Donald J. Jacobs - Publications

Affiliations: 
Information Technology (PhD) University of North Carolina, Charlotte, Charlotte, NC, United States 
Area:
Bioinformatics Biology, Computer Science

85 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
2018 Singer CM, Joy D, Jacobs DJ, Nesmelova IV. Rigidity and flexibility characteristics of DD[E/D]-transposases Mos1 and Sleeping Beauty. Proteins. PMID 30582767 DOI: 10.1002/Prot.25653  0.319
2017 David CC, Singam ERA, Jacobs DJ. JED: a Java Essential Dynamics Program for comparative analysis of protein trajectories. Bmc Bioinformatics. 18: 271. PMID 28545397 DOI: 10.1186/S12859-017-1676-Y  0.371
2017 Kanwal F, Jacobs D. Revealing the Mechanism of Binding Selectivity in Undecaprenyl Diphosphate Synthase Biophysical Journal. 112: 317a. DOI: 10.1016/J.Bpj.2016.11.1719  0.413
2016 Srivastava A, Tracka MB, Uddin S, Casas-Finet J, Livesay DR, Jacobs DJ. Mutations in Antibody Fragments Modulate Allosteric Response Via Hydrogen-Bond Network Fluctuations. Biophysical Journal. 110: 1933-42. PMID 27166802 DOI: 10.1016/J.Bpj.2016.03.033  0.401
2016 Green SB, Farmer J, Jacobs DJ. Universal Scaling of Cavity Volume Pathways in Globular Proteins Biophysical Journal. 110: 329a. DOI: 10.1016/J.Bpj.2015.11.1769  0.348
2016 Joy D, Singer CM, Godfrey DP, Jacobs DJ, Nesmelova IV. Investigation and Comparison of the Flexibility and Dynamics of Tc1/Mariner Transposases Biophysical Journal. 110: 224a. DOI: 10.1016/J.Bpj.2015.11.1241  0.345
2015 Li T, Tracka MB, Uddin S, Casas-Finet J, Jacobs DJ, Livesay DR. Rigidity Emerges during Antibody Evolution in Three Distinct Antibody Systems: Evidence from QSFR Analysis of Fab Fragments. Plos Computational Biology. 11: e1004327. PMID 26132144 DOI: 10.1371/Journal.Pcbi.1004327  0.37
2015 González LC, Wang H, Livesay DR, Jacobs DJ. A virtual pebble game to ensemble average graph rigidity. Algorithms For Molecular Biology : Amb. 10: 11. PMID 25904973 DOI: 10.1186/S13015-015-0039-3  0.357
2015 Smith BK, Jacobs DJ, Livesay DR. Fluctuations within the Hydrogen Bond Network Modulate Cooperativity Across the Conformational Ensemble of Protein Structures Biophysical Journal. 108: 61a. DOI: 10.1016/J.Bpj.2014.11.368  0.417
2015 Godfrey DP, Singer CM, Jacobs DJ, Nesmelova IV. Mos1 Transposase Thermodynamic Stability and Flexibility Biophysical Journal. 108: 521a. DOI: 10.1016/J.Bpj.2014.11.2859  0.339
2015 Srivastava A, Tracka MB, Uddin S, Casas-Finet J, Livesay DR, Jacobs DJ. Dynamic Characteristics of Allosteric Pathways in scFv Antibody Fragments Biophysical Journal. 108: 377a. DOI: 10.1016/J.Bpj.2014.11.2069  0.394
2014 Li T, Tracka MB, Uddin S, Casas-Finet J, Jacobs DJ, Livesay DR. Redistribution of flexibility in stabilizing antibody fragment mutants follows Le Châtelier's principle. Plos One. 9: e92870. PMID 24671209 DOI: 10.1371/Journal.Pone.0092870  0.386
2014 Verma D, Guo JT, Jacobs DJ, Livesay DR. Towards comprehensive analysis of protein family quantitative stability-flexibility relationships using homology models. Methods in Molecular Biology (Clifton, N.J.). 1084: 239-54. PMID 24061925 DOI: 10.1007/978-1-62703-658-0_13  0.615
