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PubMed1993

Molecular dynamics with weighted time-averaged restraints for a DNA octamer. Dynamic interpretation of nuclear magnetic resonance data.

For conformationally flexible molecules in solution, NMR-derived distance restraints are time-averaged. In contrast to deriving structures from NMR distance constraints via conventional restrained molecular dynamics (rMD), the range of conformational flexibility may be better represented by MD simulations using weighted time-averaged restrains (MD-tar). This approach has been utilized for dynamic structure refinement of the DNA octamer [d(GTATAATG].[d(CATATTAC)] which contains the Pribnow box consensus sequence. An improved set of distance restraints was calculated via complete relaxation matrix analysis utilizing the solution structure of the octamer which was determined previously by rMD as a starting model. MD-tar calculations were performed with the program AMBER4 under various conditions, some including explicit solvent. All trajectories generated via MD-tar exhibited reduced constraint energies and average deviations for the distances compared to standard rMD. Quantitative comparison with experimental data, i.e. two-dimensional NOE intensities and COSY-derived coupling constants yielded a significant improvement for MD-tar simulated structures relative to rMD-derived structures. The conformational envelope of the MD-tar structures is wider than that from rMD and even unrestrained MD. Explicit solvent force-fields tightened the conformational envelope, leading to even better agreement with experimental data. All MD-tar simulations exhibit sugar repuckering for basically all residues, yielding a minor population in the low N-region and one or more S-conformers. For most backbone torsion angles, one or more minor conformers were found, while the major conformations generally coincided with those obtained in standard rMD. Distributions of helical parameters for MD-tar trajectories are rather symmetric but slightly broader than those for rMD. Average values and associated standard deviations are discussed with respect to sequence-dependent variations. All trajectories obtained with an explicit solvent force field exhibited a narrower minor groove compared to in vacuo calculations.

Carbohydrate Conformation↗
PubMed2004

Molecular-dynamics simulations with explicit hydrodynamics I: on the friction coefficients of deformed polymers.

We implement large-scale Molecular-Dynamics (MD) simulations which incorporate hydrodynamic interactions via the inclusion of explicit Lennard-Jones solvent to examine the behaviour of polymer chains in sieving media. We begin by examining the friction coefficients of polymers in long-lived states responsible for inducing length-dependent mobility, i.e., allowing separation of polymers (or polyelectrolytes) by molecular weight. In particular, the conformations we examine occur in devices which utilize arrays of molecular obstacles or dilute solutions of polymers. We compare the results from our MD simulations with expressions from macroscopic hydrodynamics for four specific cases: i) a random coil excluded-volume Zimm polymer, ii) a rigid polymer moving perpendicular to its major axis iii) a rigid polymer moving parallel to its major axis and iv) a rigid polymer, folded at different points along its contour. We also examine the behaviour of the friction coefficient of a fully flexible molecule pulled by its middle monomer as a function of an applied force F and show that there are several distinct frictional regimes.

Journal Article↗
PubMed2006

Detection of second hydration shells in ionic solutions by XANES: computed spectra for Ni2+ in water based on molecular dynamics.

A general procedure to compute X-ray absorption near-edge structure (XANES) spectra within multiple-scattering theory starting from molecular dynamics (MD) structural data has been developed and applied to the study of a Ni(2+) aqueous solution. This method allows one to perform a quantitative analysis of the XANES spectra of disordered systems using a proper description of the thermal and structural fluctuations. The XANES spectrum of Ni(2+) in aqueous solution has been calculated using the structural information obtained from the MD simulations without carrying out any minimization in the structural parameter space. A very good reproduction of the experimental data was obtained including the second-shell water molecules in the calculation, thus showing that the second hydration shell provides a detectable contribution to the XANES spectra of ionic solutions. The analysis including the first-shell cluster only permitted us to quantitatively determine the effect of disorder on the amplitude of the XANES spectra for molecular complexes. These results simultaneously confirm the reliability of the procedure and the structural results obtained from MD simulations. The combination of MD and XANES is found to be very helpful to get important new insights into the quantitative estimation of structural properties of disordered systems.

