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Items: 1 to 50 of 295


Framework based on communicability and flow to analyze complex network dynamics.

Gilson M, Kouvaris NE, Deco G, Zamora-López G.

Phys Rev E. 2018 May;97(5-1):052301. doi: 10.1103/PhysRevE.97.052301.


Automating Installation of the Integrating Biology and the Bedside (i2b2) Platform.

Wagholikar KB, Mendis M, Dessai P, Sanz J, Law S, Gilson M, Sanders S, Vangala M, Bell DS, Murphy SN.

Biomed Inform Insights. 2018 Jun 4;10:1178222618777749. doi: 10.1177/1178222618777749. eCollection 2018. Review.


Bind3P: Optimization of a Water Model Based on Host-Guest Binding Data.

Yin J, Henriksen NM, Muddana HS, Gilson MK.

J Chem Theory Comput. 2018 Jun 6. doi: 10.1021/acs.jctc.8b00318. [Epub ahead of print]


Extracting orthogonal subject- and condition-specific signatures from fMRI data using whole-brain effective connectivity.

Pallarés V, Insabato A, Sanjuán A, Kühn S, Mantini D, Deco G, Gilson M.

Neuroimage. 2018 May 22;178:238-254. doi: 10.1016/j.neuroimage.2018.04.070. [Epub ahead of print]


Motor-like Properties of Nonmotor Enzymes.

Slochower DR, Gilson MK.

Biophys J. 2018 May 8;114(9):2174-2179. doi: 10.1016/j.bpj.2018.02.008.


An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorder.

Werling DM, Brand H, An JY, Stone MR, Zhu L, Glessner JT, Collins RL, Dong S, Layer RM, Markenscoff-Papadimitriou E, Farrell A, Schwartz GB, Wang HZ, Currall BB, Zhao X, Dea J, Duhn C, Erdman CA, Gilson MC, Yadav R, Handsaker RE, Kashin S, Klei L, Mandell JD, Nowakowski TJ, Liu Y, Pochareddy S, Smith L, Walker MF, Waterman MJ, He X, Kriegstein AR, Rubenstein JL, Sestan N, McCarroll SA, Neale BM, Coon H, Willsey AJ, Buxbaum JD, Daly MJ, State MW, Quinlan AR, Marth GT, Roeder K, Devlin B, Talkowski ME, Sanders SJ.

Nat Genet. 2018 May;50(5):727-736. doi: 10.1038/s41588-018-0107-y. Epub 2018 Apr 26.


Effective Connectivity in Depression.

Rolls ET, Cheng W, Gilson M, Qiu J, Hu Z, Ruan H, Li Y, Huang CC, Yang AC, Tsai SJ, Zhang X, Zhuang K, Lin CP, Deco G, Xie P, Feng J.

Biol Psychiatry Cogn Neurosci Neuroimaging. 2018 Feb;3(2):187-197. doi: 10.1016/j.bpsc.2017.10.004. Epub 2017 Oct 23.


Substrate-driven chemotactic assembly in an enzyme cascade.

Zhao X, Palacci H, Yadav V, Spiering MM, Gilson MK, Butler PJ, Hess H, Benkovic SJ, Sen A.

Nat Chem. 2018 Mar;10(3):311-317. doi: 10.1038/nchem.2905. Epub 2017 Dec 18.


Stereotypical modulations in dynamic functional connectivity explained by changes in BOLD variance.

Glomb K, Ponce-Alvarez A, Gilson M, Ritter P, Deco G.

Neuroimage. 2018 May 1;171:40-54. doi: 10.1016/j.neuroimage.2017.12.074. Epub 2017 Dec 30.


Task-related effective connectivity reveals that the cortical rich club gates cortex-wide communication.

Senden M, Reuter N, van den Heuvel MP, Goebel R, Deco G, Gilson M.

Hum Brain Mapp. 2018 Mar;39(3):1246-1262. doi: 10.1002/hbm.23913. Epub 2017 Dec 8.


Accounting for apparent deviations between calorimetric and van't Hoff enthalpies.

Kantonen SA, Henriksen NM, Gilson MK.

Biochim Biophys Acta. 2018 Mar;1862(3):692-704. doi: 10.1016/j.bbagen.2017.11.020. Epub 2017 Dec 6.


D3R Grand Challenge 2: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies.

Gaieb Z, Liu S, Gathiaka S, Chiu M, Yang H, Shao C, Feher VA, Walters WP, Kuhn B, Rudolph MG, Burley SK, Gilson MK, Amaro RE.

J Comput Aided Mol Des. 2018 Jan;32(1):1-20. doi: 10.1007/s10822-017-0088-4. Epub 2017 Dec 4.


Analysis of fMRI data using noise-diffusion network models: a new covariance-coding perspective.

