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For: Baker D, Sali A. Protein structure prediction and structural genomics. Science 2001;294:93-6. [PMID: 11588250 DOI: 10.1126/science.1065659] [Citation(s) in RCA: 1030] [Impact Index Per Article: 42.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Number Cited by Other Article(s)
201
Huang YT, Chen JM, Ho BC, Wu ZY, Kuo RC, Liu PY. Genome Sequencing and Comparative Analysis of Stenotrophomonas acidaminiphila Reveal Evolutionary Insights Into Sulfamethoxazole Resistance. Front Microbiol 2018;9:1013. [PMID: 29867899 PMCID: PMC5966563 DOI: 10.3389/fmicb.2018.01013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 04/30/2018] [Indexed: 11/23/2022]  Open
202
Setiawan D, Brender J, Zhang Y. Recent advances in automated protein design and its future challenges. Expert Opin Drug Discov 2018;13:587-604. [PMID: 29695210 DOI: 10.1080/17460441.2018.1465922] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
203
AIMOES: Archive information assisted multi-objective evolutionary strategy for ab initio protein structure prediction. Knowl Based Syst 2018. [DOI: 10.1016/j.knosys.2018.01.028] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
204
Nicoludis JM, Gaudet R. Applications of sequence coevolution in membrane protein biochemistry. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2018;1860:895-908. [PMID: 28993150 PMCID: PMC5807202 DOI: 10.1016/j.bbamem.2017.10.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 09/28/2017] [Accepted: 10/02/2017] [Indexed: 12/22/2022]
205
Manavalan B, Lee J. SVMQA: support-vector-machine-based protein single-model quality assessment. Bioinformatics 2018;33:2496-2503. [PMID: 28419290 DOI: 10.1093/bioinformatics/btx222] [Citation(s) in RCA: 130] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 04/12/2017] [Indexed: 01/03/2023]  Open
206
Fanuel S, Tabesh S, Mokhtarian K, Saroddiny E, Fazlollahi MR, Pourpak Z, Falak R, Kardar GA. Construction of a recombinant B-cell epitope vaccine based on a Der p1-derived hypoallergen: a bioinformatics approach. Immunotherapy 2018;10:537-553. [PMID: 29569512 DOI: 10.2217/imt-2017-0163] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]  Open
207
Kato Y, Kihara H, Fukui K, Kojima M. A ternary complex model of Sirtuin4-NAD+-Glutamate dehydrogenase. Comput Biol Chem 2018;74:94-104. [PMID: 29571013 DOI: 10.1016/j.compbiolchem.2018.03.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 11/09/2017] [Accepted: 03/08/2018] [Indexed: 10/17/2022]
208
Correnti CE, Gewe MM, Mehlin C, Bandaranayake AD, Johnsen WA, Rupert PB, Brusniak MY, Clarke M, Burke SE, De Van Der Schueren W, Pilat K, Turnbaugh SM, May D, Watson A, Chan MK, Bahl CD, Olson JM, Strong RK. Screening, large-scale production and structure-based classification of cystine-dense peptides. Nat Struct Mol Biol 2018;25:270-278. [PMID: 29483648 PMCID: PMC5840021 DOI: 10.1038/s41594-018-0033-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 01/23/2018] [Indexed: 12/04/2022]
209
Nielsen JT, Mulder FAA. POTENCI: prediction of temperature, neighbor and pH-corrected chemical shifts for intrinsically disordered proteins. JOURNAL OF BIOMOLECULAR NMR 2018;70:141-165. [PMID: 29399725 DOI: 10.1007/s10858-018-0166-5] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 01/25/2018] [Indexed: 05/04/2023]
210
Moult J, Fidelis K, Kryshtafovych A, Schwede T, Tramontano A. Critical assessment of methods of protein structure prediction (CASP)-Round XII. Proteins 2018;86 Suppl 1:7-15. [PMID: 29082672 PMCID: PMC5897042 DOI: 10.1002/prot.25415] [Citation(s) in RCA: 219] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 10/25/2017] [Accepted: 10/27/2017] [Indexed: 12/24/2022]
211
Álvarez Ó, Fernández-Martínez JL, Fernández-Brillet C, Cernea A, Fernández-Muñiz Z, Kloczkowski A. Principal component analysis in protein tertiary structure prediction. J Bioinform Comput Biol 2018;16:1850005. [PMID: 29566640 DOI: 10.1142/s0219720018500051] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
212
Wang X, Zhang D, Huang SY. New Knowledge-Based Scoring Function with Inclusion of Backbone Conformational Entropies from Protein Structures. J Chem Inf Model 2018;58:724-732. [DOI: 10.1021/acs.jcim.7b00601] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
213
