| P50 | author | Carlo Camilloni | Q41044981 |
| | Guido Tiana | Q55222631 |
| | Gennady Verkhivker | Q58883705 |
| P2093 | author name string | Davide Provasi | |
| | Ricardo A Broglia | |
| P2860 | cites work | HIV-1 protease molecular dynamics of a wild-type and of the V82F/I84V mutant: possible contributions to drug resistance and a potential new target site for drugs | Q24646227 |
| | Active human immunodeficiency virus protease is required for viral infectivity | Q24647696 |
| | Human immunodeficiency virus has an aspartic-type protease that can be inhibited by pepstatin A | Q24649411 |
| | Solution structure of the mature HIV-1 protease monomer: insight into the tertiary fold and stability of a precursor | Q27641889 |
| | Conformational flexibility in the flap domains of ligand-free HIV protease | Q27646822 |
| | The three-dimensional structure of the aspartyl protease from the HIV-1 isolate BRU | Q27648999 |
| | Novel binding mode of highly potent HIV-proteinase inhibitors incorporating the (R)-hydroxyethylamine isostere | Q27656274 |
| | Conserved folding in retroviral proteases: crystal structure of a synthetic HIV-1 protease | Q27696384 |
| | X-ray analysis of HIV-1 proteinase at 2.7 A resolution confirms structural homology among retroviral enzymes | Q27703747 |
| | ABT-538 is a potent inhibitor of human immunodeficiency virus protease and has high oral bioavailability in humans | Q27729982 |
| | Crystal structure at 1.9-A resolution of human immunodeficiency virus (HIV) II protease complexed with L-735,524, an orally bioavailable inhibitor of the HIV proteases | Q27730719 |
| | Viracept (nelfinavir mesylate, AG1343): a potent, orally bioavailable inhibitor of HIV-1 protease | Q27748305 |
| | Scalable molecular dynamics with NAMD | Q27860718 |
| | GROMACS: fast, flexible, and free | Q27860998 |
| | A synthetic HIV-1 protease inhibitor with antiviral activity arrests HIV-like particle maturation | Q28336106 |
| | Development and testing of a general amber force field | Q29547642 |
| | Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models | Q29616389 |
| | Low-throughput model design of protein folding inhibitors. | Q30158062 |
| | HIV-1 protease substrate binding and product release pathways explored with coarse-grained molecular dynamics | Q30479516 |
| | HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations | Q31029932 |
| | Inhibitors of HIV-1 protease: a major success of structure-assisted drug design | Q32059371 |
| | Folding regulates autoprocessing of HIV-1 protease precursor | Q33210584 |
| | Rapid synthesis and in situ screening of potent HIV-1 protease dimerization inhibitors | Q33240785 |
| | Folding funnels, binding funnels, and protein function | Q33674287 |
| | Folding and binding cascades: shifts in energy landscapes | Q33723481 |
| | Folding and binding cascades: dynamic landscapes and population shifts | Q33876426 |
| | Protein folding: binding of conformationally fluctuating building blocks via population selection | Q34449519 |
| | The GROMOS software for biomolecular simulation: GROMOS05. | Q34457783 |
| | Curling of flap tips in HIV-1 protease as a mechanism for substrate entry and tolerance of drug resistance | Q34513432 |
| | Gated binding of ligands to HIV-1 protease: Brownian dynamics simulations in a coarse-grained model | Q34600960 |
| | Speeding up parallel GROMACS on high-latency networks | Q34615212 |
| | Speeding molecular recognition by using the folding funnel: the fly-casting mechanism | Q35189399 |
| | Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand binding | Q35612259 |
| | Protein topology determines binding mechanism | Q35734060 |
| | Insight into the folding inhibition of the HIV-1 protease by a small peptide | Q36008703 |
| | Crystal structures of a multidrug-resistant human immunodeficiency virus type 1 protease reveal an expanded active-site cavity | Q36529238 |
| | Dimerization inhibitors of HIV-1 reverse transcriptase, protease and integrase: a single mode of inhibition for the three HIV enzymes? | Q36548868 |
| | A solution NMR study of the binding kinetics and the internal dynamics of an HIV-1 protease-substrate complex | Q36572105 |
| | Rapid structural fluctuations of the free HIV protease flaps in solution: relationship to crystal structures and comparison with predictions of dynamics calculations | Q36639010 |
| | Calculation of protein-ligand binding affinities. | Q36698596 |
| | HIV-1 protease: structure, dynamics, and inhibition | Q36857092 |
| | HIV-1 protease flaps spontaneously close to the correct structure in simulations following manual placement of an inhibitor into the open state | Q36914395 |
| | Deciphering common failures in molecular docking of ligand-protein complexes. | Q38305525 |
| | Discovery and selection of TMC114, a next generation HIV-1 protease inhibitor | Q40446011 |
| | Hydrophobic sliding: a possible mechanism for drug resistance in human immunodeficiency virus type 1 protease | Q42634144 |
| | "Wide-open" 1.3 A structure of a multidrug-resistant HIV-1 protease as a drug target | Q42675231 |
| | Design of HIV-1-PR inhibitors that do not create resistance: blocking the folding of single monomers | Q43057874 |
| | Fly-casting in protein-DNA binding: frustration between protein folding and electrostatics facilitates target recognition | Q43496890 |
