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Influence of the Length of the Alanine Spacer on the Acidic-Basic Properties of the Ac-Lys-(Ala)(n)-Lys-NH(2) Peptides (n = 0, 1, 2, …, 5).

Journal of solution chemistry

Makowska J, Liwo A, Chmurzyński L, Scheraga HA.
PMID: 23204596
J Solution Chem. 2012 Nov;41(10):1738-1746. doi: 10.1007/s10953-012-9903-7. Epub 2012 Oct 13.

By using the potentiometric titration method, we have determined the pK(a) values of the two terminal lysine groups in six alanine-based peptides differing in the length of the alanine chain: Ac-Lys-Lys-NH(2) (KK), Ac-Lys-Ala-Lys-NH(2) (KAK), Ac-Lys-Ala-Ala-Lys-NH(2) (KAK2), Ac-Lys-Ala-Ala-Ala-Lys-NH(2) (KAK3), Ac-Lys-Ala-Ala-Ala-Ala-Lys-NH(2)...

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Makowska J, Liwo A, Chmurzyński L, et al. Influence of the Length of the Alanine Spacer on the Acidic-Basic Properties of the Ac-Lys-(Ala)(n)-Lys-NH(2) Peptides (n = 0, 1, 2, …, 5). J Solution Chem. 2012;41(10):1738-1746doi: 10.1007/s10953-012-9903-7.
Makowska, J., Liwo, A., Chmurzyński, L., & Scheraga, H. A. (2012). Influence of the Length of the Alanine Spacer on the Acidic-Basic Properties of the Ac-Lys-(Ala)(n)-Lys-NH(2) Peptides (n = 0, 1, 2, …, 5). Journal of solution chemistry, 41(10), 1738-1746. https://doi.org/10.1007/s10953-012-9903-7
Makowska, Joanna, et al. "Influence of the Length of the Alanine Spacer on the Acidic-Basic Properties of the Ac-Lys-(Ala)(n)-Lys-NH(2) Peptides (n = 0, 1, 2, …, 5)." Journal of solution chemistry vol. 41,10 (2012): 1738-1746. doi: https://doi.org/10.1007/s10953-012-9903-7
Makowska J, Liwo A, Chmurzyński L, Scheraga HA. Influence of the Length of the Alanine Spacer on the Acidic-Basic Properties of the Ac-Lys-(Ala)(n)-Lys-NH(2) Peptides (n = 0, 1, 2, …, 5). J Solution Chem. 2012 Nov;41(10):1738-1746. doi: 10.1007/s10953-012-9903-7. Epub 2012 Oct 13. PMID: 23204596; PMCID: PMC3510421.
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Determination of effective potentials for the stretching of C(α) ⋯ C(α) virtual bonds in polypeptide chains for coarse-grained simulations of proteins from ab initio energy surfaces of N-methylacetamide and N-acetylpyrrolidine.

Journal of chemical theory and computation

Sieradzan AK, Scheraga HA, Liwo A.
PMID: 23087598
J Chem Theory Comput. 2012 Apr 10;8(4):1334-1343. doi: 10.1021/ct2008439. Epub 2012 Feb 24.

The potentials of mean force (PMF's) for the deformation of the C(α) ⋯ C(α) virtual bonds in polypeptide chains were determined from the diabatic energy surfaces of N-methylacetamide (modeling regular peptide groups) and N-acetylpyrrolidine (modeling the peptide groups preceding...

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Sieradzan AK, Scheraga HA, Liwo A. Determination of effective potentials for the stretching of C(α) ⋯ C(α) virtual bonds in polypeptide chains for coarse-grained simulations of proteins from ab initio energy surfaces of N-methylacetamide and N-acetylpyrrolidine. J Chem Theory Comput. 2012;8(4):1334-1343doi: 10.1021/ct2008439.
Sieradzan, A. K., Scheraga, H. A., & Liwo, A. (2012). Determination of effective potentials for the stretching of C(α) ⋯ C(α) virtual bonds in polypeptide chains for coarse-grained simulations of proteins from ab initio energy surfaces of N-methylacetamide and N-acetylpyrrolidine. Journal of chemical theory and computation, 8(4), 1334-1343. https://doi.org/10.1021/ct2008439
Sieradzan, Adam K, et al. "Determination of effective potentials for the stretching of C(α) ⋯ C(α) virtual bonds in polypeptide chains for coarse-grained simulations of proteins from ab initio energy surfaces of N-methylacetamide and N-acetylpyrrolidine." Journal of chemical theory and computation vol. 8,4 (2012): 1334-1343. doi: https://doi.org/10.1021/ct2008439
Sieradzan AK, Scheraga HA, Liwo A. Determination of effective potentials for the stretching of C(α) ⋯ C(α) virtual bonds in polypeptide chains for coarse-grained simulations of proteins from ab initio energy surfaces of N-methylacetamide and N-acetylpyrrolidine. J Chem Theory Comput. 2012 Apr 10;8(4):1334-1343. doi: 10.1021/ct2008439. Epub 2012 Feb 24. PMID: 23087598; PMCID: PMC3475191.
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Extension of UNRES force field to treat polypeptide chains with D-amino-acid residues.