dos Santos RN, Ferrari AJR, de Jesus HCR, Gozzo FC, Morcos F, Martínez L. Enhancing protein fold determination by exploring the complementary information of chemical cross-linking and coevolutionary signals. Bioinformatics 2018;34:2201-2208. [DOI: 10.1093/bioinformatics/bty074] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 02/10/2018] [Indexed: 11/13/2022]  Open
214
Guardiani C, Fedorenko OA, Roberts SK, Khovanov IA. On the selectivity of the NaChBac channel: an integrated computational and experimental analysis of sodium and calcium permeation. Phys Chem Chem Phys 2018;19:29840-29854. [PMID: 29090695 DOI: 10.1039/c7cp05928k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
215
Schneider J, Korshunova K, Musiani F, Alfonso-Prieto M, Giorgetti A, Carloni P. Predicting ligand binding poses for low-resolution membrane protein models: Perspectives from multiscale simulations. Biochem Biophys Res Commun 2018;498:366-374. [PMID: 29409902 DOI: 10.1016/j.bbrc.2018.01.160] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Revised: 01/24/2018] [Accepted: 01/25/2018] [Indexed: 12/21/2022]
216
Li B, Fooksa M, Heinze S, Meiler J. Finding the needle in the haystack: towards solving the protein-folding problem computationally. Crit Rev Biochem Mol Biol 2018;53:1-28. [PMID: 28976219 PMCID: PMC6790072 DOI: 10.1080/10409238.2017.1380596] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 08/22/2017] [Accepted: 09/13/2017] [Indexed: 12/22/2022]
217
Antunes D, Jorge NAN, Caffarena ER, Passetti F. Using RNA Sequence and Structure for the Prediction of Riboswitch Aptamer: A Comprehensive Review of Available Software and Tools. Front Genet 2018;8:231. [PMID: 29403526 PMCID: PMC5780412 DOI: 10.3389/fgene.2017.00231] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 12/21/2017] [Indexed: 12/14/2022]  Open
218
Marks C, Nowak J, Klostermann S, Georges G, Dunbar J, Shi J, Kelm S, Deane CM. Sphinx: merging knowledge-based and ab initio approaches to improve protein loop prediction. Bioinformatics 2018;33:1346-1353. [PMID: 28453681 PMCID: PMC5408792 DOI: 10.1093/bioinformatics/btw823] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 01/09/2017] [Indexed: 01/31/2023]  Open
219
Assessing Exhaustiveness of Stochastic Sampling for Integrative Modeling of Macromolecular Structures. Biophys J 2018;113:2344-2353. [PMID: 29211988 DOI: 10.1016/j.bpj.2017.10.005] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 09/22/2017] [Accepted: 10/02/2017] [Indexed: 12/22/2022]  Open
220
Slater PG, Gutierrez-Maldonado SE, Gysling K, Lagos CF. Molecular Modeling of Structures and Interaction of Human Corticotropin-Releasing Factor (CRF) Binding Protein and CRF Type-2 Receptor. Front Endocrinol (Lausanne) 2018;9:43. [PMID: 29515519 PMCID: PMC5826306 DOI: 10.3389/fendo.2018.00043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
221
Goh HH, Ng CL, Loke KK. Functional Genomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018;1102:11-30. [PMID: 30382566 DOI: 10.1007/978-3-319-98758-3_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
222
Loo JSE, Emtage AL, Ng KW, Yong ASJ, Doughty SW. Assessing GPCR homology models constructed from templates of various transmembrane sequence identities: Binding mode prediction and docking enrichment. J Mol Graph Model 2017;80:38-47. [PMID: 29306746 DOI: 10.1016/j.jmgm.2017.12.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 11/27/2017] [Accepted: 12/26/2017] [Indexed: 11/15/2022]
223
Suplatov D, Sharapova Y, Timonina D, Kopylov K, Švedas V. The visualCMAT: A web-server to select and interpret correlated mutations/co-evolving residues in protein families. J Bioinform Comput Biol 2017;16:1840005. [PMID: 29361894 DOI: 10.1142/s021972001840005x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
224
Deng L, Fan C, Zeng Z. A sparse autoencoder-based deep neural network for protein solvent accessibility and contact number prediction. BMC Bioinformatics 2017;18:569. [PMID: 29297299 PMCID: PMC5751690 DOI: 10.1186/s12859-017-1971-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]  Open
225
Kaushik R, Singh A, Jayaram B. Where Informatics Lags Chemistry Leads. Biochemistry 2017;57:503-506. [DOI: 10.1021/acs.biochem.7b01073] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
226
