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Homayoun Valafar - Publications

Affiliations: 
Computer Science & Engineering University of South Carolina, Columbia, SC 
Area:
Computer Science, Artificial Intelligence
Website:
https://www.cse.sc.edu/~homayoun/
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43 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Abdollahi H, Prestegard JH, Valafar H. Computational modeling multiple conformational states of proteins with residual dipolar coupling data. Current Opinion in Structural Biology. 82: 102655. PMID 37454402 DOI: 10.1016/j.sbi.2023.102655  0.382
2022 Omar H, Hein A, Cole CA, Valafar H. Concurrent Identification and Characterization of Protein Structure and Continuous Internal Dynamics with REDCRAFT. Frontiers in Molecular Biosciences. 9: 806584. PMID 35187082 DOI: 10.3389/fmolb.2022.806584  0.382
2021 Cole CA, Daigham NS, Liu G, Montelione GT, Valafar H. REDCRAFT: A computational platform using residual dipolar coupling NMR data for determining structures of perdeuterated proteins in solution. Plos Computational Biology. 17: e1008060. PMID 33524015 DOI: 10.1371/journal.pcbi.1008060  0.582
2020 Cole C, Parks C, Rachele J, Valafar H. Increased usability, algorithmic improvements and incorporation of data mining for structure calculation of proteins with REDCRAFT software package. Bmc Bioinformatics. 21: 204. PMID 33272215 DOI: 10.1186/s12859-020-3522-x  0.511
2020 Nag A, Valafar H, Pandala N. A Study of Nonstructural Protein 1 of SARS Coronavirus The Faseb Journal. 34: 1-1. DOI: 10.1096/Fasebj.2020.34.S1.02728  0.447
2019 Sala D, Huang YJ, Cole CA, Snyder D, Liu G, Ishida Y, Swapna GVT, Brock KP, Sander C, Fidelis K, Kryshtafovych A, Inouye M, Tejero R, Valafar H, Rosato A, et al. Protein Structure Prediction Assisted with Sparse NMR Data in CASP13. Proteins. PMID 31603581 DOI: 10.1002/Prot.25837  0.5
2016 Cole CA, Mukhopadhyay R, Omar H, Hennig M, Valafar H. Structure Calculation and Reconstruction of Discrete State Dynamics from Residual Dipolar Couplings. Journal of Chemical Theory and Computation. PMID 26984680 DOI: 10.1021/Acs.Jctc.5B01091  0.655
2016 Fahim A, Irausquin S, Valafar H. nD-PDPA: n-Dimensional Probability Density Profile Analysis Emerging Trends in Applications and Infrastructures For Computational Biology, Bioinformatics, and Systems Biology: Systems and Applications. 181-196. DOI: 10.1016/B978-0-12-804203-8.00013-4  0.477
2016 Cole CA, Ishimaru D, Hennig M, Valafar H. Structure Calculation of α, α/β, β Proteins from Residual Dipolar Coupling Data Using Redcraft Emerging Trends in Applications and Infrastructures For Computational Biology, Bioinformatics, and Systems Biology: Systems and Applications. 75-89. DOI: 10.1016/B978-0-12-804203-8.00006-7  0.383
2014 Simin M, Irausquin S, Cole CA, Valafar H. Improvements to REDCRAFT: a software tool for simultaneous characterization of protein backbone structure and dynamics from residual dipolar couplings. Journal of Biomolecular Nmr. 60: 241-64. PMID 25403759 DOI: 10.1007/S10858-014-9871-X  0.594
2014 Mukhopadhyay R, Irausquin S, Schmidt C, Valafar H. Dynafold: a dynamic programming approach to protein backbone structure determination from minimal sets of Residual Dipolar Couplings. Journal of Bioinformatics and Computational Biology. 12: 1450002. PMID 24467760 DOI: 10.1142/S0219720014500024  0.7
2013 Schmidt C, Irausquin SJ, Valafar H. Advances in the REDCAT software package. Bmc Bioinformatics. 14: 302. PMID 24098943 DOI: 10.1186/1471-2105-14-302  0.498
2013 Fahim A, Mukhopadhyay R, Yandle R, Prestegard JH, Valafar H. Protein structure validation and identification from unassigned residual dipolar coupling data using 2D-PDPA. Molecules (Basel, Switzerland). 18: 10162-88. PMID 23973992 DOI: 10.3390/Molecules180910162  0.733