Journal Article↗
PubMed2007

Molecular dynamics simulations of RNA: an in silico single molecule approach.

RNA molecules are now known to be involved in the processing of genetic information at all levels, taking on a wide variety of central roles in the cell. Understanding how RNA molecules carry out their biological functions will require an understanding of structure and dynamics at the atomistic level, which can be significantly improved by combining computational simulation with experiment. This review provides a critical survey of the state of molecular dynamics (MD) simulations of RNA, including a discussion of important current limitations of the technique and examples of its successful application. Several types of simulations are discussed in detail, including those of structured RNA molecules and their interactions with the surrounding solvent and ions, catalytic RNAs, and RNA-small molecule and RNA-protein complexes. Increased cooperation between theorists and experimentalists will allow expanded judicious use of MD simulations to complement conceptually related single molecule experiments. Such cooperation will open the door to a fundamental understanding of the structure-function relationships in diverse and complex RNA molecules. .

Catalysis↗
PubMed2003

Molecular dynamics simulation of the unfolding of the human prion protein domain under low pH and high temperature conditions.

Four 10-ns molecular dynamics (MD) simulations of the human prion protein domain (HuPrP 125-228) in explicit water solution have been performed. Each of the simulations mimicked a different environment of the protein: the neutral pH environment was simulated with all histidine residues neutral and bearing a ND proton and with other titratable side chains charged, the weakly acidic environment was simulated with all titratable side chains charged, the strongly acidic environment was simulated with all titratable side chains protonated. The protein in neutral pH environment was simulated at both ambient (298 K) and higher (350 K) temperatures. The native fold is stable in the neutral pH/ambient temperature simulation. Through out all other simulations, a quite stable core consisted of 10-20 residues around the disulfide bond retain their initial conformations. However, the secondary structures of the protein show changes of various degrees compared to the native fold, parts of the helices unfolded and the beta-sheets extended. Our simulations indicated that the heat-induced unfolding and acid-induced unfolding of HuPrP might follow different pathways: the initial stage of the acid-induced unfolding may include not only changes in secondary structures, but also changes in the tertiary structures. Under the strongly acidic condition, obvious tertiary structure changes take place after 10-ns simulation, the secondary structure elements and the loops becoming more parallel to each other, resulting in a compact state, which was stabilized by a large number of new, non-native side chain-side chain contacts. Such tertiary structure changes were not observed in the higher temperature simulation, and intuitively, they may favor the further extension of the beta-sheets and eventually the agglomeration of multiple protein molecules. The driving forces for this tertiary structure changes are discussed. Two additional 10-ns MD simulations, one with Asp202 protonated and the other with Glu196 protonated compared to the neutral pH simulation, were carried out. The results showed that the stability of the native fold is very subtle and can be strongly disturbed by eliminating a single negative charge at one of such key sites. Correlations of our results with previous experimental and theoretical studies are discussed.

Computer Simulation↗
PubMed2006

Hyaluronan: the local solution conformation determined by NMR and computer modeling is close to a contracted left-handed 4-fold helix.

