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201. Amaro, Rommie E., Swift, Robert V., Votapka, Lane, Li, Wilfred W., Walker, Ross C., Bush, Robin M., (2011), "Mechanism of 150-cavity formation in influenza neuraminidase.", Nature communications, 2: pg: 388, 2041-1723 (Electronic) 2041-1723 (Linking) 2041-1, (DOI: 10.1038/ncomms1390).
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202. Alexov, Emil, Mehler, Ernest L., Baker, Nathan, Baptista, Antnio M., Huang, Yong, Milletti, Francesca, Nielsen, Jens Erik, Farrell, Damien, Carstensen, Tommy, Olsson, Mats H. M., Shen, Jana K., Warwicker, Jim, Williams, Sarah, Word, J. Michael, (2011), "Progress in the prediction of pKa values in proteins.", Proteins, 79, 12: pg: 3260--75, 1097-0134 (Electronic)$\backslash$r0887-3585 (Link, (DOI: 10.1002/prot.23189).
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203. Aguado-Sierra, Jazmin, Krishnamurthy, Adarsh, Villongco, Christopher, Chuang, Joyce, Howard, Elliot, Gonzales, Matthew J., Omens, Jeff, Krummen, David E., Narayan, Sanjiv, Kerckhoffs, Roy C. P., McCulloch, Andrew D., (2011), "Patient-specific modeling of dyssynchronous heart failure: a case study.", Progress in biophysics and molecular biology, 107, 1: pg: 147--55, 1873-1732 (Electronic)$\backslash$r0079-6107 (Link, (DOI: 10.1016/j.pbiomolbio.2011.06.014).
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204. Williams, Sarah L., de Oliveira, Csar Augusto F., McCammon, J. Andrew, (2010), "Coupling Constant pH Molecular Dynamics with Accelerated Molecular Dynamics.", Journal of chemical theory and computation, 6, 2: pg: 560--568, 1549-9626, (DOI: 10.1021/ct9005294).
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205. West, John B., Fu, Zhenxing, Deerinck, Thomas J., Mackey, Mason R., Obayashi, James T., Ellisman, Mark H., (2010), "Structure-function studies of blood and air capillaries in chicken lung using 3D electron microscopy.", Respiratory physiology \& neurobiology, 170, 2: pg: 202--9, 1878-1519, (DOI: 10.1016/j.resp.2009.12.010).
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206. Wereszczynski, Jeff, McCammon, J. Andrew, (2010), "Using Selectively Applied Accelerated Molecular Dynamics to Enhance Free Energy Calculations", Journal of Chemical Theory and Computation, 6, 11: pg: 3285--3292, 1549-9618, (DOI: 10.1021/ct100322t).
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207. Tainer, John A., McCammon, J. Andrew, Ivanov, Ivaylo, (2010), "Recognition of the ring-opened state of proliferating cell nuclear antigen by replication factor C promotes eukaryotic clamp-loading.", Journal of the American Chemical Society, 132, 21: pg: 7372--8, 1520-5126, (DOI: 10.1021/ja100365x).
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208. Sung, Jeffrey C. and, (2010), "Role of secondary sialic acid binding sites in influenza N1 neuraminidase.", Journal of the American Chemical Society, 132, 9: pg: 2883--5, 1520-5126, (DOI: 10.1021/ja9073672).
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209. Sivendran, Sharmila, Jones, Victoria, Sun, Dianqing, Wang, Yi, Grzegorzewicz, Anna E., Scherman, Michael S., Napper, Andrew D., McCammon, J. Andrew, Lee, Richard E., Diamond, Scott L., McNeil, Michael, (2010), "Identification of triazinoindol-benzimidazolones as nanomolar inhibitors of the Mycobacterium tuberculosis enzyme TDP-6-deoxy-d-xylo-4-hexopyranosid-4-ulose 3,5-epimerase (RmlC).", Bioorganic \& medicinal chemistry, 18, 2: pg: 896--908, 1464-3391, (DOI: 10.1016/j.bmc.2009.11.033).
