DOI: 10.1529/biophysj.107.106369. Insight into the Folding Inhibition of the HIV-1 Protease by a Small Peptide

Insight into the Folding Inhibition of the HIV-1 Protease by a Small Peptide

10.1529/biophysj.107.106369

Crossref journal-article

Elsevier BV

Biophysical Journal (78)

Bibliography

Bonomi, M., Gervasio, F. L., Tiana, G., Provasi, D., Broglia, R. A., & Parrinello, M. (2007). Insight into the Folding Inhibition of the HIV-1 Protease by a Small Peptide. Biophysical Journal, 93(8), 2813â2821.

Authors 6

Massimiliano Bonomi (first)
Francesco L. Gervasio (additional)
Guido Tiana (additional)
Davide Provasi (additional)
Ricardo A. Broglia (additional)
Michele Parrinello (additional)

References 54 Referenced 36

10.1016/S0167-4838(99)00273-3 / Biochim. Biophys. Acta / Targeting the HIV-protease in AIDS therapy: a current clinical perspective by Tomasselli (2000)
10.1002/prot.10196 / Proteins / Folding and design of dimeric proteins by Tiana (2002)
10.1110/ps.8.8.1702 / Protein Sci. / Drug resistance mutations can affect dimer stability of HIV-1 protease at neutral pH by Xie (1999)
10.1074/jbc.M108136200 / J. Biol. Chem. / Folded monomer of HIV-1 protease by Ishima (2001)
10.1021/jp0219956 / J. Phys. Chem. B / The flexibility of monomeric and dimeric HIV-1 PR by Levy (2003)
10.1016/j.jmb.2004.04.028 / J. Mol. Biol. / The folding and dimerization of HIV-1 protease: evidence for a stable monomer from simulations by Levy (2004)
10.1110/ps.051670905 / Protein Sci. / Design of HIV-1-PR inhibitors that do not create resistance: blocking the folding of single monomers by Broglia (2005)
10.1016/S0959-440X(97)80002-4 / Curr. Opin. Struct. Biol. / Nucleation mechanisms in protein folding by Fersht (1997)
{'key': '10.1529/biophysj.107.106369_bib9', 'first-page': '489', 'article-title': 'Simulation of structural phase transitions by metadynamics', 'volume': '220', 'author': 'Martonak', 'year': '2005', 'journal-title': 'Zeitschrift fur Kristallographie'} / Zeitschrift fur Kristallographie / Simulation of structural phase transitions by metadynamics by Martonak (2005)
10.1038/349633a0 / Nature / Demonstration by NMR of folding domains in lysozyme by Miranker (1991)
10.1006/jmbi.2000.3618 / J. Mol. Biol. / Similarities between the spectrin SH3 domain denatured state and its folding transition state by Kortemme (2000)
10.1126/science.1060438 / Science / Persistence of native-like topology in a denatured protein in 8M urea by Shortle (2001)
10.1006/jmbi.2000.3816 / J. Mol. Biol. / NMR characterization of residual structure in the denatured state of protein L by Yi (2000)
10.1021/bi00199a029 / Biochemistry / Specific nucleus as the transition state for protein folding by Abkevich (1994)
10.1063/1.1337041 / J. Chem. Phys. / Statistical analysis of native contact formation in the folding of designed model proteins by Tiana (2001)
10.1063/1.1545087 / J. Chem. Phys. / Resistance proof, folding-inhibitor drugs by Broglia (2003)
10.1063/1.1361076 / J. Chem. Phys. / Hierarchy of events in the folding of model proteins by Broglia (2001)
10.1063/1.475435 / J. Chem. Phys. / Folding and misfolding of designed protein-like chains with mutations by Tiana (1998)
10.1002/prot.1049 / Proteins / Molecular dynamics studies on HIV-1 protease drug resistance and folding pathways by Cecconi (2001)
10.1126/science.273.5275.595 / Science / Mapping the protein universe by Holm (1996)
10.1103/PhysRevLett.80.2733 / Phys. Rev. Lett. / Vibrational dynamics of folded proteins: significance of slow and fast motions in relation to function and stability by Bahar (1998)
10.1093/protein/11.11.999 / Protein Eng. / A cooperative folding unit in HIV-1 protease. Implications for protein stability and occurrence of drug-induced mutations by Wallqvist (1998)
10.1128/JVI.73.7.6197-6202.1999 / J. Virol. / Identification of biased amino acid substitution patterns in human immunodeficiency virus type 1 isolates from patients treated with protease inhibitors by Shafer (1999)
10.1002/prot.20849 / Proteins / A folding inhibitor of the HIV-1 protease by Broglia (2006)
{'key': '10.1529/biophysj.107.106369_bib25', 'series-title': '14th Conference on Retroviruses and Opportunistic Infections (CROI)', 'article-title': 'Susceptibility to a non-conventional (folding) protease inhibitor of human immunodeficiency virus type 1 isolates in vitro', 'author': 'Rusconi', 'year': '2007'} / 14th Conference on Retroviruses and Opportunistic Infections (CROI) / Susceptibility to a non-conventional (folding) protease inhibitor of human immunodeficiency virus type 1 isolates in vitro by Rusconi (2007)
Cicero, M. L. 2007. Efficacia in vitro di un piccolo peptide nell’inibizione del folding conformazionale della proteasi di HIV-1. PhD thesis. University of Milano, Milan, Italy.