The polysaccharide hyaluronan (HA) is a ubiquitous component of the vertebrate extracellular matrix with diverse physiological roles from space-filling to acting as a scaffold for other macromolecules. The molecular interactions responsible for these solution properties have been the subject of much debate and, primarily due to the lack of residue-specific experimental data, no consensus model for the three-dimensional conformation nor dynamics of HA in solution has emerged. Here, the solution conformation of HA is investigated using molecular dynamics (MD) simulations and high-field nuclear magnetic resonance (NMR). In contrast to previous studies, MD simulations incorporated explicit water molecules and sodium ions, while NMR experiments utilized (15)N-enriched oligosaccharides to allow residue-specific information to be obtained. The resultant average conformation is predicted to be almost a contracted left-handed 4-fold helix; i.e. similar to that observed for sodium hyaluronate fibers by X-ray diffraction, but with the acetamido side-chain trans to H(2). The glycosidic linkages and acetamido side-chains are predicted to have standard deviation rotations of 13 degrees and 18 degrees around their mean conformations in free solution, respectively, and are not observed to be stabilized by strong intramolecular hydrogen bonds as X-ray fiber diffraction refinements describe for the solid-state. Rather, weak and transient hydrogen bonds that are in rapid interchange with solvent molecules are predicted. These predictions are quantitatively consistent with demanding residue-specific NMR data and correspond to an HA molecule that is rod-like as an oligosaccharide and behaves as a stiffened random coil at large molecular mass, in close agreement with previous hydrodynamic observations. This new description of the solution conformation of HA is consistent with all available experimental data and accounts for its viscoelastic space-filling properties. This representation can be used as a basis for modeling the association between HA and proteins, which will elucidate important aspects of extracellular matrix assembly.

Animals↗
PubMed2004

Temperature-dependent quantum pair potentials and their application to dense partially ionized hydrogen plasmas.

Extending our previous work [J. Phys. A 36, 5957 (2003)]], we present a detailed discussion of accuracy and practical applications of finite-temperature pseudopotentials for two-component Coulomb systems. Different pseudopotentials are discussed: (i) the diagonal Kelbg potential, (ii) the off-diagonal Kelbg potential, (iii) the improved diagonal Kelbg potential, (iv) an effective potential obtained with the Feynman-Kleinert variational principle, and (v) the "exact" quantum pair potential derived from the two-particle density matrix. For the improved diagonal Kelbg potential, a simple temperature-dependent fit is derived which accurately reproduces the "exact" pair potential in the whole temperature range. The derived pseudopotentials are then used in path integral Monte Carlo and molecular-dynamics (MD) simulations to obtain thermodynamical properties of strongly coupled hydrogen. It is demonstrated that classical MD simulations with spin-dependent interaction potentials for the electrons allow for an accurate description of the internal energy of hydrogen in the difficult regime of partial ionization down to the temperatures of about 60 000 K. Finally, we point out an interesting relationship between the quantum potentials and the effective potentials used in density-functional theory.

Journal Article↗
PubMed2005

Comparison of multiple molecular dynamics trajectories calculated for the drug-resistant HIV-1 integrase T66I/M154I catalytic domain.

HIV-1 integrase (IN) is an essential enzyme for the viral replication and an interesting target for the design of new pharmaceuticals for multidrug therapy of AIDS. Single and multiple mutations of IN at residues T66, S153, or M154 confer degrees of resistance to several inhibitors that prevent the enzyme from performing its normal strand transfer activity. Four different conformations of IN were chosen from a prior molecular dynamics (MD) simulation on the modeled IN T66I/M154I catalytic core domain as starting points for additional MD studies. The aim of this article is to understand the dynamic features that may play roles in the catalytic activity of the double mutant enzyme in the absence of any inhibitor. Moreover, we want to verify the influence of using different starting points on the MD trajectories and associated dynamical properties. By comparison of the trajectories obtained from these MD simulations we have demonstrated that the starting point does not affect the conformational space explored by this protein and that the time of the simulation is long enough to achieve convergence for this system.

Biophysics↗
PubMed2005

Membrane protein structure quality in molecular dynamics simulation.

Our goal was to assess the relationship between membrane protein quality, output from protein quality checkers and output from molecular dynamics (MD) simulations. Membrane transport proteins are essential for a wide range of cellular processes. Structural features of integral membrane proteins are still under-explored due to experimental limitations in structure determination. Computational techniques can be used to exploit biochemical and medium resolution structural data, as well as sequence homology to known structures, and enable us to explore the structure-function relationships in several transmembrane proteins. The quality of the models produced is vitally important to obtain reliable predictions. An examination of the relationship between model stability in molecular dynamics (MD) simulations derived from RMSD (root mean squared deviation) and structure quality assessment from various protein quality checkers was undertaken. The results were compared to membrane protein structures, solved at various resolution, by either X-ray or electron diffraction techniques. The checking programs could predict the potential success of MD in making functional conclusions. MD stability was shown to be a good indicator for the quality of structures. The quality was also shown to be dependent on the resolution at which the structures were determined.