Journal of chemical theory and computation

Sieradzan AK, Hansmann UH, Scheraga HA, Liwo A.
PMID: 24729761
J Chem Theory Comput. 2012 Nov 13;8(11):4746-4757. doi: 10.1021/ct3005563.

Coarse-grained force fields for protein simulations are usually designed and parameterized to treat proteins composed of natural L-amino-acid residues. However, D-amino-acid residues occur in bacterial, fungal (e.g., gramicidins), as well as human-designed proteins. For this reason, we have extended...

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Sieradzan AK, Hansmann UH, Scheraga HA, et al. Extension of UNRES force field to treat polypeptide chains with D-amino-acid residues. J Chem Theory Comput. 2012;8(11):4746-4757doi: 10.1021/ct3005563.
Sieradzan, A. K., Hansmann, U. H., Scheraga, H. A., & Liwo, A. (2012). Extension of UNRES force field to treat polypeptide chains with D-amino-acid residues. Journal of chemical theory and computation, 8(11), 4746-4757. https://doi.org/10.1021/ct3005563
Sieradzan, Adam K, et al. "Extension of UNRES force field to treat polypeptide chains with D-amino-acid residues." Journal of chemical theory and computation vol. 8,11 (2012): 4746-4757. doi: https://doi.org/10.1021/ct3005563
Sieradzan AK, Hansmann UH, Scheraga HA, Liwo A. Extension of UNRES force field to treat polypeptide chains with D-amino-acid residues. J Chem Theory Comput. 2012 Nov 13;8(11):4746-4757. doi: 10.1021/ct3005563. PMID: 24729761; PMCID: PMC3982868.
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Dynamic and conformational switching in proteins.

Biopolymers

Scheraga HA, Rackovsky S.
PMID: 33270217
Biopolymers. 2021 Oct;112(10):e23411. doi: 10.1002/bip.23411. Epub 2020 Dec 03.

Using bioinformatic methods for treating protein dynamics, developed in earlier work, we study the relationship between sequence mobility and dynamics in proteins. It is shown that sequence mobility drives a transition between two dynamic regimes in proteins, and that...

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Scheraga HA, Rackovsky S. Dynamic and conformational switching in proteins. Biopolymers. 2020;112(10):e23411doi: 10.1002/bip.23411.
Scheraga, H. A., & Rackovsky, S. (2021). Dynamic and conformational switching in proteins. Biopolymers, 112(10), e23411. https://doi.org/10.1002/bip.23411
Scheraga, H A, and Rackovsky, S. "Dynamic and conformational switching in proteins." Biopolymers vol. 112,10 (2021): e23411. doi: https://doi.org/10.1002/bip.23411
Scheraga HA, Rackovsky S. Dynamic and conformational switching in proteins. Biopolymers. 2021 Oct;112(10):e23411. doi: 10.1002/bip.23411. Epub 2020 Dec 03. PMID: 33270217; PMCID: PMC8172660.
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Occurrence of a phase transition in nucleic acid models.

The Journal of chemical physics

Poland D, Scheraga HA.
PMID: 5920201
J Chem Phys. 1966 Sep 01;45(5):1464-9. doi: 10.1063/1.1727786.

No abstract available.

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Poland D, Scheraga HA. Occurrence of a phase transition in nucleic acid models. J Chem Phys. 1966;45(5):1464-9doi: 10.1063/1.1727786.
Poland, D., & Scheraga, H. A. (1966). Occurrence of a phase transition in nucleic acid models. The Journal of chemical physics, 45(5), 1464-9. https://doi.org/10.1063/1.1727786
Poland, D, and Scheraga, H A. "Occurrence of a phase transition in nucleic acid models." The Journal of chemical physics vol. 45,5 (1966): 1464-9. doi: https://doi.org/10.1063/1.1727786
Poland D, Scheraga HA. Occurrence of a phase transition in nucleic acid models. J Chem Phys. 1966 Sep 01;45(5):1464-9. doi: 10.1063/1.1727786. PMID: 5920201.
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Crystal structure prediction of small organic molecules: a second blind test.