Glusman G, Rose PW, Prlić A, Dougherty J, Duarte JM, Hoffman AS, Barton GJ, Bendixen E, Bergquist T, Bock C, Brunk E, Buljan M, Burley SK, Cai B, Carter H, Gao J, Godzik A, Heuer M, Hicks M, Hrabe T, Karchin R, Leman JK, Lane L, Masica DL, Mooney SD, Moult J, Omenn GS, Pearl F, Pejaver V, Reynolds SM, Rokem A, Schwede T, Song S, Tilgner H, Valasatava Y, Zhang Y, Deutsch EW. Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework. Genome Med 2017;9:113. [PMID: 29254494 PMCID: PMC5735928 DOI: 10.1186/s13073-017-0509-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]  Open
227
Dai T, Yan X, Li Q, Li T, Liu C, McClements DJ, Chen J. Characterization of binding interaction between rice glutelin and gallic acid: Multi-spectroscopic analyses and computational docking simulation. Food Res Int 2017;102:274-281. [DOI: 10.1016/j.foodres.2017.09.020] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 09/02/2017] [Accepted: 09/08/2017] [Indexed: 10/18/2022]
228
Gludovacz E, Maresch D, Lopes de Carvalho L, Puxbaum V, Baier LJ, Sützl L, Guédez G, Grünwald-Gruber C, Ulm B, Pils S, Ristl R, Altmann F, Jilma B, Salminen TA, Borth N, Boehm T. Oligomannosidic glycans at Asn-110 are essential for secretion of human diamine oxidase. J Biol Chem 2017;293:1070-1087. [PMID: 29187599 DOI: 10.1074/jbc.m117.814244] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 11/14/2017] [Indexed: 01/28/2023]  Open
229
Hydrophobicity of proteins and nanostructured solutes is governed by topographical and chemical context. Proc Natl Acad Sci U S A 2017;114:13345-13350. [PMID: 29158409 DOI: 10.1073/pnas.1700092114] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
230
Martínez-Archundia M, Colín-Astudillo B, Moreno-Vargas LM, Ramírez-Galicia G, Garduño-Juárez R, Deeb O, Contreras-Romo MC, Quintanar-Stephano A, Abarca-Rojano E, Correa-Basurto J. Ligand recognition properties of the vasopressin V2 receptor studied under QSAR and molecular modeling strategies. Chem Biol Drug Des 2017;90:840-853. [DOI: 10.1111/cbdd.13005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 04/06/2017] [Accepted: 04/08/2017] [Indexed: 11/28/2022]
231
Xie H, Zeng D, Chen X, Huo D, Liu L, Zhang D, Jin Q, Ke K, Hu M. Prediction on the risk population of idiosyncratic adverse reactions based on molecular docking with mutant proteins. Oncotarget 2017;8:95568-95576. [PMID: 29221149 PMCID: PMC5707043 DOI: 10.18632/oncotarget.21509] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 09/20/2017] [Indexed: 01/11/2023]  Open
232
Kihara D, Yang YD, Hawkins T. Bioinformatics Resources for Cancer Research with an Emphasis on Gene Function and Structure Prediction Tools. Cancer Inform 2017. [DOI: 10.1177/117693510600200020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]  Open
233
Poondla V, Chikati R, Kallubai M, Chennupati V, Subramanyam R, Obulam VSR. Characterization and molecular modeling of polygalacturonase isoforms from Saccharomyces cerevisiae. 3 Biotech 2017;7:285. [PMID: 28828292 DOI: 10.1007/s13205-017-0912-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Accepted: 08/02/2017] [Indexed: 10/19/2022]  Open
234
Zeng J, Zhu Q, Wu Y, Chen H, Lin X. Characterization of a polycyclic aromatic ring-hydroxylation dioxygenase from Mycobacterium sp. NJS-P. CHEMOSPHERE 2017;185:67-74. [PMID: 28686888 DOI: 10.1016/j.chemosphere.2017.07.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 06/01/2017] [Accepted: 07/01/2017] [Indexed: 06/07/2023]
235
Monzon AM, Zea DJ, Marino-Buslje C, Parisi G. Homology modeling in a dynamical world. Protein Sci 2017;26:2195-2206. [PMID: 28815769 DOI: 10.1002/pro.3274] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 08/09/2017] [Accepted: 08/09/2017] [Indexed: 12/31/2022]
236
Fierro F, Suku E, Alfonso-Prieto M, Giorgetti A, Cichon S, Carloni P. Agonist Binding to Chemosensory Receptors: A Systematic Bioinformatics Analysis. Front Mol Biosci 2017;4:63. [PMID: 28932739 PMCID: PMC5592726 DOI: 10.3389/fmolb.2017.00063] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 08/22/2017] [Indexed: 12/17/2022]  Open
237
Terashi G, Kihara D. Protein structure model refinement in CASP12 using short and long molecular dynamics simulations in implicit solvent. Proteins 2017;86 Suppl 1:189-201. [PMID: 28833585 DOI: 10.1002/prot.25373] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 08/01/2017] [Accepted: 08/18/2017] [Indexed: 12/21/2022]