10.1021/ja062463w / J. Am. Chem. Soc. / Free-energy landscape for β hairpin folding from combined parallel tempering and metadynamics by Bussi (2006)
10.1073/pnas.202427399 / Proc. Natl. Acad. Sci. USA / Escaping free-energy minima by Laio (2002)
10.1103/PhysRevLett.90.238302 / Phys. Rev. Lett. / Efficient exploration of reactive potential energy surfaces using Car-Parrinello molecular dynamics by Iannuzzi (2003)
10.1002/cphc.200400063 / ChemPhysChem. / Azulene-to-naphthalene rearrangement: the Car-Parrinello metadynamics method explores various reaction mechanisms by Stirling (2004)
10.1021/jp037935x / J. Phys. Chem. B / Ab initio study of dehydroxylation-carbonation reaction on brucite surface by Churakov (2004)
10.1002/chem.200400171 / Chem. Eur. J. / Influence of DNA structure on the reactivity of the guanine radical cation by Gervasio (2004)
10.1021/ja048285t / J. Am. Chem. Soc. / A minimum free energy reaction path for the E2 reaction between fluoro ethane and a fluoride ion by Ensing (2004)
10.1073/pnas.0408094102 / Proc. Natl. Acad. Sci. USA / Chemical theory and computation special feature: perspective on the reactions between F− and CH3CH2F: the free energy landscape of the E2 and SN2 reaction channels by Ensing (2005)
10.1063/1.1765651 / J. Chem. Phys. / Mapping potential energy surfaces by Wu (2004)
10.1529/biophysj.103.037283 / Biophys. J. / Microscopic mechanism of antibiotics translocation through a porin by Ceccarelli (2004)
10.1021/ja0445950 / J. Am. Chem. Soc. / Flexible docking in solution using metadynamics by Gervasio (2005)
10.1021/ja0512780 / J. Am. Chem. Soc. / The role of the peripheral anionic site and cation-interactions in the ligand penetration of the human AChE gorge by Branduardi (2005)
10.1529/biophysj.106.086611 / Biophys. J. / Using metadynamics to understand the mechanism of calmodulin/target recognition at atomic detail by Fiorin (2006)
{'key': '10.1529/biophysj.107.106369_bib40', 'first-page': '75503', 'article-title': 'A molecular dynamics method for simulations in the canonical ensemble', 'volume': '90', 'author': 'Martonak', 'year': '2003', 'journal-title': 'Phys. Rev. Lett.'} / Phys. Rev. Lett. / A molecular dynamics method for simulations in the canonical ensemble by Martonak (2003)
10.1002/anie.200462760 / Angew. Chem. Int. Ed. Engl. / Exploring polymorphism: the case of benzene by Raiteri (2005)
10.1103/PhysRevLett.96.090601 / Phys. Rev. Lett. / Equilibrium free energies from nonequilibrium metadynamics by Bussi (2006)
10.1016/S0009-2614(97)01198-6 / Chem. Phys. Lett. / Parallel tempering algorithm for conformational studies of biological molecules by Hansmann (1997)
10.1016/S0009-2614(99)01123-9 / Chem. Phys. Lett. / Replica-exchange molecular dynamics method for protein folding by Sugita (1999)
10.1063/1.2393236 / J. Chem. Phys. / The free energy landscape of small peptides as obtained from metadynamics with umbrella sampling corrections by Babin (2006)
10.1002/prot.1158 / Proteins / Reading the three-dimensional structure of a protein from its amino acid sequence by Tiana (2001)
10.1021/jp984837g / J. Phys. Chem. B / Kinetic pathways of ion pair dissociation in water by Geissler (1999)
10.1002/(SICI)1096-987X(19971130)18:15<1848::AID-JCC2>3.0.CO;2-O / J. Comp. Chem. / ORAC: a molecular dynamics program to simulate complex molecular systems with realistic electrostatic interactions by Procacci (1997)
10.1002/pro.5560050311 / Protein Sci. / Three-dimensional solution structure of the HIV-1 protease complexed with DMP323, a novel cyclic urea-type inhibitor, determined by nuclear magnetic resonance spectroscopy by Yamazaki (1996)
{'key': '10.1529/biophysj.107.106369_bib50', 'series-title': 'Classical and Quantum Dynamics in Condensed Phase Simulations', 'article-title': 'Nudged elastic band method for finding minimum energy paths of transitions', 'author': 'Jonsson', 'year': '1998'} / Classical and Quantum Dynamics in Condensed Phase Simulations / Nudged elastic band method for finding minimum energy paths of transitions by Jonsson (1998)
10.1063/1.1323224 / J. Chem. Phys. / Improved tangent estimate in the nudged elastic band method for finding minimum energy paths and saddle points by Henkelman (2000)
10.1063/1.1730390 / J. Chem. Phys. / Theory of the phase transition between helix and random coil in polypeptide chains by Zimm (1959)
{'key': '10.1529/biophysj.107.106369_bib53', 'series-title': 'Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding', 'author': 'Fersht', 'year': '1998'} / Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding by Fersht (1998)
10.1016/0263-7855(96)00018-5 / J. Mol. Graph. / VMD – Visual Molecular Dynamics by Humphrey (1996)