Acta crystallographica. Section B, Structural science

Motherwell WD, Ammon HL, Dunitz JD, Dzyabchenko A, Erk P, Gavezzotti A, Hofmann DW, Leusen FJ, Lommerse JP, Mooij WT, Price SL, Scheraga H, Schweizer B, Schmidt MU, van Eijck BP, Verwer P, Williams DE.
PMID: 12149555
Acta Crystallogr B. 2002 Aug;58:647-61. doi: 10.1107/s0108768102005669. Epub 2002 Jul 30.

The first collaborative workshop on crystal structure prediction (CSP1999) has been followed by a second workshop (CSP2001) held at the Cambridge Crystallographic Data Centre. The 17 participants were given only the chemical diagram for three organic molecules and were...

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Motherwell WD, Ammon HL, Dunitz JD, et al. Crystal structure prediction of small organic molecules: a second blind test. Acta Crystallogr B. 2002;58:647-61doi: 10.1107/s0108768102005669.
Motherwell, W. D., Ammon, H. L., Dunitz, J. D., Dzyabchenko, A., Erk, P., Gavezzotti, A., Hofmann, D. W., Leusen, F. J., Lommerse, J. P., Mooij, W. T., Price, S. L., Scheraga, H., Schweizer, B., Schmidt, M. U., van Eijck, B. P., Verwer, P., & Williams, D. E. (2002). Crystal structure prediction of small organic molecules: a second blind test. Acta crystallographica. Section B, Structural science, 58647-61. https://doi.org/10.1107/s0108768102005669
Motherwell, W D Sam, et al. "Crystal structure prediction of small organic molecules: a second blind test." Acta crystallographica. Section B, Structural science vol. 58 (2002): 647-61. doi: https://doi.org/10.1107/s0108768102005669
Motherwell WD, Ammon HL, Dunitz JD, Dzyabchenko A, Erk P, Gavezzotti A, Hofmann DW, Leusen FJ, Lommerse JP, Mooij WT, Price SL, Scheraga H, Schweizer B, Schmidt MU, van Eijck BP, Verwer P, Williams DE. Crystal structure prediction of small organic molecules: a second blind test. Acta Crystallogr B. 2002 Aug;58:647-61. doi: 10.1107/s0108768102005669. Epub 2002 Jul 30. PMID: 12149555.
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Correction to Maximum Likelihood Calibration of the UNRES Force Field for Simulation of Protein Structure and Dynamics.

Journal of chemical information and modeling

Krupa P, Hałabis A, Żmudzińska W, Ołdziej S, Scheraga HA, Liwo A.
PMID: 29283263
J Chem Inf Model. 2018 Jan 22;58(1):206. doi: 10.1021/acs.jcim.7b00716. Epub 2017 Dec 28.

No abstract available.

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Krupa P, Hałabis A, Żmudzińska W, et al. Correction to Maximum Likelihood Calibration of the UNRES Force Field for Simulation of Protein Structure and Dynamics. J Chem Inf Model. 2017;58(1):206doi: 10.1021/acs.jcim.7b00716.
Krupa, P., Hałabis, A., Żmudzińska, W., Ołdziej, S., Scheraga, H. A., & Liwo, A. (2018). Correction to Maximum Likelihood Calibration of the UNRES Force Field for Simulation of Protein Structure and Dynamics. Journal of chemical information and modeling, 58(1), 206. https://doi.org/10.1021/acs.jcim.7b00716
Krupa, Paweł, et al. "Correction to Maximum Likelihood Calibration of the UNRES Force Field for Simulation of Protein Structure and Dynamics." Journal of chemical information and modeling vol. 58,1 (2018): 206. doi: https://doi.org/10.1021/acs.jcim.7b00716
Krupa P, Hałabis A, Żmudzińska W, Ołdziej S, Scheraga HA, Liwo A. Correction to Maximum Likelihood Calibration of the UNRES Force Field for Simulation of Protein Structure and Dynamics. J Chem Inf Model. 2018 Jan 22;58(1):206. doi: 10.1021/acs.jcim.7b00716. Epub 2017 Dec 28. PMID: 29283263.
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Detection of methylation, acetylation and glycosylation of protein residues by monitoring (13)C chemical-shift changes: A quantum-chemical study.