2014 Brown MC, Verma D, Russell C, Jacobs DJ, Livesay DR. A case study comparing quantitative stability-flexibility relationships across five metallo-β-lactamases highlighting differences within NDM-1. Methods in Molecular Biology (Clifton, N.J.). 1084: 227-38. PMID 24061924 DOI: 10.1007/978-1-62703-658-0_12  0.611
2014 David CC, Jacobs DJ. Principal component analysis: a method for determining the essential dynamics of proteins. Methods in Molecular Biology (Clifton, N.J.). 1084: 193-226. PMID 24061923 DOI: 10.1007/978-1-62703-658-0_11  0.356
2014 Li T, Verma D, Tracka MB, Casas-Finet J, Livesay DR, Jacobs DJ. Thermodynamic stability and flexibility characteristics of antibody fragment complexes. Protein and Peptide Letters. 21: 752-65. PMID 23855672 DOI: 10.2174/09298665113209990051  0.567
2014 Singer C, Herring C, Ermakova E, Khairutdinov B, Zuev Y, Jacobs D, Nesmelova I. Stabilization Effects of Disulfide Bonds and Dimerization on Cxcl7 Biophysical Journal. 106: 667a. DOI: 10.1016/J.Bpj.2013.11.3695  0.422
2013 Deng S, Xue C, Baumketner A, Jacobs D, Cai W. Generalized image charge solvation model for electrostatic interactions in molecular dynamics simulations of aqueous solutions. Journal of Computational Physics. 245: 84-106. PMID 23913979 DOI: 10.1016/J.Jcp.2013.03.027  0.322
2013 Verma D, Jacobs DJ, Livesay DR. Variations within class-A β-lactamase physiochemical properties reflect evolutionary and environmental patterns, but not antibiotic specificity. Plos Computational Biology. 9: e1003155. PMID 23874193 DOI: 10.1371/Journal.Pcbi.1003155  0.558
2013 Song W, Lin Y, Baumketner A, Deng S, Cai W, Jacobs DJ. Effect of the Reaction Field on Molecular Forces and Torques Revealed by an Image-Charge Solvation Model. Communications in Computational Physics. 13: 129-149. PMID 23833681 DOI: 10.4208/Cicp.290711.180711S  0.324
2013 Baker K, Baumketner A, Lin Y, Deng S, Jacobs D, Cai W. ICSM: An order N method for calculating electrostatic interactions added to TINKER. Computer Physics Communications. 184: 19-26. PMID 23087451 DOI: 10.1016/J.Cpc.2012.08.003  0.325
2013 Barlowe S, Yang J, Jacobs DJ, Livesay DR, Alsakran J, Zhao Y, Verma D, Mottonen J. A visual analytics approach to exploring protein flexibility subspaces Ieee Pacific Visualization Symposium. 193-200. DOI: 10.1109/PacificVis.2013.6596145  0.535
2013 Herring CA, Singer CM, Jacobs DJ, Nesmelova IV. Thermodynamic Stability and Flexibility of CXC Chemokines Biophysical Journal. 104: 60a. DOI: 10.1016/J.Bpj.2012.11.368  0.422
2013 Song W, Brettin A, Jacobs DJ. Image Charge Solvation Model (ICSM) with Improved Boundary Conditions Biophysical Journal. 104: 507a. DOI: 10.1016/J.Bpj.2012.11.2798  0.314
2013 Jacobs DJ. Free Energy Driven Geometrical Simulation of Protein Dynamics Biophysical Journal. 104: 370a. DOI: 10.1016/J.Bpj.2012.11.2056  0.434
2012 Verma D, Jacobs DJ, Livesay DR. Changes in Lysozyme Flexibility upon Mutation Are Frequent, Large and Long-Ranged. Plos Computational Biology. 8: e1002409. PMID 22396637 DOI: 10.1371/Journal.Pcbi.1002409  0.58
2012 González LC, Wang H, Livesay DR, Jacobs DJ. Calculating ensemble averaged descriptions of protein rigidity without sampling. Plos One. 7: e29176. PMID 22383947 DOI: 10.1371/Journal.Pone.0029176  0.388