Dates

Type	When
Created	18 years, 2 months ago (June 16, 2007, 8:11 a.m.)
Deposited	1 year, 5 months ago (March 4, 2024, 3:59 p.m.)
Indexed	1 year ago (Aug. 12, 2024, 7:49 a.m.)
Issued	17 years, 10 months ago (Oct. 1, 2007)
Published	17 years, 10 months ago (Oct. 1, 2007)
Published Print	17 years, 10 months ago (Oct. 1, 2007)

Funders 0

None

BibTeX

@article{Bonomi_2007, title={Insight into the Folding Inhibition of the HIV-1 Protease by a Small Peptide}, volume={93}, ISSN={0006-3495}, url={http://dx.doi.org/10.1529/biophysj.107.106369}, DOI={10.1529/biophysj.107.106369}, number={8}, journal={Biophysical Journal}, publisher={Elsevier BV}, author={Bonomi, Massimiliano and Gervasio, Francesco L. and Tiana, Guido and Provasi, Davide and Broglia, Ricardo A. and Parrinello, Michele}, year={2007}, month=oct, pages={2813–2821} }

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      "article-title": "Folded monomer of HIV-1 protease",
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      "author": "Ishima",
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      "volume": "340",
      "author": "Levy",
      "year": "2004",
      "journal-title": "J. Mol. Biol."
    },
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      "article-title": "Design of HIV-1-PR inhibitors that do not create resistance: blocking the folding of single monomers",
      "volume": "14",
      "author": "Broglia",
      "year": "2005",
      "journal-title": "Protein Sci."
    },
    {
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      "author": "Fersht",
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      "journal-title": "Curr. Opin. Struct. Biol."
    },
    {
      "key": "10.1529/biophysj.107.106369_bib9",
      "first-page": "489",
      "article-title": "Simulation of structural phase transitions by metadynamics",
      "volume": "220",
      "author": "Martonak",
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    {
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      "author": "Miranker",
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      "author": "Shortle",
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      "author": "Tiana",
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      "article-title": "Resistance proof, folding-inhibitor drugs",
      "volume": "118",
      "author": "Broglia",
      "year": "2003",
      "journal-title": "J. Chem. Phys."
    },
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      "author": "Broglia",
      "year": "2001",
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      "volume": "80",
      "author": "Bahar",
      "year": "1998",
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    },
    {
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      "DOI": "10.1093/protein/11.11.999",
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      "volume": "11",
      "author": "Wallqvist",
      "year": "1998",
      "journal-title": "Protein Eng."
    },
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      "first-page": "6197",
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      "volume": "73",
      "author": "Shafer",
      "year": "1999",
      "journal-title": "J. Virol."
    },
    {
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      "doi-asserted-by": "crossref",
      "first-page": "928",
      "DOI": "10.1002/prot.20849",
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      "volume": "62",
      "author": "Broglia",
      "year": "2006",
      "journal-title": "Proteins"
    },
    {
      "key": "10.1529/biophysj.107.106369_bib25",
      "series-title": "14th Conference on Retroviruses and Opportunistic Infections (CROI)",