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210. Sierecki, Emma, Sinko, William, McCammon, J. Andrew, Newton, Alexandra C., (2010), "Discovery of small molecule inhibitors of the PH domain leucine-rich repeat protein phosphatase (PHLPP) by chemical and virtual screening.", Journal of medicinal chemistry, 53, 19: pg: 6899--911, 0022-2623 1520-4804, (DOI: 10.1021/jm100331d).
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211. Setny, Piotr, Baron, Riccardo, McCammon, J. Andrew, (2010), "How Can Hydrophobic Association Be Enthalpy Driven?", Journal of Chemical Theory and Computation, 6, 9: pg: 2866--2871, 1549-9618, (DOI: 10.1021/ct1003077).
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212. Rouffet, Matthieu, de Oliveira, Csar Augusto F., Udi, Yael, Agrawal, Arpita, Sagi, Irit, McCammon, J. Andrew, Cohen, Seth M., (2010), "From sensors to silencers: quinoline- and benzimidazole-sulfonamides as inhibitors for zinc proteases.", Journal of the American Chemical Society, 132, 24: pg: 8232--3, 1520-5126, (DOI: 10.1021/ja101088j).
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213. Ren, Jingyuan, Xie, Lei, Li, Wilfred W., Bourne, Philip E., (2010), "SMAP-WS: a parallel web service for structural proteome-wide ligand-binding site comparison.", Nucleic acids research, 38, Web Server issue: pg: W441--4, 1362-4962 (Electronic)$\backslash$r0305-1048 (Link, (DOI: 10.1093/nar/gkq400).
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214. Ren, Jingyuan, Williams, Nadya, Clementi, Luca, Krishnan, Sriram, Li, Wilfred W., (2010), "Opal web services for biomedical applications.", Nucleic acids research, 38, Web Server issue: pg: W724--31, 1362-4962 (Linking) 1362-4962, (DOI: 10.1093/nar/gkq503).
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215. Qin, Sanbo, Minh, David D. L., McCammon, J. Andrew, Zhou, Huan-Xiang, (2010), "Method to Predict Crowding Effects by Postprocessing Molecular Dynamics Trajectories: Application to the Flap Dynamics of HIV-1 Protease.", The journal of physical chemistry letters, 1, 1: pg: 107--110, 1948-7185 (Print)$\backslash$r1948-7185 (Linking) (DOI: 10.1021/jz900023w).
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216. Perryman, Alexander L., Zhang, Qing, Soutter, Holly H., Rosenfeld, Robin, McRee, Duncan E., Olson, Arthur J., Elder, John E., Stout, C. David, (2010), "Fragment-based screen against HIV protease.", Chemical biology \& drug design, 75, 3: pg: 257--68, 1747-0285, (DOI: 10.1111/j.1747-0285.2009.00943.x).
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217. Perryman, Alex L., Forli, Stefano, Morris, Garrett M., Burt, Catherine, Cheng, Yuhui, Palmer, Michael J., Whitby, Kevin, McCammon, J. Andrew, Phillips, Chris, Olson, Arthur J., (2010), "A dynamic model of HIV integrase inhibition and drug resistance.", Journal of molecular biology, 397, 2: pg: 600--15, 1089-8638, (DOI: 10.1016/j.jmb.2010.01.033).
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218. Perkins, Guy A., Tjong, Jonathan, Brown, Joshua M., Poquiz, Patrick H., Scott, Raymond T., Kolson, Douglas R., Ellisman, Mark H., Spirou, George A., (2010), "The micro-architecture of mitochondria at active zones: electron tomography reveals novel anchoring scaffolds and cristae structured for high-rate metabolism.", The Journal of neuroscience : the official journal of the Society for Neuroscience, 30, 3: pg: 1015--26, 1529-2401, (DOI: 10.1523/JNEUROSCI.1517-09.2010).