238
Sirovetz BJ, Schafer NP, Wolynes PG. Protein structure prediction: making AWSEM AWSEM-ER by adding evolutionary restraints. Proteins 2017;85:2127-2142. [PMID: 28799172 DOI: 10.1002/prot.25367] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 07/29/2017] [Accepted: 08/08/2017] [Indexed: 11/07/2022]
239
Xiong D, Mao W, Gong H. Predicting the helix-helix interactions from correlated residue mutations. Proteins 2017;85:2162-2169. [PMID: 28833538 DOI: 10.1002/prot.25370] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 08/03/2017] [Accepted: 08/13/2017] [Indexed: 12/30/2022]
240
Colas C, Schlessinger A, Pajor AM. Mapping Functionally Important Residues in the Na+/Dicarboxylate Cotransporter, NaDC1. Biochemistry 2017;56:4432-4441. [PMID: 28731330 DOI: 10.1021/acs.biochem.7b00503] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
241
Lam SD, Das S, Sillitoe I, Orengo C. An overview of comparative modelling and resources dedicated to large-scale modelling of genome sequences. Acta Crystallogr D Struct Biol 2017;73:628-640. [PMID: 28777078 PMCID: PMC5571743 DOI: 10.1107/s2059798317008920] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 06/14/2017] [Indexed: 12/02/2022]  Open
242
Kim HS, Asmis R. Mitogen-activated protein kinase phosphatase 1 (MKP-1) in macrophage biology and cardiovascular disease. A redox-regulated master controller of monocyte function and macrophage phenotype. Free Radic Biol Med 2017;109:75-83. [PMID: 28330703 PMCID: PMC5462841 DOI: 10.1016/j.freeradbiomed.2017.03.020] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 03/03/2017] [Accepted: 03/17/2017] [Indexed: 12/21/2022]
243
Gaded V, Anand R. Selective Deamination of Mutagens by a Mycobacterial Enzyme. J Am Chem Soc 2017;139:10762-10768. [DOI: 10.1021/jacs.7b04967] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
244
Raghuraman P, Jesu Jaya Sudan R, Lesitha Jeeva Kumari J, Sudandiradoss C. Systematic prioritization of functional hotspot in RIG-1 domains using pattern based conventional molecular dynamic simulation. Life Sci 2017;184:58-70. [PMID: 28705469 DOI: 10.1016/j.lfs.2017.07.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 06/29/2017] [Accepted: 07/09/2017] [Indexed: 10/19/2022]
245
Sharifi M. Computational approaches to understand the adverse drug effect on potassium, sodium and calcium channels for predicting TdP cardiac arrhythmias. J Mol Graph Model 2017;76:152-160. [PMID: 28756335 DOI: 10.1016/j.jmgm.2017.06.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Revised: 06/08/2017] [Accepted: 06/10/2017] [Indexed: 02/08/2023]
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Brodie NI, Popov KI, Petrotchenko EV, Dokholyan NV, Borchers CH. Solving protein structures using short-distance cross-linking constraints as a guide for discrete molecular dynamics simulations. SCIENCE ADVANCES 2017;3:e1700479. [PMID: 28695211 PMCID: PMC5501500 DOI: 10.1126/sciadv.1700479] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 05/19/2017] [Indexed: 05/21/2023]
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Adsorption of a hydrophobic cationic polypeptide onto acidic lipid membrane. POLYMER 2017. [DOI: 10.1016/j.polymer.2017.06.058] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Shams H, Soheilypour M, Peyro M, Moussavi-Baygi R, Mofrad MRK. Looking "Under the Hood" of Cellular Mechanotransduction with Computational Tools: A Systems Biomechanics Approach across Multiple Scales. ACS Biomater Sci Eng 2017;3:2712-2726. [PMID: 33418698 DOI: 10.1021/acsbiomaterials.7b00117] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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HÖft TA, Alpert BK. FAST UPDATING MULTIPOLE COULOMBIC POTENTIAL CALCULATION. SIAM JOURNAL ON SCIENTIFIC COMPUTING : A PUBLICATION OF THE SOCIETY FOR INDUSTRIAL AND APPLIED MATHEMATICS 2017;39:https://doi.org/10.1137/16M1096189. [PMID: 33088167 PMCID: PMC7574401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
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Deciphering MCR-2 Colistin Resistance. mBio 2017;8:mBio.00625-17. [PMID: 28487432 PMCID: PMC5424208 DOI: 10.1128/mbio.00625-17] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]  Open
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