| | Folded monomer of HIV-1 protease | Q43764692 |
| | Monte Carlo simulations of the peptide recognition at the consensus binding site of the constant fragment of human immunoglobulin G: the energy landscape analysis of a hot spot at the intermolecular interface | Q43814574 |
| | Optimization and computational evaluation of a series of potential active site inhibitors of the V82F/I84V drug-resistant mutant of HIV-1 protease: an application of the relaxed complex method of structure-based drug design | Q43909316 |
| | Computational detection of the binding-site hot spot at the remodeled human growth hormone-receptor interface. | Q44175684 |
| | Revisiting monomeric HIV-1 protease. Characterization and redesign for improved properties | Q44240364 |
| | Fast peptidyl cis-trans isomerization within the flexible Gly-rich flaps of HIV-1 protease | Q44647434 |
| | Computational analysis of ligand binding dynamics at the intermolecular hot spots with the aid of simulated tempering and binding free energy calculations | Q44853004 |
| | Lessons learned fighting HIV can be applied to anti-cancer drug design | Q45254499 |
| | Computational characterization of structural role of the non-active site mutation M36I of human immunodeficiency virus type 1 protease | Q45403633 |
| | HIVdb: a database of the structures of human immunodeficiency virus protease | Q45730318 |
| | Binding pathways of ligands to HIV-1 protease: coarse-grained and atomistic simulations | Q46077493 |
| | In silico profiling of tyrosine kinases binding specificity and drug resistance using Monte Carlo simulations with the ensembles of protein kinase crystal structures. | Q46079038 |
| | Restrained molecular dynamics simulations of HIV-1 protease: the first step in validating a new target for drug design | Q46172149 |
| | Computational proteomics of biomolecular interactions in the sequence and structure space of the tyrosine kinome: deciphering the molecular basis of the kinase inhibitors selectivity | Q46486140 |
| | Molecular dynamics and free energy studies on the wild-type and double mutant HIV-1 protease complexed with amprenavir and two amprenavir-related inhibitors: mechanism for binding and drug resistance | Q46523471 |
| | A folding inhibitor of the HIV-1 protease. | Q46873034 |
| | The folding and dimerization of HIV-1 protease: evidence for a stable monomer from simulations | Q47378914 |
| | Closing of the flaps of HIV-1 protease induced by substrate binding: a model of a flap closing mechanism in retroviral aspartic proteases. | Q50479299 |
| | Flap opening mechanism of HIV-1 protease. | Q50482899 |
| | Molecular dynamics simulations of HIV-1 protease monomer: Assembly of N-terminus and C-terminus into beta-sheet in water solution. | Q50923985 |
| | Disruption of the HIV-1 protease dimer with interface peptides: structural studies using NMR spectroscopy combined with [2-(13)C]-Trp selective labeling. | Q52576370 |
| | Flap opening in HIV-1 protease simulated by 'activated' molecular dynamics. | Q53849991 |
| | Prediction of HIV-1 protease inhibitor resistance using a protein-inhibitor flexible docking approach. | Q53867047 |
| | Structural Insights into the Mechanisms of Drug Resistance in HIV-1 Protease NL4-3 | Q57976076 |
| | Flap opening dynamics in HIV-1 protease explored with a coarse-grained model | Q58022446 |
| | Flap opening and dimer-interface flexibility in the free and inhibitor-bound HIV protease, and their implications for function | Q73047075 |
| | Cooperative fluctuations of unliganded and substrate-bound HIV-1 protease: a structure-based analysis on a variety of conformations from crystallography and molecular dynamics simulations | Q73271590 |
| | Determining the 3D structure of HIV-1 protease | Q73905414 |
| | Continuum solvent studies of the stability of RNA hairpin loops and helices | Q74532607 |
| | A cooperative folding unit in HIV-1 protease. Implications for protein stability and occurrence of drug-induced mutations | Q77757692 |
| | Molecular tongs containing amino acid mimetic fragments: new inhibitors of wild-type and mutated HIV-1 protease dimerization | Q79946013 |
| | Mutational and structural studies aimed at characterizing the monomer of HIV-1 protease and its precursor | Q80107609 |
| | An alternative strategy for inhibiting multidrug-resistant mutants of the dimeric HIV-1 protease by targeting the subunit interface | Q80354592 |
| | A molecular dynamics study comparing a wild-type with a multiple drug resistant HIV protease: differences in flap and aspartate 25 cavity dimensions | Q80595817 |
| | Solvation influences flap collapse in HIV-1 protease | Q80947725 |
| | Molecular dynamics studies on HIV-1 protease: a comparison of the flap motions between wild type protease and the M46I/G51D double mutant | Q81041303 |
| | A diverse view of protein dynamics from NMR studies of HIV-1 protease flaps | Q81349949 |
| | Mechanism of drug resistance revealed by the crystal structure of the unliganded HIV-1 protease with F53L mutation | Q82994000 |
| P433 | issue | 2 | |
| P407 | language of work or name | English | Q1860 |
| P304 | page(s) | 550-562 | |
| P577 | publication date | 2008-03-28 | |
| P1433 | published in | Biophysical Journal | Q2032955 |
| P1476 | title | Atomistic simulations of the HIV-1 protease folding inhibition | |
| P478 | volume | 95 | |