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219. Peng, Lili X., Ivetac, Anthony, Chaudhari, Akshay S., Van, Sang, Zhao, Gang, Yu, Lei, Howell, Stephen B., McCammon, J. Andrew, Gough, David A., (2010), "Characterization of a clinical polymer-drug conjugate using multiscale modeling.", Biopolymers, 93, 11: pg: 936--51, 0006-3525, (DOI: 10.1002/bip.21474).
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220. Markwick, Phineus R. L., Cervantes, Carla F., Abel, Barrett L., Komives, Elizabeth A., Blackledge, Martin, McCammon, J. Andrew, (2010), "Enhanced conformational space sampling improves the prediction of chemical shifts in proteins.", Journal of the American Chemical Society, 132, 4: pg: 1220--1, 1520-5126, (DOI: 10.1021/ja9093692).
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221. Lukman, Suryani, Grant, Barry J., Gorfe, Alemayehu A., Grant, Guy H., McCammon, J. Andrew, (2010), "The distinct conformational dynamics of K-Ras and H-Ras A59G.", PLoS computational biology, 6, 9: pg: e1000922, 1553-7358, (DOI: 10.1371/journal.pcbi.1000922).
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222. Lu, Benzhuo, McCammon, J. Andrew, (2010), "Kinetics of diffusion-controlled enzymatic reactions with charged substrates.", PMC biophysics, 3, 1: pg: 1, 1757-5036, (DOI: 10.1186/1757-5036-3-1).
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223. Lu, Benzhuo, Holst, Michael J., McCammon, J. Andrew, Zhou, Y. C., (2010), "Poisson-Nernst-Planck Equations for Simulating Biomolecular Diffusion-Reaction Processes I: Finite Element Solutions.", Journal of computational physics, 229, 19: pg: 6979--6994, 0021-9991, (DOI: 10.1016/j.jcp.2010.05.035).
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224. Lu, Benzhuo, Cheng, Xiaolin, Huang, Jingfang, McCammon, J. Andrew, (2010), "AFMPB: An Adaptive Fast Multipole Poisson-Boltzmann Solver for Calculating Electrostatics in Biomolecular Systems.", Computer physics communications, 181, 6: pg: 1150--1160, 0010-4655, (DOI: 10.1016/j.cpc.2010.02.015).
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225. Li, Bo, Lu, Benzhuo, Wang, Zhongming, McCammon, J. Andrew, (2010), "Solutions to a reduced Poisson-Nernst-Planck system and determination of reaction rates.", Physica A, 389, 7: pg: 1329--1345, 0378-4371, (DOI: 10.1016/j.physa.2009.12.024).
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226. Lawrenz, Morgan, Wereszczynski, Jeff, Amaro, Rommie, Walker, Ross, Roitberg, Adrian, McCammon, J. Andrew, (2010), "Impact of calcium on N1 influenza neuraminidase dynamics and binding free energy.", Proteins, 78, 11: pg: 2523--32, 1097-0134 (Electronic)$\backslash$r0887-3585 (Link, (DOI: 10.1002/prot.22761).
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227. Kerckhoffs, Roy C. P., Omens, Jeffrey H., McCulloch, Andrew D., Mulligan, Lawrence J., (2010), "Ventricular dilation and electrical dyssynchrony synergistically increase regional mechanical nonuniformity but not mechanical dyssynchrony: a computational model.", Circulation. Heart failure, 3, 4: pg: 528--36, 1941-3297, (DOI: 10.1161/CIRCHEARTFAILURE.109.862144).
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228. Ivetac, Anthony, McCammon, J. Andrew, (2010), "Mapping the druggable allosteric space of G-protein coupled receptors: a fragment-based molecular dynamics approach.", Chemical biology \& drug design, 76, 3: pg: 201--17, 1747-0285, (DOI: 10.1111/j.1747-0285.2010.01012.x).