      "article-title": "Susceptibility to a non-conventional (folding) protease inhibitor of human immunodeficiency virus type 1 isolates in vitro",
      "author": "Rusconi",
      "year": "2007"
    },
    {
      "key": "10.1529/biophysj.107.106369_bib26",
      "unstructured": "Cicero, M. L. 2007. Efficacia in vitro di un piccolo peptide nell\u2019inibizione del folding conformazionale della proteasi di HIV-1. PhD thesis. University of Milano, Milan, Italy."
    },
    {
      "key": "10.1529/biophysj.107.106369_bib27",
      "doi-asserted-by": "crossref",
      "first-page": "13435",
      "DOI": "10.1021/ja062463w",
      "article-title": "Free-energy landscape for \u03b2 hairpin folding from combined parallel tempering and metadynamics",
      "volume": "128",
      "author": "Bussi",
      "year": "2006",
      "journal-title": "J. Am. Chem. Soc."
    },
    {
      "key": "10.1529/biophysj.107.106369_bib28",
      "doi-asserted-by": "crossref",
      "first-page": "12562",
      "DOI": "10.1073/pnas.202427399",
      "article-title": "Escaping free-energy minima",
      "volume": "99",
      "author": "Laio",
      "year": "2002",
      "journal-title": "Proc. Natl. Acad. Sci. USA"
    },
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      "key": "10.1529/biophysj.107.106369_bib29",
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      "first-page": "238302",
      "DOI": "10.1103/PhysRevLett.90.238302",
      "article-title": "Efficient exploration of reactive potential energy surfaces using Car-Parrinello molecular dynamics",
      "volume": "90",
      "author": "Iannuzzi",
      "year": "2003",
      "journal-title": "Phys. Rev. Lett."
    },
    {
      "key": "10.1529/biophysj.107.106369_bib30",
      "doi-asserted-by": "crossref",
      "first-page": "1558",
      "DOI": "10.1002/cphc.200400063",
      "article-title": "Azulene-to-naphthalene rearrangement: the Car-Parrinello metadynamics method explores various reaction mechanisms",
      "volume": "5",
      "author": "Stirling",
      "year": "2004",
      "journal-title": "ChemPhysChem."
    },
    {
      "key": "10.1529/biophysj.107.106369_bib31",
      "doi-asserted-by": "crossref",
      "first-page": "11567",
      "DOI": "10.1021/jp037935x",
      "article-title": "Ab initio study of dehydroxylation-carbonation reaction on brucite surface",
      "volume": "108",
      "author": "Churakov",
      "year": "2004",
      "journal-title": "J. Phys. Chem. B"
    },
    {
      "key": "10.1529/biophysj.107.106369_bib32",
      "doi-asserted-by": "crossref",
      "first-page": "4846",
      "DOI": "10.1002/chem.200400171",
      "article-title": "Influence of DNA structure on the reactivity of the guanine radical cation",
      "volume": "10",
      "author": "Gervasio",
      "year": "2004",
      "journal-title": "Chem. Eur. J."
    },
    {
      "key": "10.1529/biophysj.107.106369_bib33",
      "doi-asserted-by": "crossref",
      "first-page": "9492",
      "DOI": "10.1021/ja048285t",
      "article-title": "A minimum free energy reaction path for the E2 reaction between fluoro ethane and a fluoride ion",
      "volume": "126",
      "author": "Ensing",
      "year": "2004",
      "journal-title": "J. Am. Chem. Soc."
    },
    {
      "key": "10.1529/biophysj.107.106369_bib34",
      "doi-asserted-by": "crossref",
      "first-page": "6755",
      "DOI": "10.1073/pnas.0408094102",
      "article-title": "Chemical theory and computation special feature: perspective on the reactions between F\u2212 and CH3CH2F: the free energy landscape of the E2 and SN2 reaction channels",
      "volume": "102",
      "author": "Ensing",
      "year": "2005",
      "journal-title": "Proc. Natl. Acad. Sci. USA"