2013 Fawcett TM, Irausquin SJ, Simin M, Valafar H. An artificial neural network approach to improving the correlation between protein energetics and the backbone structure. Proteomics. 13: 230-8. PMID 23184572 DOI: 10.1002/Pmic.201200330  0.765
2012 Shealy P, Valafar H. Multiple structure alignment with msTALI. Bmc Bioinformatics. 13: 105. PMID 22607234 DOI: 10.1186/1471-2105-13-105  0.792
2012 Valafar H, Irausquin SJ. Structure and Dynamics of Proteins from Nuclear Magnetic Resonance Spectroscopy Intech. 43. DOI: 10.5772/38682  0.525
2012 Valafar H, Simin M, Irausquin S. A Review of REDCRAFT. Simultaneous Investigation of Structure and Dynamics of Proteins from RDC Restraints Annual Reports On Nmr Spectroscopy. 76: 23-66. DOI: 10.1016/B978-0-12-397019-0.00002-9  0.595
2011 Shealy P, Liu Y, Simin M, Valafar H. Backbone resonance assignment and order tensor estimation using residual dipolar couplings. Journal of Biomolecular Nmr. 50: 357-69. PMID 21667298 DOI: 10.1007/S10858-011-9521-5  0.798
2011 Fawcett TM, Irausquin S, Simin M, Valafar H. An artificial neural network based approach for identification of native protein structures using an extended forcefield Proceedings - 2011 Ieee International Conference On Bioinformatics and Biomedicine, Bibm 2011. 500-505. DOI: 10.1109/BIBM.2011.53  0.743
2010 Shealy P, Simin M, Park SH, Opella SJ, Valafar H. Simultaneous structure and dynamics of a membrane protein using REDCRAFT: membrane-bound form of Pf1 coat protein. Journal of Magnetic Resonance (San Diego, Calif. : 1997). 207: 8-16. PMID 20829084 DOI: 10.1016/J.Jmr.2010.07.016  0.794
2009 Park SH, Son WS, Mukhopadhyay R, Valafar H, Opella SJ. Phage-induced alignment of membrane proteins enables the measurement and structural analysis of residual dipolar couplings with dipolar waves and lambda-maps. Journal of the American Chemical Society. 131: 14140-1. PMID 19761238 DOI: 10.1021/Ja905640D  0.622
2009 Mukhopadhyay R, Miao X, Shealy P, Valafar H. Efficient and accurate estimation of relative order tensors from lambda-maps. Journal of Magnetic Resonance (San Diego, Calif. : 1997). 198: 236-47. PMID 19345125 DOI: 10.1016/J.Jmr.2009.02.014  0.749
2008 Miao X, Mukhopadhyay R, Valafar H. Estimation of relative order tensors, and reconstruction of vectors in space using unassigned RDC data and its application. Journal of Magnetic Resonance (San Diego, Calif. : 1997). 194: 202-11. PMID 18692422 DOI: 10.1016/J.Jmr.2008.07.005  0.764
2008 Miao X, Waddell PJ, Valafar H. TALI: local alignment of protein structures using backbone torsion angles. Journal of Bioinformatics and Computational Biology. 6: 163-81. PMID 18324751 DOI: 10.1142/S0219720008003370  0.708
2008 Bansal S, Miao X, Adams MW, Prestegard JH, Valafar H. Rapid classification of protein structure models using unassigned backbone RDCs and probability density profile analysis (PDPA). Journal of Magnetic Resonance (San Diego, Calif. : 1997). 192: 60-8. PMID 18321742 DOI: 10.1016/J.Jmr.2008.01.014  0.758
2008 Bryson M, Tian F, Prestegard JH, Valafar H. REDCRAFT: a tool for simultaneous characterization of protein backbone structure and motion from RDC data. Journal of Magnetic Resonance (San Diego, Calif. : 1997). 191: 322-34. PMID 18258464 DOI: 10.1016/J.Jmr.2008.01.007  0.537
2008 Timko E, Shealy P, Bryson M, Valafar H. Minimum data requirements and supplemental angle constraints for protein structure prediction with REDCRAFT Proceedings of the 2008 International Conference On Bioinformatics and Computational Biology, Biocomp 2008. 738-744.  0.819
2008 Shealy P, Mukhopadhyay R, Smith S, Valafar H. Automated assignment of backbone resonances using residual dipolar couplings acquired from a protein with known structure Proceedings of the 2008 International Conference On Bioinformatics and Computational Biology, Biocomp 2008. 646-652.  0.816
