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| 213. | N. Eswar, A. Sali.
Protein Structure Modeling.
In: Integrating Crystallography in Drug Discovery.
2008. |
| 212. | M.F. Kim, A. Sali, V. Dötsch, M.L. Reese.
Efficient computational identification and docking of macromolecular interfaces using ambiguous NMR constraints.
submitted,
|
| 211. | U. Pieper, R. Chiang, J.J. Seffernick, S.D. Brown, M.E. Glasner, N. Eswar, M. Sauder, S.K. Burley, S. Almo, J.A. Gerlt, F. Raushel, B.K. Shoichet, M.P. Jacobson, P.P. Babbitt, A. Sali.
Target Selection and Annotation for the Structural Genomics of Enolases and Amidohydrolases.
submitted,
|
| 210. | M.S. Madhusudhan, M.A. Marti-Renom, N. Eswar, A. Sali.
Alignment of multiple protein structures based on sequence and structure features.
submitted,
|
| 209. | C.M. Anderson, D. Korkin, D.L. Smith, S. Makovets, J.J. Seidel, A. Sali, E.H. Blackburn.
Tel2 mediates activation and localization of ATM/Tel1 kinase to a double-strand break.
Genes Dev. 22,
854-859, 2008. |
| 208. | K. Lasker, M. Topf, A. Sali, H. Wolfson.
Fitting multiple components into a cryoEM map of their assembly.
submitted,
|
| 207. | F. Förster, B. Webb, K.A. Krukenberg, H. Tsuruta, D.A. Agard, A. Sali.
Integration of small angle X-ray scattering and protein structure modeling.
submitted,
|
| 206. | L. Kelly, U. Pieper, F. Hays, N. Eswar, D. Kroetz, K. Giacomini, R. Stroud, A. Sali.
A taxonomic profile of the membrane protein universe .
submitted,
|
| 205. | D. Eramian, N. Eswar, M-Y. Shen, A. Sali.
Can the accuracy of comparative protein structure models be predicted?.
submitted,
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| 204. | K.A. Krukenberg, F. Förster, L.M. Rice, A. Sali, D.A. Agard.
A novel conformation of E. coli Hsp90 in solution: insights into the conformational dynamics of Hsp90.
Structure 16,
755-765, 2008. |
| 203. | R. Karchin, M. Agarwal, Sali, F.A. Couch, M.S. Beattie.
Classifying Variants of Undetermined Significance in BRCA2 with Protein Likelihood Ratios.
Cancer Informatics 4,
203-216, 2008. |
| 202. | F. Agüero, B. Al-Lazikani, M. Berriman, F.S. Buckner, B. Campbell, S. Carmona, FengChen, G.J. Crowther, C. Hertz-Fowler, A.L. Hopkins, G. McAllister, S. Nwaka, J. Overington, A. Pain, G.V. Paolini, U. Pieper, S.A. Ralph, A. Riechers, D.S. Roos, A. Sali, D. Shanmugam, T. Suzuki, W.C. VanVoorhis, C.L. Verlinde.
Genomic-scale Prioritization of Drug Targets: TDRtargets.org.
submitted,
|
| 201. | J. Espadaler, N. Eswar, E. Querol, F.X. Aviles, A. Sali, M. Marti-Renom, B. Oliva.
Prediction of enzyme function by combining sequence similarity and protein interactions.
BMC Bioinformatics 9,
249, 2008. |
| 200. | F. Alber, S. Dokudovskaya, L. Veenhoff, W. Zhang, J. Kipper, D. Devos, A. Suprapto, O. Karni, R. Williams, B.T. Chait, M.P Rout, A. Sali.
Determining the architectures of macromolecular assemblies.
Nature 450,
683-694, 2007. NPC
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| 199. | F. Alber, S. Dokudovskaya, L. Veenhoff, W. Zhang, J. Kipper, D. Devos, A. Suprapto, O. Karni, R. Williams, B.T. Chait, A. Sali, M.P. Rout.
The Molecular Architecture of the Nuclear Pore Complex.
Nature 450,
695-701, 2007. NPC
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| 198. | C.V. Robinson, A. Sali, W. Baumeister.
Molecular sociology of the cell.
Nature 450,
973-982, 2007.Nature
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| 197. | M. Topf, K. Lasker, B. Webb, H. Wolfson, W. Chiu, A. Sali.
Protein Structure Fitting and Refinement Guided by cryoEM Density.
Structure 16,
295-307, 2008.
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| 196. | F. Alber, F. Förster, D. Korkin, M. Topf, A. Sali.
Integrating Diverse Data for Structure Determination of Macromolecular Assemblies.
Annual Review of Biochemistry 77,
11.1–11.35, 2008. |
| 195. | N. Eswar, B. Webb, M.A. Marti-Renom, M.S. Madhusudhan, D. Eramian, M-Y. Shen, U. Pieper, A. Sali.