PeerJ

Garay PG, Martin OA, Scheraga HA, Vila JA.
PMID: 27547559
PeerJ. 2016 Jul 21;4:e2253. doi: 10.7717/peerj.2253. eCollection 2016.

Post-translational modifications of proteins expand the diversity of the proteome by several orders of magnitude and have a profound effect on several biological processes. Their detection by experimental methods is not free of limitations such as the amount of...

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Garay PG, Martin OA, Scheraga HA, et al. Detection of methylation, acetylation and glycosylation of protein residues by monitoring (13)C chemical-shift changes: A quantum-chemical study. PeerJ. 2016;4:e2253doi: 10.7717/peerj.2253.
Garay, P. G., Martin, O. A., Scheraga, H. A., & Vila, J. A. (2016). Detection of methylation, acetylation and glycosylation of protein residues by monitoring (13)C chemical-shift changes: A quantum-chemical study. PeerJ, 4e2253. https://doi.org/10.7717/peerj.2253
Garay, Pablo G, et al. "Detection of methylation, acetylation and glycosylation of protein residues by monitoring (13)C chemical-shift changes: A quantum-chemical study." PeerJ vol. 4 (2016): e2253. doi: https://doi.org/10.7717/peerj.2253
Garay PG, Martin OA, Scheraga HA, Vila JA. Detection of methylation, acetylation and glycosylation of protein residues by monitoring (13)C chemical-shift changes: A quantum-chemical study. PeerJ. 2016 Jul 21;4:e2253. doi: 10.7717/peerj.2253. eCollection 2016. PMID: 27547559; PMCID: PMC4963218.
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Limiting Values of the one-bond C-H Spin-Spin Coupling Constants of the Imidazole Ring of Histidine at High-pH.

Journal of molecular structure

Vila JA, Scheraga HA.
PMID: 28919647
J Mol Struct. 2017 Apr 15;1134:576-581. doi: 10.1016/j.molstruc.2017.01.022. Epub 2017 Jan 08.

Assessment of the relative amounts of the forms of the imidazole ring of Histidine (His), namely the protonated (H

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Vila JA, Scheraga HA. Limiting Values of the one-bond C-H Spin-Spin Coupling Constants of the Imidazole Ring of Histidine at High-pH. J Mol Struct. 2017;1134:576-581doi: 10.1016/j.molstruc.2017.01.022.
Vila, J. A., & Scheraga, H. A. (2017). Limiting Values of the one-bond C-H Spin-Spin Coupling Constants of the Imidazole Ring of Histidine at High-pH. Journal of molecular structure, 1134576-581. https://doi.org/10.1016/j.molstruc.2017.01.022
Vila, Jorge A, and Scheraga, Harold A. "Limiting Values of the one-bond C-H Spin-Spin Coupling Constants of the Imidazole Ring of Histidine at High-pH." Journal of molecular structure vol. 1134 (2017): 576-581. doi: https://doi.org/10.1016/j.molstruc.2017.01.022
Vila JA, Scheraga HA. Limiting Values of the one-bond C-H Spin-Spin Coupling Constants of the Imidazole Ring of Histidine at High-pH. J Mol Struct. 2017 Apr 15;1134:576-581. doi: 10.1016/j.molstruc.2017.01.022. Epub 2017 Jan 08. PMID: 28919647; PMCID: PMC5596661.
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A new approach to empirical intermolecular and conformational potential energy functions. I. Description of model and derivation of parameters.

Proceedings of the National Academy of Sciences of the United States of America

Shipman LL, Burgess AW, Scheraga HA.
PMID: 16592221
Proc Natl Acad Sci U S A. 1975 Feb;72(2):543-7. doi: 10.1073/pnas.72.2.543.

An empirical potential energy function based on the interactions of the electrons and nuclei in molecules has been developed and tested. The potential energy of interaction is approximated by the sum of the coulombic interactions between all point charge...