2012 Jacobs DJ, Livesay DR, Mottonen JM, Vorov OK, Istomin AY, Verma D. Ensemble properties of network rigidity reveal allosteric mechanisms. Methods in Molecular Biology (Clifton, N.J.). 796: 279-304. PMID 22052496 DOI: 10.1007/978-1-61779-334-9_15  0.628
2011 David CC, Jacobs DJ. Characterizing protein motions from structure. Journal of Molecular Graphics & Modelling. 31: 41-56. PMID 21893421 DOI: 10.1016/J.Jmgm.2011.08.004  0.428
2011 Vorov OK, Livesay DR, Jacobs DJ. Nonadditivity in conformational entropy upon molecular rigidification reveals a universal mechanism affecting folding cooperativity. Biophysical Journal. 100: 1129-38. PMID 21320459 DOI: 10.1016/J.Bpj.2011.01.027  0.416
2011 Jacobs DJ, Trivedi D, David C, Yengo CM. Kinetics and thermodynamics of the rate-limiting conformational change in the actomyosin V mechanochemical cycle. Journal of Molecular Biology. 407: 716-30. PMID 21315083 DOI: 10.1016/J.Jmb.2011.02.001  0.357
2011 Wood GG, Clinkenbeard DA, Jacobs DJ. Nonadditivity in the alpha-helix to coil transition. Biopolymers. 95: 240-53. PMID 21280020 DOI: 10.1002/Bip.21572  0.366
2011 Barlowe S, Liu Y, Yang J, Livesay DR, Jacobs DJ, Mottonen J, Verma D. WaveMap: Interactively discovering features from protein flexibility matrices using wavelet-based visual analytics Computer Graphics Forum. 30: 1001-1010. DOI: 10.1111/j.1467-8659.2011.01949.x  0.523
2011 Trivedi DV, David C, Rösgen J, Jacobs DJ, Yengo CM. The Switch II Region is Critical for the Formation of the Open Cleft Weak Binding Conformation in Myosin V Biophysical Journal. 100: 117a. DOI: 10.1016/J.Bpj.2010.12.846  0.329
2011 Verma D, Jacobs DJ, Livesay DR. Elucidating the Effects of Mutation upon C-Type Lysozyme through Quantitative Stability/Flexibility Relationships Biophysical Journal. 100: 400a. DOI: 10.1016/J.Bpj.2010.12.2376  0.601
2011 David C, Jacobs DJ. A Model Comparison for Characterizing Protein Motions from Structure Biophysical Journal. 100: 172a. DOI: 10.1016/J.Bpj.2010.12.1161  0.432
2011 Song W, Lin Y, Baumketner A, Cai W, Jacobs DJ. Optimized Image Charges for Reaction Field Calculations Biophysical Journal. 100: 157a. DOI: 10.1016/J.Bpj.2010.12.1073  0.304
2010 Vasilache S, Mirshahi N, Ji SY, Mottonen J, Jacobs DJ, Najarian K. A signal processing method to explore similarity in protein flexibility. Advances in Bioinformatics. 454671. PMID 21197478 DOI: 10.1155/2010/454671  0.369
2010 Jacobs DJ. Ensemble-based methods for describing protein dynamics. Current Opinion in Pharmacology. 10: 760-9. PMID 20965786 DOI: 10.1016/J.Coph.2010.09.014  0.448
2010 Mottonen JM, Jacobs DJ, Livesay DR. Allosteric response is both conserved and variable across three CheY orthologs. Biophysical Journal. 99: 2245-54. PMID 20923659 DOI: 10.1016/J.Bpj.2010.07.043  0.381
2010 Verma D, Jacobs DJ, Livesay DR. Predicting the melting point of human C-type lysozyme mutants. Current Protein & Peptide Science. 11: 562-72. PMID 20887260 DOI: 10.2174/138920310794109210  0.588
2010 Verma D, Jacobs DJ, Guo J, Livesay DR. Towards Comprehensive Analysis of Protein Family Quantitative Stability/flexibility Relationships Biophysical Journal. 98: 637a. DOI: 10.1016/J.Bpj.2009.12.3489  0.6