Computer Simulation↗
PubMed2006

Dynamics of benzene guest inside a self-assembled cylindrical capsule: a combined solid-state 2H NMR and molecular dynamics simulation study.

The reorientational dynamics of benzene-d(6) molecules hosted into the cavity of a cavitand-based, self-assembled capsule was investigated by Molecular Dynamics (MD) simulations and temperature-dependent solid-state (2)H NMR spectroscopy. MD simulations were preliminarily performed to assess the motional models of the guest molecules inside the capsules. An in-plane fast reorientation of the benzene guest around the C(6) symmetry axis (B1 motion), characterized by correlation times of the order of picoseconds, was predicted with an activation barrier ( approximately 8 kJ/mol) very similar to that found for neat benzene in the liquid state. An out-of-plane reorientation corresponding to a nutation of the C(6) symmetry axis in a cone angle of 39 degrees (B2 motion, 373 K) with an activation barrier ( approximately 39 kJ/mol) definitely larger than that of liquid benzene was also anticipated. In the temperature range 293-373 K correlation times of the order of a nanosecond have been calculated and a transition from fast to slow regime in the (2)H NMR scale has been predicted between 293 and 173 K. (2)H NMR spectroscopic analysis, carried out in the temperature range 173-373 K on the solid capsules containing the perdeuterated guest (two benzene molecules/capsule), confirmed the occurrence of the B1 and B2 motions found in slow exchange in the (2)H NMR time scale. Line shape simulation of the (2)H NMR spectral lines permitted defining a cone angle value of 39 degrees at 373 K and 35 degrees at 173 K for the nutation axis. The T(1) values measured for the (2)H nuclei of the encapsulated aromatic guest gave correlation times and energetic barrier for the in-plane motion B1 in fine agreement with theoretical calculation. The experimental correlation time for B2 as well as the corresponding energetic barrier are in the same range found for B1. A molecular mechanism for the encapsulated guest accounting for the B1 and B2 motions was also provided.

Journal Article↗
PubMed2005

Dynamic mechanism for the autophosphorylation of CheA histidine kinase: molecular dynamics simulations.

The two-component system (TCS) is an important signal transduction component for most bacteria. This signaling pathway is mediated by histidine kinases via autophosphorylation between P1 and P4 domains. Taking chemotaxis protein CheA as a model of TCS, the autophosphorylation mechanism of the TCS histidine kinases has been investigated in this study by using a computational approach integrated homology modeling, ligand-protein docking, protein-protein docking, and molecular dynamics (MD) simulations. Four nanosecond-scale MD simulations were performed on the free P4 domain, P4-ATP, P4-TNPATP, and P1-P4-ATP complexes, respectively. Upon its binding to the binding pocket of P4 with a folded conformation, ATP gradually extends to an open state with help from a water molecule. Meanwhile, ATP forms two hydrogen bonds with His413 and Lys494 at this state. Because of the lower energy of the folded conformations, ATP shrinks back to its folded conformations, leading to the rupture of the hydrogen bond between ATP and Lys494. Consequently, Lys494 moves away from the pocket entrance, resulting in an open of the ATP lid of P4. It is the open state of P4 that can bind tightly to P1, where the His45 of P1 occupies a favorable position for its autophosphorylation from ATP. This indicates that ATP is not only a phosphoryl group donor but also an activator for CheA phosphorylation. Accordingly, a mechanism of the autophosphorylation of CheA is proposed as that the ATP conformational switch triggers the opening of the ATP lid of P4, leading to P1 binding tightly, and subsequently autophosphorylation from ATP to P1.

