN, Forli S, Olson AJ, Levy RM.

J Comput Aided Mol Des. 2014 Apr;28(4):475-90. doi: 10.1007/s10822-014-9711-9. Epub 2014 Feb 7.

25.

Correction: Chimeric Rhinoviruses Displaying MPER Epitopes Elicit Anti-HIV Neutralizing Responses.

Yi G, Lapelosa M, Bradley R, Mariano TM, Dietz DE, Hughes S, Wrin T, Petropoulos C, Gallicchio E, Levy RM, Arnold E, Arnold GF.

PLoS One. 2013 Sep 27;8(9). doi: 10.1371/annotation/57fc0148-19fe-4b8b-b2f4-bb5f60baa971. eCollection 2013.

26.

Chimeric rhinoviruses displaying MPER epitopes elicit anti-HIV neutralizing responses.

Yi G, Lapelosa M, Bradley R, Mariano TM, Dietz DE, Hughes S, Wrin T, Petropoulos C, Gallicchio E, Levy RM, Arnold E, Arnold GF.

PLoS One. 2013 Sep 6;8(9):e72205. doi: 10.1371/journal.pone.0072205. eCollection 2013.

28.

Theory of binless multi-state free energy estimation with applications to protein-ligand binding.

Tan Z, Gallicchio E, Lapelosa M, Levy RM.

J Chem Phys. 2012 Apr 14;136(14):144102. doi: 10.1063/1.3701175.

29.

Conformational Transitions and Convergence of Absolute Binding Free Energy Calculations.

Lapelosa M, Gallicchio E, Levy RM.

J Chem Theory Comput. 2012 Jan 10;8(1):47-60.

30.

Prediction of SAMPL3 host-guest affinities with the binding energy distribution analysis method (BEDAM).

Gallicchio E, Levy RM.

J Comput Aided Mol Des. 2012 May;26(5):505-16. doi: 10.1007/s10822-012-9552-3. Epub 2012 Feb 22.

31.

The linear interaction energy method for the prediction of protein stability changes upon mutation.

Wickstrom L, Gallicchio E, Levy RM.

Proteins. 2012 Jan;80(1):111-25. doi: 10.1002/prot.23168. Epub 2011 Oct 31.

32.

Recent theoretical and computational advances for modeling protein-ligand binding affinities.

Gallicchio E, Levy RM.

Adv Protein Chem Struct Biol. 2011;85:27-80. doi: 10.1016/B978-0-12-386485-7.00002-8. Review.

33.

Insights into the dynamics of HIV-1 protease: a kinetic network model constructed from atomistic simulations.

Deng NJ, Zheng W, Gallicchio E, Levy RM.

J Am Chem Soc. 2011 Jun 22;133(24):9387-94. doi: 10.1021/ja2008032. Epub 2011 May 25.

34.

Advances in all atom sampling methods for modeling protein-ligand binding affinities.

Gallicchio E, Levy RM.

Curr Opin Struct Biol. 2011 Apr;21(2):161-6. doi: 10.1016/j.sbi.2011.01.010. Epub 2011 Feb 19. Review.

35.

Kinetic network study of the diversity and temperature dependence of Trp-Cage folding pathways: combining transition path theory with stochastic simulations.

Zheng W, Gallicchio E, Deng N, Andrec M, Levy RM.

J Phys Chem B. 2011 Feb 17;115(6):1512-23. doi: 10.1021/jp1089596. Epub 2011 Jan 21.

36.

The Binding Energy Distribution Analysis Method (BEDAM) for the Estimation of Protein-Ligand Binding Affinities.

Gallicchio E, Lapelosa M, Levy RM.

J Chem Theory Comput. 2010 Sep 14;6(9):2961-2977.

37.

The AGBNP2 Implicit Solvation Model.

Gallicchio E, Paris K, Levy RM.

J Chem Theory Comput. 2009 Jul 31;5(9):2544-2564.

38.

Antigenic characteristics of rhinovirus chimeras designed in silico for enhanced presentation of HIV-1 gp41 epitopes [corrected].

Lapelosa M, Arnold GF, Gallicchio E, Arnold E, Levy RM.

J Mol Biol. 2010 Apr 2;397(3):752-66. doi: 10.1016/j.jmb.2010.01.064. Epub 2010 Feb 4. Erratum in: J Mol Biol. 2010 May 14;398(4):623-4.

39.

Conformational populations of ligand-sized molecules by replica exchange molecular dynamics and temperature reweighting.

Okumura H, Gallicchio E, Levy RM.

J Comput Chem. 2010 May;31(7):1357-67. doi: 10.1002/jcc.21419.

41.

Recovering kinetics from a simplified protein folding model using replica exchange simulations: a kinetic network and effective stochastic dynamics.

Zheng W, Andrec M, Gallicchio E, Levy RM.

J Phys Chem B. 2009 Aug 27;113(34):11702-9. doi: 10.1021/jp900445t.

42.

In silico vaccine design based on molecular simulations of rhinovirus chimeras presenting HIV-1 gp41 epitopes.

Lapelosa M, Gallicchio E, Arnold GF, Arnold E, Levy RM.

J Mol Biol. 2009 Jan 16;385(2):675-91. doi: 10.1016/j.jmb.2008.10.089. Epub 2008 Nov 8.

43.

Prediction of Protein Loop Conformations using the AGBNP Implicit Solvent Model and Torsion Angle Sampling.

Felts AK, Gallicchio E, Chekmarev D, Paris KA, Friesner RA, Levy RM.

J Chem Theory Comput. 2008;4(5):855-868.

44.

Exploring structural variability in X-ray crystallographic models using protein local optimization by torsion-angle sampling.

Knight JL, Zhou Z, Gallicchio E, Himmel DM, Friesner RA, Arnold E, Levy RM.

Acta Crystallogr D Biol Crystallogr. 2008 Apr;64(Pt 4):383-96. doi: 10.1107/S090744490800070X. Epub 2008 Mar 19.

45.

Simple continuous and discrete models for simulating replica exchange simulations of protein folding.

Zheng W, Andrec M, Gallicchio E, Levy RM.

J Phys Chem B. 2008 May 15;112(19):6083-93. doi: 10.1021/jp076377+. Epub 2008 Feb 6.

46.

Simulating replica exchange simulations of protein folding with a kinetic network model.

Zheng W, Andrec M, Gallicchio E, Levy RM.

Proc Natl Acad Sci U S A. 2007 Sep 25;104(39):15340-5. Epub 2007 Sep 18.

47.

Asynchronous replica exchange for molecular simulations.

Gallicchio E, Levy RM, Parashar M.

J Comput Chem. 2008 Apr 15;29(5):788-94.

48.

Conformational dynamics of substrate in the active site of cytochrome P450 BM-3/NPG complex: insights from NMR order parameters.

Ravindranathan KP, Gallicchio E, McDermott AE, Levy RM.

J Am Chem Soc. 2007 Jan 24;129(3):474-5. No abstract available.

49.

Linear Interaction Energy (LIE) Models for Ligand Binding in Implicit Solvent:  Theory and Application to the Binding of NNRTIs to HIV-1 Reverse Transcriptase.

Su Y, Gallicchio E, Das K, Arnold E, Levy RM.

J Chem Theory Comput. 2007 Jan;3(1):256-77. doi: 10.1021/ct600258e.

PMID:
26627170
50.

Temperature weighted histogram analysis method, replica exchange, and transition paths.

Gallicchio E, Andrec M, Felts AK, Levy RM.

J Phys Chem B. 2005 Apr 14;109(14):6722-31.

PMID:
16851756

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