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Shipman LL, Burgess AW, Scheraga HA. A new approach to empirical intermolecular and conformational potential energy functions. I. Description of model and derivation of parameters. Proc Natl Acad Sci U S A. 1975;72(2):543-7doi: 10.1073/pnas.72.2.543.
Shipman, L. L., Burgess, A. W., & Scheraga, H. A. (1975). A new approach to empirical intermolecular and conformational potential energy functions. I. Description of model and derivation of parameters. Proceedings of the National Academy of Sciences of the United States of America, 72(2), 543-7. https://doi.org/10.1073/pnas.72.2.543
Shipman, L L, et al. "A new approach to empirical intermolecular and conformational potential energy functions. I. Description of model and derivation of parameters." Proceedings of the National Academy of Sciences of the United States of America vol. 72,2 (1975): 543-7. doi: https://doi.org/10.1073/pnas.72.2.543
Shipman LL, Burgess AW, Scheraga HA. A new approach to empirical intermolecular and conformational potential energy functions. I. Description of model and derivation of parameters. Proc Natl Acad Sci U S A. 1975 Feb;72(2):543-7. doi: 10.1073/pnas.72.2.543. PMID: 16592221; PMCID: PMC432349.
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Description of hydration free energy density as a function of molecular physical properties.

Biophysical chemistry

No KT, Kim SG, Cho KH, Scheraga HA.
PMID: 17030307
Biophys Chem. 1999 Apr 05;78(1):127-45. doi: 10.1016/s0301-4622(98)00225-7.

A method to calculate the solvation free energy density (SFED) at any point in the cavity surface or solvent volume surrounding a solute is proposed. In the special case in which the solvent is water, the SFED is referred...

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No KT, Kim SG, Cho KH, et al. Description of hydration free energy density as a function of molecular physical properties. Biophys Chem. 1999;78(1):127-45doi: 10.1016/s0301-4622(98)00225-7.
No, K. T., Kim, S. G., Cho, K. H., & Scheraga, H. A. (1999). Description of hydration free energy density as a function of molecular physical properties. Biophysical chemistry, 78(1), 127-45. https://doi.org/10.1016/s0301-4622(98)00225-7
No, K T, et al. "Description of hydration free energy density as a function of molecular physical properties." Biophysical chemistry vol. 78,1 (1999): 127-45. doi: https://doi.org/10.1016/s0301-4622(98)00225-7
No KT, Kim SG, Cho KH, Scheraga HA. Description of hydration free energy density as a function of molecular physical properties. Biophys Chem. 1999 Apr 05;78(1):127-45. doi: 10.1016/s0301-4622(98)00225-7. PMID: 17030307.
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Systematic review on the recurrence of postoperative nausea and vomiting after a first episode in the recovery room - implications for the treatment of PONV and related clinical trials.

BMC anesthesiology

Eberhart LH, Frank S, Lange H, Morin AM, Scherag A, Wulf H, Kranke P.
PMID: 17166262
BMC Anesthesiol. 2006 Dec 13;6:14. doi: 10.1186/1471-2253-6-14.

BACKGROUND: Despite the presence of a plethora of publications on the prevention of postoperative nausea and vomiting (PONV) only little is known how to treat established symptoms. Besides the high effort of performing these efficacy trials (much more patients...

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Eberhart LH, Frank S, Lange H, et al. Systematic review on the recurrence of postoperative nausea and vomiting after a first episode in the recovery room - implications for the treatment of PONV and related clinical trials. BMC Anesthesiol. 2006;6:14doi: 10.1186/1471-2253-6-14.
Eberhart, L. H., Frank, S., Lange, H., Morin, A. M., Scherag, A., Wulf, H., & Kranke, P. (2006). Systematic review on the recurrence of postoperative nausea and vomiting after a first episode in the recovery room - implications for the treatment of PONV and related clinical trials. BMC anesthesiology, 614. https://doi.org/10.1186/1471-2253-6-14
Eberhart, Leopold H J, et al. "Systematic review on the recurrence of postoperative nausea and vomiting after a first episode in the recovery room - implications for the treatment of PONV and related clinical trials." BMC anesthesiology vol. 6 (2006): 14. doi: https://doi.org/10.1186/1471-2253-6-14
Eberhart LH, Frank S, Lange H, Morin AM, Scherag A, Wulf H, Kranke P. Systematic review on the recurrence of postoperative nausea and vomiting after a first episode in the recovery room - implications for the treatment of PONV and related clinical trials. BMC Anesthesiol. 2006 Dec 13;6:14. doi: 10.1186/1471-2253-6-14. PMID: 17166262; PMCID: PMC1712223.
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Showing 1 to 12 of 55 entries