2010 Wang H, Du C, Livesay DR, Jacobs DJ. Fast Prediction of Protein Thermodynamics Biophysical Journal. 98: 635a. DOI: 10.1016/J.Bpj.2009.12.3479  0.422
2010 Song W, Qin P, Lin Y, Baumketner A, Cai W, Jacobs D. Testing a Hybrid Solvation Model with a Transition Layer Via Molecular Dynamics Simulation Biophysical Journal. 98: 575a. DOI: 10.1016/J.Bpj.2009.12.3124  0.312
2010 Trivedi DV, David C, Jacobs DJ, Yengo C. Coupling the Actin Binding Cleft and Nucleotide Binding Pocket in Myosin V Biophysical Journal. 98: 562a. DOI: 10.1016/J.Bpj.2009.12.3046  0.308
2010 David CC, Yengo CM, Jacobs DJ. Critical Assessment of the Statistical Significance of Simulated Motions in Myosin V Biophysical Journal. 98: 27a-28a. DOI: 10.1016/J.Bpj.2009.12.163  0.35
2009 Lin Y, Baumketner A, Deng S, Xu Z, Jacobs D, Cai W. An image-based reaction field method for electrostatic interactions in molecular dynamics simulations of aqueous solutions. The Journal of Chemical Physics. 131: 154103. PMID 20568843 DOI: 10.1063/1.3245232  0.3
2009 Rahman MBA, Karjiban RA, Salleh AB, Jacobs D, Basri M, Chor ALT, Wahab HA, Rahman RNZRA. Deciphering the flexibility and dynamics of Geobacillus zalihae strain T1 lipase at high temperatures by molecular dynamics simulation. Protein and Peptide Letters. 16: 1360-1370. PMID 20001926 DOI: 10.2174/092986609789353763  0.301
2009 Vorov OK, Livesay DR, Jacobs DJ. Helix/coil nucleation: a local response to global demands. Biophysical Journal. 97: 3000-9. PMID 19948130 DOI: 10.1016/J.Bpj.2009.09.013  0.418
2009 Jasuja R, Ulloor J, Yengo CM, Choong K, Istomin AY, Livesay DR, Jacobs DJ, Swerdloff RS, Miksovská J, Larsen RW, Bhasin S. Kinetic and thermodynamic characterization of dihydrotestosterone-induced conformational perturbations in androgen receptor ligand-binding domain. Molecular Endocrinology (Baltimore, Md.). 23: 1231-41. PMID 19443608 DOI: 10.1210/Me.2008-0304  0.31
2009 Abedi Karjiban R, Abdul Rahman MB, Basri M, Salleh AB, Jacobs D, Abdul Wahab H. Molecular dynamics study of the structure, flexibility and dynamics of thermostable L1 lipase at high temperatures Protein Journal. 28: 14-23. PMID 19130194 DOI: 10.1007/S10930-008-9159-7  0.321
2009 Mottonen JM, Xu M, Jacobs DJ, Livesay DR. Unifying mechanical and thermodynamic descriptions across the thioredoxin protein family. Proteins. 75: 610-27. PMID 19004018 DOI: 10.1002/prot.22273  0.342
2009 Trivedi D, David C, Rose M, Jacobs DJ, Yengo C. Temperature Dependent Energy Transfer Measurements Reveal Flexibility in the Upper 50 kDa Domain of Myosin V Biophysical Journal. 96: 139a. DOI: 10.1016/J.Bpj.2008.12.3869  0.305
2009 Mottonen JM, Jacobs DJ, Livesay DR. Assessing Mechanical And Thermodynamic Response Upon Allosteric Perturbation Biophysical Journal. 96: 568a. DOI: 10.1016/J.Bpj.2008.12.3724  0.384
2009 Wang H, Farchild M, Livesay DR, Jacobs DJ. Molecular Partition Functions For Amino Acids And Beyond Biophysical Journal. 96: 80a. DOI: 10.1016/J.Bpj.2008.12.314  0.393
2009 Qin P, Xu Z, Cai W, Jacobs DJ. Image Charge Methods for a Hybrid Solvation Model with Transition Layer Biophysical Journal. 96: 3-3. DOI: 10.1016/J.Bpj.2008.12.1506  0.301
