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Hammad Naveed, Ph.D. - Publications

Affiliations: 
2012 Bioengineering University of Illinois at Chicago, Chicago, IL, United States 
Area:
Bioinformatics Biology, General Biophysics, Biochemistry
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39 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 Tian W, Lin M, Tang K, Barse M, Naveed H, Liang J. 3D-BMPP: 3D Beta-Barrel Membrane Protein Predictor. Methods in Molecular Biology (Clifton, N.J.). 2627: 321-328. PMID 36959455 DOI: 10.1007/978-1-0716-2974-1_17  0.577
2021 Mushtaq M, Naveed H, Khalid Z. Computational Prediction of lncRNA-Protein Interactions using Machine learning. Annual International Conference of the Ieee Engineering in Medicine and Biology Society. Ieee Engineering in Medicine and Biology Society. Annual International Conference. 2021: 2100-2103. PMID 34891703 DOI: 10.1109/EMBC46164.2021.9630282  0.335
2020 Iftikhar H, Ali HN, Farooq S, Naveed H, Shahzad-Ul-Hussan S. Identification of potential inhibitors of three key enzymes of SARS-CoV2 using computational approach. Computers in Biology and Medicine. 122: 103848. PMID 32658735 DOI: 10.1016/J.Compbiomed.2020.103848  0.304
2020 Bausewein T, Naveed H, Liang J, Nussberger S. The structure of the TOM core complex in the mitochondrial outer membrane. Biological Chemistry. PMID 32142473 DOI: 10.1515/Hsz-2020-0104  0.608
2019 Tian W, Naveed H, Lin M, Liang J. GeTFEP: A general transfer free energy profile of transmembrane proteins. Protein Science : a Publication of the Protein Society. PMID 31658402 DOI: 10.1002/Pro.3763  0.615
2018 Tian W, Lin M, Tang K, Liang J, Naveed H. High-resolution structure prediction of β-barrel membrane proteins. Proceedings of the National Academy of Sciences of the United States of America. PMID 29378944 DOI: 10.1073/Pnas.1716817115  0.569
2017 Tian W, Lin M, Naveed H, Liang J. Efficient computation of transfer free energies of amino acids in beta-barrel membrane proteins. Bioinformatics (Oxford, England). PMID 28158457 DOI: 10.1093/Bioinformatics/Btx053  0.575
2017 Tian W, Naveed H, Liang J. Improving 3D Structure Prediction of Beta-Barrel Membrane Proteins Biophysical Journal. 112: 55a. DOI: 10.1016/J.Bpj.2016.11.333  0.65
2016 Hashemifar S, Ma J, Naveed H, Canzar S, Xu J. ModuleAlign: module-based global alignment of protein-protein interaction networks. Bioinformatics (Oxford, England). 32: i658-i664. PMID 27587686 DOI: 10.1093/Bioinformatics/Btw447  0.407
2016 Lin M, Gessmann D, Naveed H, Liang J. Outer membrane protein folding and topology from a computational transfer free energy scale. Journal of the American Chemical Society. PMID 26860422 DOI: 10.1021/Jacs.5B10307  0.584
2016 Tian W, Liang J, Naveed H. Improved 3D Structure Prediction of Beta-Barrel Membrane Proteins by using Evolutionary Coupling Constraints, Reduced State Space and an Empirical Potential Function Biophysical Journal. 110: 56a. DOI: 10.1016/J.Bpj.2015.11.370  0.662
2015 Liang J, Cao Y, Gursoy G, Naveed H, Terebus A, Zhao J. Multiscale Modeling of Cellular Epigenetic States: Stochasticity in Molecular Networks, Chromatin Folding in Cell Nuclei, and Tissue Pattern Formation of Cells. Critical Reviews in Biomedical Engineering. 43: 323-46. PMID 27480462 DOI: 10.1615/Critrevbiomedeng.2016016559  0.666
2015 Naveed H, Hameed US, Harrus D, Bourguet W, Arold ST, Gao X. An integrated structure- and system-based framework to identify new targets of metabolites and known drugs. Bioinformatics (Oxford, England). 31: 3922-9. PMID 26286808 DOI: 10.1093/Bioinformatics/Btv477  0.317