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229. Ishizuka, Ryosuke, Huber, Gary A., McCammon, J. Andrew, (2010), "Solvation Effect on the Conformations of Alanine Dipeptide: Integral Equation Approach.", The journal of physical chemistry letters, 1, 15: pg: 2279--2283, 1948-7185, (DOI: 10.1021/jz100665c).
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230. Huber, Gary A., McCammon, J. Andrew, (2010), "Browndye: A Software Package for Brownian Dynamics.", Computer physics communications, 181, 11: pg: 1896--1905, 0010-4655, (DOI: 10.1016/j.cpc.2010.07.022).
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231. Holst, Michael, Tsogtgerel, Gantumur, Zhu, Yunrong, (2010), "Local Convergence of Adaptive Methods for Nonlinear Partial Differential Equations", Convergence, 74, Pde 2: pg: viii+80
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232. Grant, Barry J., McCammon, J. Andrew, Gorfe, Alemayehu A., (2010), "Conformational selection in G-proteins: lessons from Ras and Rho.", Biophysical journal, 99, 11: pg: L87--9, 1542-0086 (Electronic)$\backslash$r0006-3495 (Link, (DOI: 10.1016/j.bpj.2010.10.020).
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233. Grant, Barry J., Gorfe, Alemayehu a, McCammon, J. Andrew, (2010), "Large conformational changes in proteins: signaling and other functions.", Current opinion in structural biology, 20, 2: pg: 142--7, 1879-033X, (DOI: 10.1016/j.sbi.2009.12.004).
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234. Fitzpatrick, Kathleen, Skasko, Mark, Deerinck, Thomas J., Crum, John, Ellisman, Mark H., Guatelli, John, (2010), "Direct restriction of virus release and incorporation of the interferon-induced protein BST-2 into HIV-1 particles.", PLoS pathogens, 6, 3: pg: e1000701, 1553-7374 (Electronic)$\backslash$r1553-7366 (Link, (DOI: 10.1371/journal.ppat.1000701).
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235. Feala, Jacob D., Cortes, Jorge, Duxbury, Phillip M., Piermarocchi, Carlo, McCulloch, Andrew D., Paternostro, Giovanni, (2010), "Systems approaches and algorithms for discovery of combinatorial therapies.", Wiley interdisciplinary reviews. Systems biology and medicine, 2, 2: pg: 181--93, 1939-005X, (DOI: 10.1002/wsbm.51).
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236. Durrant, Jacob D., Urbaniak, Michael D., Ferguson, Michael A. J., McCammon, J. Andrew, (2010), "Computer-aided identification of Trypanosoma brucei uridine diphosphate galactose 4'-epimerase inhibitors: toward the development of novel therapies for African sleeping sickness.", Journal of medicinal chemistry, 53, 13: pg: 5025--32, 0022-2623 1520-4804, (DOI: 10.1021/jm100456a).
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237. Durrant, Jacob D., McCammon, J. Andrew, (2010), "Computer-aided drug-discovery techniques that account for receptor flexibility.", Current opinion in pharmacology, 10, 6: pg: 770--4, 1471-4973, (DOI: 10.1016/j.coph.2010.09.001).
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238. Durrant, Jacob D., McCammon, J. Andrew, (2010), "NNScore: A Neural-Network-Based Scoring Function for the Characterization of Protein−Ligand Complexes", Journal of Chemical Information and Modeling, 50, 10: pg: 1865--1871, 1549-9596, (DOI: 10.1021/ci100244v).
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239. Durrant, Jacob D., McCammon, J. Andrew, (2010), "Potential drug-like inhibitors of Group 1 influenza neuraminidase identified through computer-aided drug design.", Computational biology and chemistry, 34, 2: pg: 97--105, 1476-928X, (DOI: 10.1016/j.compbiolchem.2010.03.005).