2009 Verma D, Jacobs DJ, Livesay DR. Predicting Protein Mutant Stability With A Combined Experimental/theoretical Approach Biophysical Journal. 96: 301a-302a. DOI: 10.1016/J.Bpj.2008.12.1499  0.612
2008 Vorov OK, Livesay DR, Jacobs DJ. Conformational Entropy of an Ideal Cross-Linking Polymer Chain. Entropy (Basel, Switzerland). 10: 285-308. PMID 19777088 DOI: 10.3390/E10030285  0.343
2008 Livesay DR, Huynh DH, Dallakyan S, Jacobs DJ. Hydrogen bond networks determine emergent mechanical and thermodynamic properties across a protein family. Chemistry Central Journal. 2: 17. PMID 18700034 DOI: 10.1186/1752-153X-2-17  0.388
2008 Sun M, Rose MB, Ananthanarayanan SK, Jacobs DJ, Yengo CM. Characterization of the pre-force-generation state in the actomyosin cross-bridge cycle. Proceedings of the National Academy of Sciences of the United States of America. 105: 8631-6. PMID 18552179 DOI: 10.1073/Pnas.0710793105  0.3
2008 Istomin AY, Gromiha MM, Vorov OK, Jacobs DJ, Livesay DR. New insight into long-range nonadditivity within protein double-mutant cycles. Proteins. 70: 915-24. PMID 17803237 DOI: 10.1002/Prot.21620  0.398
2007 Istomin AY, Jacobs DJ, Livesay DR. On the role of structural class of a protein with two-state folding kinetics in determining correlations between its size, topology, and folding rate. Protein Science : a Publication of the Protein Society. 16: 2564-9. PMID 17962408 DOI: 10.1110/Ps.073124507  0.346
2006 Livesay DR, Jacobs DJ, Kanjanapangka J, Chea E, Cortez H, Garcia J, Kidd P, Marquez MP, Pande S, Yang D. Elucidating the Conformational Dependence of Calculated pKa Values. Journal of Chemical Theory and Computation. 2: 927-38. PMID 26633052 DOI: 10.1021/Ct600066Z  0.359
2006 Jacobs DJ, Livesay DR, Hules J, Tasayco ML. Elucidating quantitative stability/flexibility relationships within thioredoxin and its fragments using a distance constraint model. Journal of Molecular Biology. 358: 882-904. PMID 16542678 DOI: 10.1016/J.Jmb.2006.02.015  0.413
2006 Livesay DR, Jacobs DJ. Conserved quantitative stability/flexibility relationships (QSFR) in an orthologous RNase H pair. Proteins. 62: 130-43. PMID 16287093 DOI: 10.1002/Prot.20745  0.397
2005 Jacobs DJ, Dallakyan S. Elucidating protein thermodynamics from the three-dimensional structure of the native state using network rigidity. Biophysical Journal. 88: 903-15. PMID 15542549 DOI: 10.1529/Biophysj.104.048496  0.43
2004 Livesay DR, Dallakyan S, Wood GG, Jacobs DJ. A flexible approach for understanding protein stability Febs Letters. 576: 468-476. PMID 15498582 DOI: 10.1016/J.Febslet.2004.09.057  0.395
2004 Jacobs DJ, Wood GG. Understanding the alpha-helix to coil transition in polypeptides using network rigidity: predicting heat and cold denaturation in mixed solvent conditions. Biopolymers. 75: 1-31. PMID 15307195 DOI: 10.1002/Bip.20102  0.41
2004 Hespenheide BM, Jacobs DJ, Thorpe MF. Structural rigidity in the capsid assembly of cowpea chlorotic mottle virus Journal of Physics Condensed Matter. 16. DOI: 10.1088/0953-8984/16/44/003  0.306
2004 Lee MS, Wood GG, Jacobs DJ. Investigations on the alpha-helix to coil transition in HP heterogeneous polypeptides using network rigidity Journal of Physics Condensed Matter. 16. DOI: 10.1088/0953-8984/16/44/001  0.352