Comparative Protein Structure Modeling Using MODELLER.
Ed: Coligan JE, Dunn BM, Speicher DW, Wingfield PT. Current Protocols in Protein Science Unit 2.9 1-31,
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| 194. | P. Chandramouli, M. Topf, J.F. Ménétret, N. Eswar, R.R. Gutell, A. Sali, C.W. Akey.
Structure of the Mammalian 80S Ribosome at 8.7Ĺ Resolution .
Structure 16,
535-548, 2008.
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| 193. | A. Sali, C.D. Lima, M. Kostic.
Structural genomics.
Structure 15,
1341, 2007.
|
| 192. | F. Melo, A. Sali.
Fold Assessment for Comparative Protein Structure Modelling.
Protein Science 16,
2412-2426, 2007.
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| 191. | F. Alber, B.T. Chait, M.P. Rout, A. Sali.
Integrative Structure Determination of Protein Assemblies by Satisfaction of Spatial Restraints.
In: Protein-protein interactions and networks: identification, characterization and prediction.
Ed: Panchenko, A. and Przytycka, T. Cambridge University Press, Cambridge, UK.
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| 190. | S.K. Burley, S.C. Almo, J.B. Bonanno, M.R Chance, S. Emtage, A. Fiser, A. Sali, J.M. Sauder, S. Swaminathan.
Structural Genomics of Protein Superfamilies.
Structural Bioinformatics, 2nd Edition in press,
|
| 189. | S.C. Almo, J.B. Bonanno, J.M. Sauder, S. Emtage, T.P. Dilorenzo, V. Malashkevich, S.R. Wasserman, S. Swaminathan, S. Eswaramoorthy, R. Agarwal, D. Kumaran, M. Madegowda, S. Ragumani, Y. Patskovsky, J. Alvarado, U.A. Ramagopal, J. Faber-Barata, M.R. Chance, A. Sali, A. Fiser, Z.Y. Zhang, D.S. Lawrence, S.K. Burley.
Structural genomics of protein phosphatases.
Journal of Structural and Functional Genomics 8,
121-140, 2007.
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| 188. | C.R. Booth, A.S. Meyer, Y. Cong, M. Topf, A. Sali, S.J. Ludtke, W. Chiu, J. Frydman.
Mechanism of lid closure in the eukaryotic chaperonin TRiC/CCT.
Nature Structural and Molecular Biology in press,
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| 187. | F.P. Davis, D.T. Barkan, N. Eswar, J.H. McKerrow, A. Sali.
Host-Pathogen Protein Interactions Predicted by Comparative Modeling.
Protein Science 16,
2585-2596, 2007.
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| 186. | M.A. Marti-Renom, U. Pieper, M.S Madhusudhan, A. Rossi, N. Eswar, F.P. Davis, F. Al-Shahrour, J. Dopazo, A. Sali.
DBAli tools: mining the protein structure space.
Nucleic Acids Research 35,
W393-W397, 2007.
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| 185. | Y. Cong, M. Topf, A. Sali, P. Matsudaira, M.T. Dougherty, W. Chiu, M.F. Schmid.
Crystallographic Conformers of Actin in a Biologically Active Bundle of Filaments.
J. Mol. Biol. 375,
331-6, 2008.
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| 184. | M.A. Marti-Renom, A. Rossi, F. Al-Shahrour, F.P. Davis, U. Pieper, J. Dopazo, A. Sali.
The AnnoLite and AnnoLyze Programs for Comparative Annotation of Protein Structures.
BMC Bioinformatics 8 Suppl 4,
2007.
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| 183. | R. Aragues, A. Sali, M.A. Marti-Renom, B. Oliva.
Characterization of protein network hubs by inferring interacting motifs from binary protein interactions.
PLoS Comp. Biol. 3,
1761-1771, 2007. |
| 182. | T. Schwede, A. Sali, N. Eswar, M.C. Peitsch.
Protein Structure Modeling.
In: Computational Structure Biology.
Ed: T. Schwede, M.C. Peitsch, World Scientific Publishing Ltd. |
| 181. | N. Eswar, D.Eramian , B.Webb , M.Shen , A. Sali.
Protein Structure Modeling With MODELLER.
In: Methods in Molecular Biology: Structural Proteomics - High-throughput Methods.
Ed: Kobe B, Guss M, Huber T. 2007.
|
| 180. | K. Bajaj, M.S. Madhusudhan, B.V. Adkar, P. Chakrabarti, C. Ramakrishnan, A. Sali, R. Varadarajan.
Stereochemical criteria for prediction of the effects of Proline mutations on protein stability.