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240. Durrant, Jacob D., Kernen, Henrik, Wilson, Benjamin A., McCammon, J. Andrew, (2010), "Computational identification of uncharacterized cruzain binding sites.", PLoS neglected tropical diseases, 4, 5: pg: e676, 1935-2735 (Electronic)$\backslash$n1935-2727 (Link, (DOI: 10.1371/journal.pntd.0000676).
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241. Durrant, Jacob D., Amaro, Rommie E., Xie, Lei, Urbaniak, Michael D., Ferguson, Michael A. J., Haapalainen, Antti, Chen, Zhijun and, (2010), "A multidimensional strategy to detect polypharmacological targets in the absence of structural and sequence homology.", PLoS computational biology, 6, 1: pg: e1000648, 1553-7358 (Electronic)$\backslash$r1553-734X (Link, (DOI: 10.1371/journal.pcbi.1000648).
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242. Cheng, Yuhui, Yu, Zeyun, Hoshijima, Masahiko, Holst, Michael J., McCulloch, Andrew D., McCammon, J. Andrew, Michailova, Anushka P., (2010), "Numerical analysis of Ca2+ signaling in rat ventricular myocytes with realistic transverse-axial tubular geometry and inhibited sarcoplasmic reticulum.", PLoS computational biology, 6, 10: pg: e1000972, 1553-7358, (DOI: 10.1371/journal.pcbi.1000972).
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243. Chen, Zhan, Baker, Nathan A., Wei, G. W., (2010), "Differential geometry based solvation model I: Eulerian formulation.", Journal of computational physics, 229, 22: pg: 8231--8258, 0021-9991, (DOI: 10.1016/j.jcp.2010.06.036).
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244. Campbell, Stuart G., Lionetti, Fred V., Campbell, Kenneth S., McCulloch, Andrew D., (2010), "Coupling of adjacent tropomyosins enhances cross-bridge-mediated cooperative activation in a markov model of the cardiac thin filament.", Biophysical journal, 98, 10: pg: 2254--64, 1542-0086 (Electronic)$\backslash$r0006-3495 (Link, (DOI: 10.1016/j.bpj.2010.02.010).
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245. Callenberg, Keith M., Choudhary, Om P., de Forest, Gabriel L., Gohara, David W., Baker, Nathan A., Grabe, Michael, (2010), "APBSmem: a graphical interface for electrostatic calculations at the membrane.", PloS one, 5, 9: 1932-6203, (DOI: 10.1371/journal.pone.0012722).
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246. Bauler, Patricia, Huber, Gary, Leyh, Thomas, McCammon, J. Andrew, (2010), "Channeling by Proximity: The Catalytic Advantages of Active Site Colocalization Using Brownian Dynamics.", The journal of physical chemistry letters, 1, 9: pg: 1332--1335, 1948-7185 (Electronic)$\backslash$r1948-7185 (Link, (DOI: 10.1021/jz1002007).
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247. Baron, Riccardo, Setny, Piotr, McCammon, J. Andrew, (2010), "Water in cavity-ligand recognition.", Journal of the American Chemical Society, 132, 34: pg: 12091--7, 1520-5126, (DOI: 10.1021/ja1050082).
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248. Ambrus, Gza, Whitby, Landon R., Singer, Eric L., Trott, Oleg, Choi, Euna, Olson, Arthur J., Boger, Dale L., Gerace, Larry, (2010), "Small molecule peptidomimetic inhibitors of importin $\alpha$/$\beta$ mediated nuclear transport.", Bioorganic \& medicinal chemistry, 18, 21: pg: 7611--20, 1858784913 1464-3391, (DOI: 10.1016/j.bmc.2010.08.038).
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249. Amaro, Rommie E., Li, Wilfred W., (2010), "Emerging methods for ensemble-based virtual screening.", Current topics in medicinal chemistry, 10, 1: pg: 3--13, 1873-4294
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250. Aksoylu, Burak, Holst, Michael, (2010), "An Odyssey into Local Refinement and Multilevel Preconditioning Ii: Stabilizing Hierarchical Basis Methods", Preprint: pg: 1--22
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