2015 Cui X, Naveed H, Gao X. Finding optimal interaction interface alignments between biological complexes. Bioinformatics (Oxford, England). 31: i133-i141. PMID 26072475 DOI: 10.1093/Bioinformatics/Btv242  0.387
2015 Kachalo S, Naveed H, Cao Y, Zhao J, Liang J. Mechanical model of geometric cell and topological algorithm for cell dynamics from single-cell to formation of monolayered tissues with pattern. Plos One. 10: e0126484. PMID 25974182 DOI: 10.1371/Journal.Pone.0126484  0.457
2014 Li Y, Naveed H, Kachalo S, Xu LX, Liang J. Mechanisms of regulating tissue elongation in Drosophila wing: impact of oriented cell divisions, oriented mechanical forces, and reduced cell size. Plos One. 9: e86725. PMID 24504016 DOI: 10.1371/Journal.Pone.0086725  0.429
2014 Naveed H, Liang J. Weakly stable regions and protein-protein interactions in beta-barrel membrane proteins. Current Pharmaceutical Design. 20: 1268-73. PMID 23713778 DOI: 10.2174/13816128113199990071  0.623
2013 Cao Y, Naveed H, Liang C, Liang J. Modeling spatial population dynamics of stem cell lineage in wound healing and cancerogenesis. Conference Proceedings : ... Annual International Conference of the Ieee Engineering in Medicine and Biology Society. Ieee Engineering in Medicine and Biology Society. Annual Conference. 2013: 5550-3. PMID 24110994 DOI: 10.1109/EMBC.2013.6610807  0.333
2013 Zhao J, Naveed H, Kachalo S, Cao Y, Tian W, Liang J. Dynamic mechanical finite element model of biological cells for studying cellular pattern formation. Conference Proceedings : ... Annual International Conference of the Ieee Engineering in Medicine and Biology Society. Ieee Engineering in Medicine and Biology Society. Annual Conference. 2013: 4517-20. PMID 24110738 DOI: 10.1109/EMBC.2013.6610551  0.382
2013 Qiao N, Huang Y, Naveed H, Green CD, Han JD. CoCiter: an efficient tool to infer gene function by assessing the significance of literature co-citation. Plos One. 8: e74074. PMID 24086311 DOI: 10.1371/Journal.Pone.0074074  0.3
2013 Lin M, Naveed H, Liang J. Statistical Mechanical Model for the Transfer Free Energy of Amino Acids in the Context of Membrane Protein OmpLA Biophysical Journal. 104: 401a. DOI: 10.1016/J.Bpj.2012.11.2236  0.558
2012 Li Y, Naveed H, Kachalo S, Xu LX, Liang J. Mechanisms of regulating cell topology in proliferating epithelia: impact of division plane, mechanical forces, and cell memory. Plos One. 7: e43108. PMID 22912800 DOI: 10.1371/Journal.Pone.0043108  0.429
2012 Naveed H, Jimenez-Morales D, Tian J, Pasupuleti V, Kenney LJ, Liang J. Engineered oligomerization state of OmpF protein through computational design decouples oligomer dissociation from unfolding. Journal of Molecular Biology. 419: 89-101. PMID 22391420 DOI: 10.1016/J.Jmb.2012.02.043  0.604
2012 Naveed H, Xu Y, Jackups R, Liang J. Predicting three-dimensional structures of transmembrane domains of β-barrel membrane proteins. Journal of the American Chemical Society. 134: 1775-81. PMID 22148174 DOI: 10.1021/Ja209895M  0.756
2012 Geula S, Naveed H, Liang J, Shoshan-Barmatz V. Structure-based analysis of VDAC1 protein: defining oligomer contact sites. The Journal of Biological Chemistry. 287: 2179-90. PMID 22117062 DOI: 10.1074/Jbc.M111.268920  0.508
2012 Liang J, Naveed H, Jimenez-Morales D, Adamian L, Lin M. Computational studies of membrane proteins: models and predictions for biological understanding. Biochimica Et Biophysica Acta. 1818: 927-41. PMID 22051023 DOI: 10.1016/J.Bbamem.2011.09.026  0.658