PLoS Comp. Biol. 3,
e241, 2007.
|
| 179. | N. Soranzo, L. Kelly, L. Martinian, M-W. Burley, M. Thom, A. Sali, D.L. Kroetz, D.B. Goldstein, S.M. Sisodiya.
Lack of support for a role for RLIP76 (RALBP1) in response to treatment or predisposition to epilepsy.
Epilepsia Apr;48(4):674-83.,
2007.
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| 178. | E. Feyfant, A. Fiser, A. Sali.
Modeling mutations in protein structures.
Protein Science 16,
2030-2041, 2007.
|
| 177. | S.X. Wang, K.C. Pandey, J. Scharfstein, J. Whisstock, R.K. Huang, J. Jacobelli, R.J. Fletterick, P.J. Rosenthal, M. Abrahamson, A. Rossi, A. Sali, J.H. McKerrow.
The structure of chagasin in complex with a cysteine protease clarifies the binding mode and evolution of a new inhibitor family.
Structure 15,
535-543, 2007.
|
| 176. | M.A. Carvalho, S.M. Marsillac, R. Karchin, S. Manoukian, S. Grist, R. Swaby, T.P. Urmenyi, E. Rondinelli, R. Silva, L. Gayol, L. Baumbach, R. Sutphen, J.L. Pickard, K.L. Nathanson, A. Sali, D. Goldgar, F.J. Couch, P. Radice, A.N.A. Monteiro.
Determination of cancer risk associated with germline BRCA1 missense variants by functional analysis.
Cancer Research 15;67(4),
1494-501, 2007.
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| 175. | N. Eswar, A. Sali.
Comparative Modeling of Drug Target Proteins.
In: Volume 4 Computer-Assisted Drug Design, Comprehensive Medicinal Chemistry II.
Ed: J. Taylor, D. Triggle and J.S. Mason. Elsevier Ltd, Oxford, UK,
215-236, 2007.
|
| 174. | L. Kelly, R. Karchin, A. Sali.
Protein interactions and disease phenotypes in the ABC transporter superfamily.
Pacific Symposium on Biocomputing 12,
51-63, 2007.
|
| 173. | R. Karchin, A.N.A. Monteiro, S.V. Tavtigian, M.A. Carvalho, A. Sali.
Functional impact of missense variants in BRCA1 predicted by supervised learning.
PLoS Computational Biology 3(2): e26,
2007.
|
| 172. | M-Y. Shen, A. Sali.
Statistical Potential for Assessment and Prediction of Protein Structures.
Protein Science 15,
2507 - 2524, 2006.
|
| 171. | A. Colubri, A. Jha, M. Shen, A. Sali, R.S. Berry, T. Sosnick, K.F. Freed.
Minimalist representations and the importance of nearest neighbor effects in protein folding simulations.
Journal of Molecular Biology 363(4),
835-57, 2006.
|
| 170. | H.M. Berman, S.K. Burley, W. Chiu, A. Sali, A. Adzhubei, P.E. Bourne, S.H. Bryant, J. Roland, L. Dunbrack, K. Fidelis, J. Frank, A. Godzik, K. Henrick, A. Joachimiak, B. Heymann, D. Jones, J.L. Markley, J. Moult, G.T. Montelione, C. Orengo, M.G. Rossmann, B. Rost, H. Saibil, T. Schwede, D.M. Standley, J.D. Westbrook.
Outcome of a workshop on archiving structural models of biological macromolecules.
Structure 14,
1211-1217, 2006.
|
| 169. | T.D. Nguyen, J.M. Gow, L.W. Chinn, L. Kelly, H. Jeong, C.C. Huang, D. Stryke, M. Kawamoto, S.J. Johns, E. Carlson, T. Taylor, T.E. Ferrin, A. Sali, K.M. Giacomini, D.L. Kroetz.
PharmGKB Submission Update: IV. PMT Submissions of Genetic Variations in ATP-Binding Cassette Transporters to the PharmGKB Network.
Pharmacological Reviews 58,
1-2, 2006.
|
| 168. | V.D. Winn, R. Haimov-Kochman, A.C. Paquet, Y.J. Yang, M.S. Madhusudhan, M. Gormley, V. Feng, D.A. Bernlohr, S. McDonagh, L. Pereira, A. Sali, S.J. Fisher.
Gene Expression Profiling of the Human Maternal-Fetal Interface Over Gestation Reveals Dramatic Changes between Midgestation and Term.
Endocrinology 148,
1059-79, 2007.
|
| 167. | F.P. Davis, H. Braberg, M.Y. Shen, U. Pieper, A. Sali, M.S. Madhusudhan.
Protein complex compositions predicted by structural similarity.
Nucleic Acids Research 34,
2943-2952, 2006.
|
| 166. | A. Rossi, M.A. Marti-Renom, A. Sali.
Localization of binding sites in protein structures by optimization of a composite scoring function.
