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Jan J. Hermans, Ph.D. - Publications

Affiliations: 
1947-1953 University of Groningen, Groningen, Netherlands 
 1952-1958 Leiden University, Leiden, Netherlands 
 1968-1978 chemistry University of North Carolina, Chapel Hill, Chapel Hill, NC 
Area:
chemical physics
Website:
http://www.dwc.knaw.nl/biografie/pmknaw/?pagetype=authorDetail&aId=PE00000802
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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
2011 Hermans J. The amino acid dipeptide: small but still influential after 50 years. Proceedings of the National Academy of Sciences of the United States of America. 108: 3095-6. PMID 21310970 DOI: 10.1073/Pnas.1019470108  0.315
2005 Hu H, Hermans J, Lee AL. Relating side-chain mobility in proteins to rotameric transitions: insights from molecular dynamics simulations and NMR. Journal of Biomolecular Nmr. 32: 151-62. PMID 16034666 DOI: 10.1007/S10858-005-5366-0  0.328
2005 Butterfoss GL, Richardson JS, Hermans J. Protein imperfections: separating intrinsic from extrinsic variation of torsion angles. Acta Crystallographica. Section D, Biological Crystallography. 61: 88-98. PMID 15608380 DOI: 10.1107/S0907444904027325  0.318
2005 Maciejczyk M, Hermans J, Bierzyński A. Free energy of helix propagation in short polyalanine chains determined from peptide growth simulations of La3+-binding model peptides. Comparison with experimental data. Acta Biochimica Polonica. 53: 121-129. DOI: 10.18388/Abp.2006_3370  0.33
2003 Hu H, Clarkson MW, Hermans J, Lee AL. Increased rigidity of eglin c at acidic pH: evidence from NMR spin relaxation and MD simulations. Biochemistry. 42: 13856-68. PMID 14636053 DOI: 10.1021/Bi035015Z  0.328
2003 Butterfoss GL, Hermans J. Boltzmann-type distribution of side-chain conformation in proteins. Protein Science : a Publication of the Protein Society. 12: 2719-31. PMID 14627733 DOI: 10.1110/Ps.03273303  0.347
2003 Hu H, Elstner M, Hermans J. Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine "dipeptides" (Ace-Ala-Nme and Ace-Gly-Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution. Proteins. 50: 451-63. PMID 12557187 DOI: 10.1002/Prot.10279  0.312
2002 Vorobjev YN, Hermans J. Free energies of protein decoys provide insight into determinants of protein stability. Protein Science : a Publication of the Protein Society. 11: 994. PMID 11910042 DOI: 10.1002/Pro.110994  0.353
2002 Hu H, Yun RH, Hermans J. Reversibility of free energy simulations: Slow growth may have a unique advantage. (With a note on use of Ewald summation) Molecular Simulation. 28: 67-80. DOI: 10.1080/08927020211971  0.312
2001 Liu H, Elstner M, Kaxiras E, Frauenheim T, Hermans J, Yang W. Quantum mechanics simulation of protein dynamics on long timescale. Proteins. 44: 484-9. PMID 11484226 DOI: 10.1002/Prot.1114  0.318
2000 Mann G, Hermans J. Modeling protein-small molecule interactions: structure and thermodynamics of noble gases binding in a cavity in mutant phage T4 lysozyme L99A. Journal of Molecular Biology. 302: 979-89. PMID 10993736 DOI: 10.1006/Jmbi.2000.4064  0.325
1999 O'Connell TM, Wang L, Tropsha A, Hermans J. The "random-coil" state of proteins: comparison of database statistics and molecular simulations. Proteins. 36: 407-18. PMID 10450082 DOI: 10.1002/(Sici)1097-0134(19990901)36:4<407::Aid-Prot4>3.0.Co;2-1  0.349
1999 Vorobjev YN, Hermans J. ES/IS: estimation of conformational free energy by combining dynamics simulations with explicit solvent with an implicit solvent continuum model. Biophysical Chemistry. 78: 195-205. PMID 10343388 DOI: 10.1016/S0301-4622(98)00230-0  0.38
1999 Prins JF, Hermans J, Mann G, Nyland LS, Simons M. A virtual environment for steered molecular dynamics Future Generation Computer Systems. 15: 485-495. DOI: 10.1016/S0167-739X(99)00005-9  0.319
1998 Vorobjev YN, Almagro JC, Hermans J. Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model. Proteins. 32: 399-413. PMID 9726412 DOI: 10.1002/(Sici)1097-0134(19980901)32:4<399::Aid-Prot1>3.0.Co;2-C  0.384
1997 Hermans J, Wang L. Inclusion of Loss of Translational and Rotational Freedom in Theoretical Estimates of Free Energies of Binding. Application to a Complex of Benzene and Mutant T4 Lysozyme Journal of the American Chemical Society. 119: 2707-2714. DOI: 10.1021/Ja963568+  0.328
1996 Wang L, O'Connell T, Tropsha A, Hermans J. Energetic decomposition of the alpha-helix-coil equilibrium of a dynamic model system. Biopolymers. 39: 479-89. PMID 8837515 DOI: 10.1002/(Sici)1097-0282(199610)39:4<479::Aid-Bip1>3.0.Co;2-U  0.364
1996 Wang L, O'Connell T, Tropsha A, Hermans J. Molecular simulations of beta-sheet twisting. Journal of Molecular Biology. 262: 283-93. PMID 8831794 DOI: 10.1006/Jmbi.1996.0513  0.326