2003 Jacobs DJ, Dallakyan S, Wood GG, Heckathorne A. Network rigidity at finite temperature: relationships between thermodynamic stability, the nonadditivity of entropy, and cooperativity in molecular systems. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 68: 061109. PMID 14754182 DOI: 10.1103/Physreve.68.061109  0.401
2001 Jacobs DJ, Rader AJ, Kuhn LA, Thorpe MF. Protein flexibility predictions using graph theory. Proteins. 44: 150-65. PMID 11391777 DOI: 10.1002/Prot.1081  0.386
2001 Thorpe MF, Lei M, Rader AJ, Jacobs DJ, Kuhn LA. Protein flexibility and dynamics using constraint theory. Journal of Molecular Graphics & Modelling. 19: 60-9. PMID 11381531 DOI: 10.1016/S1093-3263(00)00122-4  0.351
2000 Jacobs DJ, Hules J. Characteristics of conformational flexibility in hinge-binding proteins: Hierarchical flexibility maps in terms of dihedral angle internal coordinates Journal of Molecular Graphics and Modelling. 18: 550-551. DOI: 10.1016/S1093-3263(00)80114-X  0.315
1999 Duxbury PM, Jacobs DJ, Thorpe M, Moukarzel C. Floppy modes and the free energy: Rigidity and connectivity percolation on Bethe lattices Physical Review E. 59: 2084-2092. DOI: 10.1103/Physreve.59.2084  0.315
1998 Jacobs DJ. Generic rigidity in three-dimensional bond-bending networks Journal of Physics a: Mathematical and General. 31: 6653-6668. DOI: 10.1088/0305-4470/31/31/012  0.315
1997 Jacobs DJ, Hendrickson B. An Algorithm for Two-Dimensional Rigidity Percolation: The Pebble Game Journal of Computational Physics. 137: 346-365. DOI: 10.1006/Jcph.1997.5809  0.331
1995 Jacobs DJ, Thorpe MF. Generic rigidity percolation: The pebble game Physical Review Letters. 75: 4051-4054. DOI: 10.1103/Physrevlett.75.4051  0.311
1995 Mukherjee S, Jacobs DJ, Nakanishi H. Diffusion on loopless critical percolation cluster Journal of Physics a: Mathematical and General. 28: 291-296. DOI: 10.1088/0305-4470/28/2/007  0.54
1994 Jacobs DJ, Masters AJ. Domain growth in a one-dimensional diffusive lattice gas with short-range attraction Physical Review E. 49: 2700-2710. DOI: 10.1103/Physreve.49.2700  0.301
1994 Jacobs DJ, Mukherjee S, Nakanishi H. Diffusion on a DLA cluster in two and three dimensions Journal of Physics a: Mathematical and General. 27: 4341-4350. DOI: 10.1088/0305-4470/27/13/010  0.535
1993 Jacobs DJ, Nakanishi H. A persistent random walk model for the frequency-dependent electrical conductivity Physica a: Statistical Mechanics and Its Applications. 197: 204-222. DOI: 10.1016/0378-4371(93)90468-J  0.521
1991 Muralidhar R, Jacobs DJ, Ramkrishna D, Nakanishi H. Diffusion on two-dimensional percolation clusters: Influence of cluster anisotropy. Physical Review. A. 43: 6503-6517. PMID 9905000 DOI: 10.1103/Physreva.43.6503  0.526
1990 Jacobs D, Nakanishi H. Autocorrelation functions for discrete random walks on disordered lattice Physical Review A. 41: 706-719. DOI: 10.1103/Physreva.41.706  0.539
1990 Muralidhar R, Ramkrishna D, Nakanishi H, Jacobs D. Anomalous diffusion: A dynamic perspective Physica a: Statistical Mechanics and Its Applications. 167: 539-559. DOI: 10.1016/0378-4371(90)90132-C  0.527
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