Gilson M.

Biol Cybern. 2018 Apr;112(1-2):153-161. doi: 10.1007/s00422-017-0741-y. Epub 2017 Dec 4.


Solvation Structure and Thermodynamic Mapping (SSTMap): An Open-Source, Flexible Package for the Analysis of Water in Molecular Dynamics Trajectories.

Haider K, Cruz A, Ramsey S, Gilson MK, Kurtzman T.

J Chem Theory Comput. 2018 Jan 9;14(1):418-425. doi: 10.1021/acs.jctc.7b00592. Epub 2017 Dec 8.


HYDROPHOBE Challenge: A Joint Experimental and Computational Study on the Host-Guest Binding of Hydrocarbons to Cucurbiturils, Allowing Explicit Evaluation of Guest Hydration Free-Energy Contributions.

Assaf KI, Florea M, Antony J, Henriksen NM, Yin J, Hansen A, Qu ZW, Sure R, Klapstein D, Gilson MK, Grimme S, Nau WM.

J Phys Chem B. 2017 Dec 14;121(49):11144-11162. doi: 10.1021/acs.jpcb.7b09175. Epub 2017 Dec 1.


Effective connectivity inferred from fMRI transition dynamics during movie viewing points to a balanced reconfiguration of cortical interactions.

Gilson M, Deco G, Friston KJ, Hagmann P, Mantini D, Betti V, Romani GL, Corbetta M.

Neuroimage. 2017 Oct 9. pii: S1053-8119(17)30810-8. doi: 10.1016/j.neuroimage.2017.09.061. [Epub ahead of print] Review.


Resting state networks in empirical and simulated dynamic functional connectivity.

Glomb K, Ponce-Alvarez A, Gilson M, Ritter P, Deco G.

Neuroimage. 2017 Oct 1;159:388-402. doi: 10.1016/j.neuroimage.2017.07.065. Epub 2017 Aug 3.


Testing inhomogeneous solvation theory in structure-based ligand discovery.

Balius TE, Fischer M, Stein RM, Adler TB, Nguyen CN, Cruz A, Gilson MK, Kurtzman T, Shoichet BK.

Proc Natl Acad Sci U S A. 2017 Aug 15;114(33):E6839-E6846. doi: 10.1073/pnas.1703287114. Epub 2017 Jul 31.


Erratum to: Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset.

Shirts MR, Klein C, Swails JM, Yin J, Gilson MK, Mobley DL, Case DA, Zhong ED.

J Comput Aided Mol Des. 2017 Aug;31(8):777. doi: 10.1007/s10822-017-0043-4. No abstract available.


Evaluating Force Field Performance in Thermodynamic Calculations of Cyclodextrin Host-Guest Binding: Water Models, Partial Charges, and Host Force Field Parameters.

Henriksen NM, Gilson MK.

J Chem Theory Comput. 2017 Sep 12;13(9):4253-4269. doi: 10.1021/acs.jctc.7b00359. Epub 2017 Aug 4.


Attach-Pull-Release Calculations of Ligand Binding and Conformational Changes on the First BRD4 Bromodomain.

Heinzelmann G, Henriksen NM, Gilson MK.

J Chem Theory Comput. 2017 Jul 11;13(7):3260-3275. doi: 10.1021/acs.jctc.7b00275. Epub 2017 Jun 13.


Attractive Interactions between Heteroallenes and the Cucurbituril Portal.

Reany O, Li A, Yefet M, Gilson MK, Keinan E.

J Am Chem Soc. 2017 Jun 21;139(24):8138-8145. doi: 10.1021/jacs.6b13005. Epub 2017 Jun 7.


Predicting Binding Free Energies: Frontiers and Benchmarks.

Mobley DL, Gilson MK.

Annu Rev Biophys. 2017 May 22;46:531-558. doi: 10.1146/annurev-biophys-070816-033654. Epub 2017 Apr 7. Review.


Bio-inspired CO2 reduction by a rhenium tricarbonyl bipyridine-based catalyst appended to amino acids and peptidic platforms: incorporating proton relays and hydrogen-bonding functional groups.

Chabolla SA, Machan CW, Yin J, Dellamary EA, Sahu S, Gianneschi NC, Gilson MK, Tezcan FA, Kubiak CP.

Faraday Discuss. 2017 Jun 2;198:279-300. doi: 10.1039/c7fd00003k.


Probing the orientation of inhibitor and epoxy-eicosatrienoic acid binding in the active site of soluble epoxide hydrolase.

Lee KS, Henriksen NM, Ng CJ, Yang J, Jia W, Morisseau C, Andaya A, Gilson MK, Hammock BD.

Arch Biochem Biophys. 2017 Jan 1;613:1-11. doi: 10.1016/ Epub 2016 Oct 29.


Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset.

Shirts MR, Klein C, Swails JM, Yin J, Gilson MK, Mobley DL, Case DA, Zhong ED.

J Comput Aided Mol Des. 2017 Jan;31(1):147-161. doi: 10.1007/s10822-016-9977-1. Epub 2016 Oct 27. Erratum in: J Comput Aided Mol Des. 2017 Jul 27;:.


D3R grand challenge 2015: Evaluation of protein-ligand pose and affinity predictions.

Gathiaka S, Liu S, Chiu M, Yang H, Stuckey JA, Kang YN, Delproposto J, Kubish G, Dunbar JB Jr, Carlson HA, Burley SK, Walters WP, Amaro RE, Feher VA, Gilson MK.

J Comput Aided Mol Des. 2016 Sep;30(9):651-668. Epub 2016 Sep 30.


Blind prediction of cyclohexane-water distribution coefficients from the SAMPL5 challenge.

Bannan CC, Burley KH, Chiu M, Shirts MR, Gilson MK, Mobley DL.

J Comput Aided Mol Des. 2016 Nov;30(11):927-944. doi: 10.1007/s10822-016-9954-8. Epub 2016 Sep 27.


Overview of the SAMPL5 host-guest challenge: Are we doing better?

Yin J, Henriksen NM, Slochower DR, Shirts MR, Chiu MW, Mobley DL, Gilson MK.

J Comput Aided Mol Des. 2017 Jan;31(1):1-19. doi: 10.1007/s10822-016-9974-4. Epub 2016 Sep 22. Review.


Non-TNF-Targeted Biologic vs a Second Anti-TNF Drug to Treat Rheumatoid Arthritis in Patients With Insufficient Response to a First Anti-TNF Drug: A Randomized Clinical Trial.

Gottenberg JE, Brocq O, Perdriger A, Lassoued S, Berthelot JM, Wendling D, Euller-Ziegler L, Soubrier M, Richez C, Fautrel B, Constantin AL, Mariette X, Morel J, Gilson M, Cormier G, Salmon JH, Rist S, Lioté F, Marotte H, Bonnet C, Marcelli C, Sellam J, Meyer O, Solau-Gervais E, Guis S, Ziza JM, Zarnitsky C, Chary-Valckenaere I, Vittecoq O, Saraux A, Pers YM, Gayraud M, Bolla G, Claudepierre P, Ardizzone M, Dernis E, Breban MA, Fain O, Balblanc JC, Aberkane O, Vazel M, Back C, Candon S, Chatenoud L, Perrodeau E, Sibilia J, Ravaud P.

JAMA. 2016 Sep 20;316(11):1172-1180. doi: 10.1001/jama.2016.13512.


The SAMPL5 host-guest challenge: computing binding free energies and enthalpies from explicit solvent simulations by the attach-pull-release (APR) method.

Yin J, Henriksen NM, Slochower DR, Gilson MK.

J Comput Aided Mol Des. 2017 Jan;31(1):133-145. doi: 10.1007/s10822-016-9970-8. Epub 2016 Sep 16.


Evaluation and Minimization of Uncertainty in ITC Binding Measurements: Heat Error, Concentration Error, Saturation, and Stoichiometry.

Kantonen SA, Henriksen NM, Gilson MK.

Biochim Biophys Acta. 2017 Feb;1861(2):485-498. doi: 10.1016/j.bbagen.2016.09.002. Epub 2016 Sep 15.


Long-term Efficacy and Safety of Mepolizumab in Patients With Severe Eosinophilic Asthma: A Multi-center, Open-label, Phase IIIb Study.

Lugogo N, Domingo C, Chanez P, Leigh R, Gilson MJ, Price RG, Yancey SW, Ortega HG.

Clin Ther. 2016 Sep;38(9):2058-2070.e1. doi: 10.1016/j.clinthera.2016.07.010. Epub 2016 Aug 21.


Erratum: "The electrostatic response of water to neutral polar solutes: Implications for continuum solvent modeling" [J. Chem. Phys. 138, 224504 (2013)].

Muddana HS, Sapra NV, Fenley AT, Gilson MK.

J Chem Phys. 2016 Jul 28;145(4):049902. doi: 10.1063/1.4960037. No abstract available.


Solvation thermodynamic mapping of molecular surfaces in AmberTools: GIST.

Ramsey S, Nguyen C, Salomon-Ferrer R, Walker RC, Gilson MK, Kurtzman T.

J Comput Chem. 2016 Aug 5;37(21):2029-37. doi: 10.1002/jcc.24417. Epub 2016 Jun 18.


Improving the Efficiency and Activity of Electrocatalysts for the Reduction of CO2 through Supramolecular Assembly with Amino Acid-Modified Ligands.