    },
    {
      "key": "10.1529/biophysj.107.106369_bib35",
      "doi-asserted-by": "crossref",
      "first-page": "1193",
      "DOI": "10.1063/1.1765651",
      "article-title": "Mapping potential energy surfaces",
      "volume": "121",
      "author": "Wu",
      "year": "2004",
      "journal-title": "J. Chem. Phys."
    },
    {
      "key": "10.1529/biophysj.107.106369_bib36",
      "doi-asserted-by": "crossref",
      "first-page": "58",
      "DOI": "10.1529/biophysj.103.037283",
      "article-title": "Microscopic mechanism of antibiotics translocation through a porin",
      "volume": "87",
      "author": "Ceccarelli",
      "year": "2004",
      "journal-title": "Biophys. J."
    },
    {
      "key": "10.1529/biophysj.107.106369_bib37",
      "doi-asserted-by": "crossref",
      "first-page": "2600",
      "DOI": "10.1021/ja0445950",
      "article-title": "Flexible docking in solution using metadynamics",
      "volume": "127",
      "author": "Gervasio",
      "year": "2005",
      "journal-title": "J. Am. Chem. Soc."
    },
    {
      "key": "10.1529/biophysj.107.106369_bib38",
      "doi-asserted-by": "crossref",
      "first-page": "9147",
      "DOI": "10.1021/ja0512780",
      "article-title": "The role of the peripheral anionic site and cation-interactions in the ligand penetration of the human AChE gorge",
      "volume": "127",
      "author": "Branduardi",
      "year": "2005",
      "journal-title": "J. Am. Chem. Soc."
    },
    {
      "key": "10.1529/biophysj.107.106369_bib39",
      "doi-asserted-by": "crossref",
      "first-page": "2768",
      "DOI": "10.1529/biophysj.106.086611",
      "article-title": "Using metadynamics to understand the mechanism of calmodulin/target recognition at atomic detail",
      "volume": "91",
      "author": "Fiorin",
      "year": "2006",
      "journal-title": "Biophys. J."
    },
    {
      "key": "10.1529/biophysj.107.106369_bib40",
      "first-page": "75503",
      "article-title": "A molecular dynamics method for simulations in the canonical ensemble",
      "volume": "90",
      "author": "Martonak",
      "year": "2003",
      "journal-title": "Phys. Rev. Lett."
    },
    {
      "key": "10.1529/biophysj.107.106369_bib41",
      "doi-asserted-by": "crossref",
      "first-page": "3769",
      "DOI": "10.1002/anie.200462760",
      "article-title": "Exploring polymorphism: the case of benzene",
      "volume": "44",
      "author": "Raiteri",
      "year": "2005",
      "journal-title": "Angew. Chem. Int. Ed. Engl."
    },
    {
      "key": "10.1529/biophysj.107.106369_bib42",
      "doi-asserted-by": "crossref",
      "first-page": "90601",
      "DOI": "10.1103/PhysRevLett.96.090601",
      "article-title": "Equilibrium free energies from nonequilibrium metadynamics",
      "volume": "96",
      "author": "Bussi",
      "year": "2006",
      "journal-title": "Phys. Rev. Lett."
    },
    {
      "key": "10.1529/biophysj.107.106369_bib43",
      "doi-asserted-by": "crossref",
      "first-page": "140",
      "DOI": "10.1016/S0009-2614(97)01198-6",
      "article-title": "Parallel tempering algorithm for conformational studies of biological molecules",
      "volume": "281",
      "author": "Hansmann",
      "year": "1997",
      "journal-title": "Chem. Phys. Lett."
    },
    {
      "key": "10.1529/biophysj.107.106369_bib44",
      "doi-asserted-by": "crossref",
      "first-page": "141",
      "DOI": "10.1016/S0009-2614(99)01123-9",
      "article-title": "Replica-exchange molecular dynamics method for protein folding",
      "volume": "314",
      "author": "Sugita",
      "year": "1999",
      "journal-title": "Chem. Phys. Lett."
    },
    {