2008 Mukhopadhyay R, Shealy P, Valafar H. Protein fold family recognition from unassigned residual dipolar coupling data Proceedings of the 2008 International Conference On Bioinformatics and Computational Biology, Biocomp 2008. 633-638.  0.802
2005 Prestegard JH, Mayer KL, Valafar H, Benison GC. Determination of protein backbone structures from residual dipolar couplings. Methods in Enzymology. 394: 175-209. PMID 15808221 DOI: 10.1016/S0076-6879(05)94007-X  0.6
2005 Wang J, Valafar H, Prestegard JH. Assessment of protein alignment using 1H-1H residual dipolar coupling measurements. Journal of Magnetic Resonance (San Diego, Calif. : 1997). 172: 85-90. PMID 15589411 DOI: 10.1016/J.Jmr.2004.03.012  0.477
2004 Valafar H, Mayer KL, Bougault CM, LeBlond PD, Jenney FE, Brereton PS, Adams MW, Prestegard JH. Backbone solution structures of proteins using residual dipolar couplings: application to a novel structural genomics target. Journal of Structural and Functional Genomics. 5: 241-54. PMID 15704012 DOI: 10.1007/S10969-005-4899-5  0.61
2004 Di Lello P, Benison GC, Valafar H, Pitts KE, Summers AO, Legault P, Omichinski JG. NMR structural studies reveal a novel protein fold for MerB, the organomercurial lyase involved in the bacterial mercury resistance system. Biochemistry. 43: 8322-32. PMID 15222745 DOI: 10.1021/Bi049669Z  0.42
2004 Valafar H, Prestegard JH. REDCAT: a residual dipolar coupling analysis tool. Journal of Magnetic Resonance (San Diego, Calif. : 1997). 167: 228-41. PMID 15040978 DOI: 10.1016/J.Jmr.2003.12.012  0.39
2004 Morris LC, Valafar H, Prestegard JH. Assignment of protein backbone resonances using connectivity, torsion angles and 13Calpha chemical shifts. Journal of Biomolecular Nmr. 29: 1-9. PMID 15017135 DOI: 10.1023/B:Jnmr.0000019500.76436.31  0.4
2004 Valafar H, Mayer KL, LeBlond PD, Bougault C, Prestegard JH. Residual dipolar couplings in high throughput backbone solution structure determination of proteins Proceedings of the International Conference On Mathematics and Engineering Techniques in Medicine and Biological Sciences, Metmbs'04. 270.  0.415
2003 Valafar H, Prestegard JH. Rapid classification of a protein fold family using a statistical analysis of dipolar couplings. Bioinformatics (Oxford, England). 19: 1549-55. PMID 12912836 DOI: 10.1093/Bioinformatics/Btg201  0.52
2003 Umemoto K, Leffler H, Venot A, Valafar H, Prestegard JH. Conformational differences in liganded and unliganded states of Galectin-3. Biochemistry. 42: 3688-95. PMID 12667058 DOI: 10.1021/Bi026671M  0.344
2002 Valafar H, Prestegard JH, Valafar F. Datamining protein structure databanks for crystallization patterns of proteins. Annals of the New York Academy of Sciences. 980: 13-22. PMID 12594078 DOI: 10.1111/J.1749-6632.2002.Tb04885.X  0.501
2001 Tian F, Valafar H, Prestegard JH. A dipolar coupling based strategy for simultaneous resonance assignment and structure determination of protein backbones. Journal of the American Chemical Society. 123: 11791-6. PMID 11716736 DOI: 10.1021/Ja011806H  0.602
2001 Prestegard JH, Valafar H, Glushka J, Tian F. Nuclear magnetic resonance in the era of structural genomics Biochemistry. 40: 8677-8685. PMID 11467927 DOI: 10.1021/Bi0102095  0.522
2000 Al-Hashimi HM, Valafar H, Terrell M, Zartler ER, Eidsness MK, Prestegard JH. Variation of molecular alignment as a means of resolving orientational ambiguities in protein structures from dipolar couplings. Journal of Magnetic Resonance (San Diego, Calif. : 1997). 143: 402-6. PMID 10729267 DOI: 10.1006/Jmre.2000.2049  0.459
1998 Cherniak R, Valafar H, Morris LC, Valafar F. Cryptococcus neoformans chemotyping by quantitative analysis of 1H nuclear magnetic resonance spectra of glucuronoxylomannans with a computer- simulated artificial neural network Clinical and Diagnostic Laboratory Immunology. 5: 146-159. PMID 9521136 DOI: 10.1128/Cdli.5.2.146-159.1998  0.426
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