Protein Science 15(10),
2366-80, 2006.
|
| 165. | N. Eswar, M.A. Marti-Renom, B. Webb, M.S. Madhusudhan, D. Eramian, M.Y. Shen, U. Pieper, A. Sali.
Comparative Protein Structure Modeling using MODELLER.
Ed: Baxevanis AD, Petsko GA, Stein LD, Stormo GD. Current Protocols in Bioinformatics John Wiley & Sons, Inc., Hoboken, NJ,
Supplement 15,
5.6.1-5.6.30, 2006.
|
| 164. | S. Dokudovskaya, R. Williams, D. Devos, A. Sali, B.T. Chait, M. Rout.
Protease Accessibility Laddering (PAL) - A Proteomic Tool for Probing Protein Structure.
Structure 14,
653-660, 2006.
|
| 163. | D. Eramian, M.Y. Shen, D. Devos, F. Melo, A. Sali, M.A. Marti-Renom.
A composite score for predicting errors in protein structure models.
Protein Science 15,
1653-66, 2006.
|
| 162. | D. Korkin, F.P. Davis, F. Alber, T. Luong, M. Shen, V. Lucic, M.B. Kennedy, A. Sali.
Structural Modeling of Protein Interactions by Analogy: Application to PSD-95.
PLoS Computational Biology 2(11); e153,
1365-1376, 2006.
|
| 161. | M. Topf, M.L. Baker, M.A. Marti-Renom, W. Chiu, A. Sali.
Refinement of Protein Structures by Iterative Comparative Modeling and CryoEM Density Fitting.
Journal of Molecular Biology 357,
1655-1668, 2006.
|
| 160. | U. Pieper, N. Eswar, F.P. Davis, H. Braberg, M.S. Madhusudhan, A. Rossi, M. Marti-Renom, R. Karchin, B.M. Webb, D. Eramian, M.Y. Shen, L. Kelly, F. Melo, A. Sali.
MODBASE, a database of annotated comparative protein structure models and associated resources.
Nucleic Acids Research 34,
D291-D295, 2006.
|
| 159. | C. Lima, J. Puglisi, A. Sali, L. Szewczak.
Editorial.
Structure 14,
801, 2006.
|
| 158. | S.A. McMahon, J.L. Miller, J.A. Lawton, D.E. Kerkow, A. Hodes, M.A. Marti-Renom, S. Doulatov, E. Narayanan, A. Sali, J.F. Miller, P. Ghosh.
The C-type lectin fold as an evolutionary solution for massive sequence variation.
Nature Structural & Molecular Biology 12,
886-892, 2005.
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| 157. | M. Topf, A. Sali.
Combining Electron Microscopy and Comparative Protein Structure Modeling.
Current Opinion in Structural Biology 15,
578-585, 2005.
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| 156. | J.B. Bonanno, S.C. Almo, A. Bresnick, M.R. Chance, A. Fiser, S. Swaminathan, J. Jiang, F.W. Studier, L. Shapiro, C. Lima, T. Gaasterland, A. Sali, K. Bain, I. Feil, X. Gao, D. Lorimer, A. Ramos, M. Sauder, S. Wasserman, S. Emtage, K. DAmico, S.K. Burley.
New York-Structural GenomiX Research Consortium (NYSGXRC): a large scale center for the protein structure initiative.
Journal of Structural and Functional Genomics 6,
225-232, 2005.
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| 155. | Min-yi Shen, F.P. Davis, A. Sali.
The optimal size of a globular protein domain: a simple sphere-packing model.
Chemical Physics Letters 405,
224-228, 2005.
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| 154. | M.S. Madhusudhan, M.A. Marti-Renom, R. Sanchez, A. Sali.
Variable gap penalty for protein sequence-structure alignment.
Protein Engineering Design & Selection 19,
129-133, 2006.
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| 153. | D. Devos, S. Dokudovskaya, R. Williams, F. Alber, N. Eswar, B.T. Chait, M.P. Rout, A. Sali.
Simple fold composition and modular architecture of the nuclear pore complex.
PNAS 14,
2172-2177, 2006.
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| 152. | D. Korkin, F.P. Davis, A. Sali.
Localization of protein-binding sites within families of proteins.
Protein Science 14,
2350-2360, 2005.
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| 151. | A. Sali, W. Chiu.
Macromolecular Assemblies Highlighted.
Structure 13,
339-341, 2005.
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| 150. | J. Dvorak, M. Delcroix, A. Rossi, V. Vopalensky, M. Pospisek, M. Sedinova, L. Mikes, M. Sajid, A. Sali, J.H. Mckerrow, P. Horak, C.R. Caffrey.
Multiple cathepsin B isoforms in schistosomula of Trichobilharzia regenti: Identification, characterization and putative role in migration and nutrition.
International Journal of Parasitology 35,
895-910, 2005.
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