      "key": "10.1529/biophysj.107.106369_bib45",
      "doi-asserted-by": "crossref",
      "first-page": "204909",
      "DOI": "10.1063/1.2393236",
      "article-title": "The free energy landscape of small peptides as obtained from metadynamics with umbrella sampling corrections",
      "volume": "125",
      "author": "Babin",
      "year": "2006",
      "journal-title": "J. Chem. Phys."
    },
    {
      "key": "10.1529/biophysj.107.106369_bib46",
      "doi-asserted-by": "crossref",
      "first-page": "421",
      "DOI": "10.1002/prot.1158",
      "article-title": "Reading the three-dimensional structure of a protein from its amino acid sequence",
      "volume": "45",
      "author": "Tiana",
      "year": "2001",
      "journal-title": "Proteins"
    },
    {
      "key": "10.1529/biophysj.107.106369_bib47",
      "doi-asserted-by": "crossref",
      "first-page": "3706",
      "DOI": "10.1021/jp984837g",
      "article-title": "Kinetic pathways of ion pair dissociation in water",
      "volume": "103",
      "author": "Geissler",
      "year": "1999",
      "journal-title": "J. Phys. Chem. B"
    },
    {
      "key": "10.1529/biophysj.107.106369_bib48",
      "doi-asserted-by": "crossref",
      "first-page": "1848",
      "DOI": "10.1002/(SICI)1096-987X(19971130)18:15<1848::AID-JCC2>3.0.CO;2-O",
      "article-title": "ORAC: a molecular dynamics program to simulate complex molecular systems with realistic electrostatic interactions",
      "volume": "18",
      "author": "Procacci",
      "year": "1997",
      "journal-title": "J. Comp. Chem."
    },
    {
      "key": "10.1529/biophysj.107.106369_bib49",
      "doi-asserted-by": "crossref",
      "first-page": "495",
      "DOI": "10.1002/pro.5560050311",
      "article-title": "Three-dimensional solution structure of the HIV-1 protease complexed with DMP323, a novel cyclic urea-type inhibitor, determined by nuclear magnetic resonance spectroscopy",
      "volume": "5",
      "author": "Yamazaki",
      "year": "1996",
      "journal-title": "Protein Sci."
    },
    {
      "key": "10.1529/biophysj.107.106369_bib50",
      "series-title": "Classical and Quantum Dynamics in Condensed Phase Simulations",
      "article-title": "Nudged elastic band method for finding minimum energy paths of transitions",
      "author": "Jonsson",
      "year": "1998"
    },
    {
      "key": "10.1529/biophysj.107.106369_bib51",
      "doi-asserted-by": "crossref",
      "first-page": "9978",
      "DOI": "10.1063/1.1323224",
      "article-title": "Improved tangent estimate in the nudged elastic band method for finding minimum energy paths and saddle points",
      "volume": "113",
      "author": "Henkelman",
      "year": "2000",
      "journal-title": "J. Chem. Phys."
    },
    {
      "key": "10.1529/biophysj.107.106369_bib52",
      "doi-asserted-by": "crossref",
      "first-page": "526",
      "DOI": "10.1063/1.1730390",
      "article-title": "Theory of the phase transition between helix and random coil in polypeptide chains",
      "volume": "31",
      "author": "Zimm",
      "year": "1959",
      "journal-title": "J. Chem. Phys."
    },
    {
      "key": "10.1529/biophysj.107.106369_bib53",
      "series-title": "Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding",
      "author": "Fersht",
      "year": "1998"
    },
    {
      "key": "10.1529/biophysj.107.106369_bib54",
      "doi-asserted-by": "crossref",
      "first-page": "33",
      "DOI": "10.1016/0263-7855(96)00018-5",
      "article-title": "VMD \u2013 Visual Molecular Dynamics",
      "volume": "14",
      "author": "Humphrey",
      "year": "1996",
      "journal-title": "J. Mol. Graph."
    }
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