1995 Wang L, O'Connell T, Tropsha A, Hermans J. Thermodynamic parameters for the helix-coil transition of oligopeptides: Molecular dynamics simulation with the peptide growth method Proceedings of the National Academy of Sciences of the United States of America. 92: 10924-10928. PMID 7479911 DOI: 10.1073/Pnas.92.24.10924  0.368
1994 Scully J, Hermans J. Backbone flexibility and stability of reverse turn conformation in a model system. Journal of Molecular Biology. 235: 682-94. PMID 8289288 DOI: 10.1006/Jmbi.1994.1020  0.363
1994 Zhang L, Hermans J. 310 Helix Versus .alpha.-Helix: A Molecular Dynamics Study of Conformational Preferences of Aib and Alanine Journal of the American Chemical Society. 116: 11915-11921. DOI: 10.1021/Ja00105A034  0.301
1993 Zhang L, Hermans J. Molecular dynamics study of structure and stability of a model coiled coil Proteins. 16: 384-392. PMID 8356033 DOI: 10.1002/Prot.340160407  0.36
1993 Scully JL, Hermans J. Multiple Time Steps: Limits on the Speedup of Molecular Dynamics Simulations of Aqueous Systems Molecular Simulation. 11: 67-77. DOI: 10.1080/08927029308022177  0.315
1993 Hermans J. Molecular dynamics simulations of helix and turn propensities in model peptides Current Opinion in Structural Biology. 3: 270-276. DOI: 10.1016/S0959-440X(05)80163-0  0.383
1992 Tropsha A, Hermans J. Application of free energy simulations to the binding of a transition-state-analogue inhibitor to HTV protease Protein Engineering, Design and Selection. 5: 29-33. PMID 1631042 DOI: 10.1093/Protein/5.1.29  0.316
1992 Hermans J, Anderson AG, Yun RH. Differential helix propensity of small apolar side chains studied by molecular dynamics simulations. Biochemistry. 31: 5646-53. PMID 1610812 DOI: 10.1021/Bi00139A031  0.345
1992 Hermans J, Yun RH, Anderson AG. Precision of free energies calculated by molecular dynamics simulations of peptides in solution Journal of Computational Chemistry. 13: 429-442. DOI: 10.1002/Jcc.540130406  0.354
1991 Yun RH, Anderson A, Hermans J. Proline in alpha-helix: stability and conformation studied by dynamics simulation. Proteins. 10: 219-28. PMID 1881878 DOI: 10.1002/Prot.340100306  0.363
1991 Yun RH, Hermans J. Conformational equilibria of valine studied by dynamics simulation. Protein Engineering. 4: 761-6. PMID 1798700 DOI: 10.1093/Protein/4.7.761  0.374
1988 Hermans J, Pathiaseril A, Anderson A. Excess free energy of liquids from molecular dynamics simulations. Application to water models. Journal of the American Chemical Society. 110: 5982-5986. PMID 22148769 DOI: 10.1021/Ja00226A009  0.331
1988 Anderson AG, Hermans J. Microfolding: conformational probability map for the alanine dipeptide in water from molecular dynamics simulations. Proteins. 3: 262-5. PMID 3420105 DOI: 10.1002/Prot.340030408  0.348
1986 Anderson A, Carson M, Hermans J. Molecular Dynamics Simulation Study of Polypeptide Conformational Equilibria: A Progress Reporta Annals of the New York Academy of Sciences. 482: 51-59. DOI: 10.1111/J.1749-6632.1986.Tb20936.X  0.336
1984 Robinson RM, Hermans J. Subunit interactions in human plasma fibronectin. Biochemical and Biophysical Research Communications. 124: 718-25. PMID 6239619 DOI: 10.1016/0006-291X(84)91017-9  0.31
1984 Hermans J, Berendsen HJC, Gunsteren WFV, Postma JPM. A Consistent Empirical Potential For Water-Protein Interactions Biopolymers. 23: 1513-1518. DOI: 10.1002/Bip.360230807  0.317
1983 van Gunsteren WF, Berendsen HJ, Hermans J, Hol WG, Postma JP. Computer simulation of the dynamics of hydrated protein crystals and its comparison with x-ray data. Proceedings of the National Academy of Sciences of the United States of America. 80: 4315-9. PMID 6576339 DOI: 10.1073/Pnas.80.14.4315  0.33
1980 Hermans J, Vacatello M. Modeling water-protein interactions in a protein crystal Biophysical Journal. 32: 87-88. PMID 19431416 DOI: 10.1016/S0006-3495(80)84922-8  0.313
1980 Feero DR, McQueen JE, McCown JT, Hermans J. Energy minimizations of rubredoxin Journal of Molecular Biology. 136: 1-18. PMID 7365789 DOI: 10.1016/0022-2836(80)90363-0  0.324
1972 Ferro DR, Hermans J. Semiempirical energy calculations on model compounds of polypeptides. Crystal structures of DL‐acetylleucine N‐methylamide and DL‐acetyl‐amino‐n‐butyric acid N‐methylamide Biopolymers. 11: 105-117. PMID 5008173 DOI: 10.1002/Bip.1972.360110108  0.345
1971 Hermans J, Puett D. Relative effects of primary and tertiary structure on helix formation in myoglobin and α‐lactalbumin Biopolymers. 10: 895-914. PMID 5572633 DOI: 10.1002/Bip.360100512  0.304
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