Machan CW, Yin J, Chabolla SA, Gilson MK, Kubiak CP.

J Am Chem Soc. 2016 Jul 6;138(26):8184-93. doi: 10.1021/jacs.6b03774. Epub 2016 Jun 23.


Evaluation of Representations and Response Models for Polarizable Force Fields.

Li A, Voronin A, Fenley AT, Gilson MK.

J Phys Chem B. 2016 Aug 25;120(33):8668-84. doi: 10.1021/acs.jpcb.6b03392. Epub 2016 Jun 16.


Enthalpic Breakdown of Water Structure on Protein Active-Site Surfaces.

Haider K, Wickstrom L, Ramsey S, Gilson MK, Kurtzman T.

J Phys Chem B. 2016 Sep 1;120(34):8743-56. doi: 10.1021/acs.jpcb.6b01094. Epub 2016 Jun 2.


Risk of postoperative infections and the discontinuation of TNF inhibitors in patients with rheumatoid arthritis: A meta-analysis.

Clay M, Mazouyes A, Gilson M, Gaudin P, Baillet A.

Joint Bone Spine. 2016 Dec;83(6):701-705. doi: 10.1016/j.jbspin.2015.10.019. Epub 2016 Apr 23. Review.


Estimation of Directed Effective Connectivity from fMRI Functional Connectivity Hints at Asymmetries of Cortical Connectome.

Gilson M, Moreno-Bote R, Ponce-Alvarez A, Ritter P, Deco G.

PLoS Comput Biol. 2016 Mar 16;12(3):e1004762. doi: 10.1371/journal.pcbi.1004762. eCollection 2016 Mar.


Erratum: Addendum: Models of Metaplasticity: A Review of Concepts.

Yger P, Gilson M.

Front Comput Neurosci. 2016 Jan 28;10:4. doi: 10.3389/fncom.2016.00004. eCollection 2016.


REM-Enriched Naps Are Associated with Memory Consolidation for Sad Stories and Enhance Mood-Related Reactivity.

Gilson M, Deliens G, Leproult R, Bodart A, Nonclercq A, Ercek R, Peigneux P.

Brain Sci. 2015 Dec 29;6(1). pii: E1. doi: 10.3390/brainsci6010001.


Editorial: Emergent Neural Computation from the Interaction of Different Forms of Plasticity.

Gilson M, Savin C, Zenke F.

Front Comput Neurosci. 2015 Nov 30;9:145. doi: 10.3389/fncom.2015.00145. eCollection 2015. No abstract available.


Spatial Decomposition of Translational Water-Water Correlation Entropy in Binding Pockets.

Nguyen CN, Kurtzman T, Gilson MK.

J Chem Theory Comput. 2016 Jan 12;12(1):414-29. doi: 10.1021/acs.jctc.5b00939. Epub 2015 Dec 4.


Models of Metaplasticity: A Review of Concepts.

Yger P, Gilson M.

Front Comput Neurosci. 2015 Nov 10;9:138. doi: 10.3389/fncom.2015.00138. eCollection 2015. Review. Erratum in: Front Comput Neurosci. 2016;10:4.


Binding enthalpy calculations for a neutral host-guest pair yield widely divergent salt effects across water models.

Gao K, Yin J, Henriksen NM, Fenley AT, Gilson MK.

J Chem Theory Comput. 2015 Oct 13;11(10):4555-64. doi: 10.1021/acs.jctc.5b00676. Epub 2015 Sep 18.


Computational Calorimetry: High-Precision Calculation of Host-Guest Binding Thermodynamics.

Henriksen NM, Fenley AT, Gilson MK.

J Chem Theory Comput. 2015 Sep 8;11(9):4377-94.


BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology.

Gilson MK, Liu T, Baitaluk M, Nicola G, Hwang L, Chong J.

Nucleic Acids Res. 2016 Jan 4;44(D1):D1045-53. doi: 10.1093/nar/gkv1072. Epub 2015 Oct 19.


Connecting proteins with drug-like compounds: Open source drug discovery workflows with BindingDB and KNIME.

Nicola G, Berthold MR, Hedrick MP, Gilson MK.

Database (Oxford). 2015 Sep 16;2015. pii: bav087. doi: 10.1093/database/bav087. Print 2015.


Prevalence of Renal Impairment in Patients With Rheumatoid Arthritis: Results From a Cross-Sectional Multicenter Study.

Couderc M, Tatar Z, Pereira B, Tiple A, Gilson M, Fautrel B, Pouplin S, Dernis E, Gossec L, Gaujoux-Viala C, Soubrier M, Dougados M.

Arthritis Care Res (Hoboken). 2016 May;68(5):638-44. doi: 10.1002/acr.22713.

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