2012 Lin M, Naveed H, Liang J. Computational Free Energy Scale of Amino Acid Residues in Membrane Protein from Statistical Mechanics Biophysical Journal. 102: 59a. DOI: 10.1016/J.Bpj.2011.11.349  0.563
2012 Li Y, Naveed H, Kachalo S, Xu LX, Liang J. On Mechanisms of Regulation of Tissue Elongation in Drosophila Wing Biophysical Journal. 102: 593a. DOI: 10.1016/J.Bpj.2011.11.3234  0.426
2012 Naveed H, Liang J. TMBB-Explorer: A Webserver to Predict the Structure, Oligomerization State, Ppi Interface, and Thermodynamic Properties of the Transmembrane Domains of Outer Membrane Proteins Biophysical Journal. 102: 469a. DOI: 10.1016/J.Bpj.2011.11.2573  0.657
2012 Naveed H, Liang J. Engineering Biological Nanopores with Enhanced Properties Biophysical Journal. 102: 188a-189a. DOI: 10.1016/J.Bpj.2011.11.1028  0.576
2011 Li Y, Naveed H, Kachalo S, Xu LX, Liang J. Mechanical forces mediate localized topological change in epithelia. Conference Proceedings : ... Annual International Conference of the Ieee Engineering in Medicine and Biology Society. Ieee Engineering in Medicine and Biology Society. Annual Conference. 2011: 178-81. PMID 22254279 DOI: 10.1109/IEMBS.2011.6089923  0.351
2011 Gessmann D, Mager F, Naveed H, Arnold T, Weirich S, Linke D, Liang J, Nussberger S. Improving the resistance of a eukaryotic β-barrel protein to thermal and chemical perturbations. Journal of Molecular Biology. 413: 150-61. PMID 21835183 DOI: 10.1016/J.Jmb.2011.07.054  0.621
2011 Adamian L, Naveed H, Liang J. Lipid-binding surfaces of membrane proteins: evidence from evolutionary and structural analysis. Biochimica Et Biophysica Acta. 1808: 1092-102. PMID 21167813 DOI: 10.1016/J.Bbamem.2010.12.008  0.548
2011 Naveed H, Xu Y, Jackups R, Liang J. Intertwined Coil Inspired Modeling of β-Barrel Membrane Protein Structures using Predicted Interstrand Interaction Constraints Biophysical Journal. 100: 206a. DOI: 10.1016/J.Bpj.2010.12.1335  0.762
2011 Li Y, Naveed H, Kachalo S, Liang J. Topological Properties and Variations of Cells in Proliferating Epithelia: Impact of Mechanical Force and Division Orientation Biophysical Journal. 100: 166a. DOI: 10.1016/J.Bpj.2010.12.1123  0.45
2010 Naveed H, Li Y, Kachalo S, Liang J. Geometric order in proliferating epithelia: impact of rearrangements and cleavage plane orientation. Conference Proceedings : ... Annual International Conference of the Ieee Engineering in Medicine and Biology Society. Ieee Engineering in Medicine and Biology Society. Annual Conference. 2010: 3808-11. PMID 21097056 DOI: 10.1109/IEMBS.2010.5627601  0.371
2010 Naveed H, Jackups R, Liang J. Accurate Ab Initio Prediction of Three Dimensional Structures of Beta-Barrel Membrane Proteins from Sequences Biophysical Journal. 98: 644a. DOI: 10.1016/J.Bpj.2009.12.3529  0.753
2009 Naveed H, Jackups R, Liang J. Predicting weakly stable regions, oligomerization state, and protein-protein interfaces in transmembrane domains of outer membrane proteins. Proceedings of the National Academy of Sciences of the United States of America. 106: 12735-40. PMID 19622743 DOI: 10.1073/Pnas.0902169106  0.758
2009 Naveed H, Jackups R, Liang J. Predicting Strained Regions for Folding and Protein-Protein Interaction in Bacterial Outer Membranes Biophysical Journal. 96: 339a. DOI: 10.1016/J.Bpj.2008.12.3824  0.756
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