Adenosine Triphosphate↗
PubMed2006

Exceptional thermodynamic stability of DNA duplexes modified by nonpolar base analogues is due to increased stacking interactions and favorable solvation: Correlated ab initio calculations and molecular dynamics simulations.

The geometries of DNA hexamer (5'-GGAACC-3') and DNA 13-mer (5'-GCGTACACATGCG-3') have been determined by molecular dynamics (MD) simulations using an empirical force field. The central canonical base pair was replaced by a pair of nonpolar base analogues, 2,2'-bipyridyl and 3-methylisocarbostyril. The stabilization energy of the model system (model A) consisting of a central base pair (base-analogue pair) and two neighboring base pairs was determined by the RI-MP2 method using an extended aug-cc-pVDZ basis set. The geometry of the model was averaged from structures determined by MD simulations. The role of the solvent was covered by the COSMO continuum solvent model and calculations were performed for a larger model system (model B) which also contained a sugar-phosphate backbone. The total stabilization energies of the unperturbed system and the system perturbed by a base-analogue pair (model A) were comparable to the stability of both duplexes experimentally determined. This is due to large stacking interaction energy of the base-analogue self-pair which compensates for the missing hydrogen-bonding energy of the replaced adenine...thymine base pair. The selectivity of the base-analogue pair was reproduced (model B) when their desolvation energy was included with the interaction energy of both strands determined by the approximate SCC-DFTB-D method.

Base Pairing↗
PubMed2026

Genomic and structural insights into the atpB L173I substitution: modulation of the F₀ rotor architecture in Mycobacterium tuberculosis ATP synthase and altered Bedaquiline binding dynamics.

The F₀F₁ ATP synthase of Mycobacterium tuberculosis (M. tuberculosis) is an essential membrane-embedded rotary motor responsible for ATP synthesis and maintenance of the proton motive force in bacteria. The transmembrane F₀ domain comprises the c-subunit (atpE) and the a-subunit (atpB). Their coordinated interactions are needed for proton translocation and torque generation. Bedaquiline (BDQ), FDA-approved diarylquinoline for the treatment of multidrug-resistant tuberculosis (MDR-TB), targets the F₀ motor by binding at the a-c interface and inhibiting rotary catalysis. To the best of our knowledge, this study represents the first attempt to analyze the effects of mutations in the atpB protein on its structural stability in the F₀ domain, thereby highlighting the novelty of this work. In this study, we integrated Indian whole-genome sequencing (WGS) datasets (PRJNA37907) with long-timescale (1000 ns) membrane-embedded molecular dynamics (MD) simulations. Among 57 atpB mutations identified from WGS analysis, L173I was selected for structural and MD analysis. L173I is located at the atpB-atpE interface near the BDQ-binding region, despite V177L and S184A showing higher prevalence. Comparative MD simulations encompassed four systems: wild-type apo, wild-type with BDQ, L173I apo, and L173I with BDQ. Structural interrogation revealed that the L173I substitution induces subtle destabilization of the global fold of the atpB-atpE complex relative to the apo state, while more critically attenuating inter-subunit contacts between the a-subunit and the c-ring. These perturbations provide a mechanistic rationale for reduced BDQ susceptibility, arising from altered interfacial dynamics rather than complete abrogation of drug binding. This integrative genomic-structural framework advances our understanding of ATP synthase-mediated resistance in M. tuberculosis.

Diarylquinolines↗
PubMed2003

A molecular dynamics simulation study of oriented DNA with polyamine and sodium counterions: diffusion and averaged binding of water and cations.

Four different molecular dynamics (MD) simulations have been performed for ordered DNA decamers, d(5'-ATGCAGTCAG)*d(5'-TGACTGCATC). The counterions were the two natural polyamines spermidine3+ (Spd3+) and putrescine2+ (Put2+), the synthetic polyamine diaminopropane2+ (DAP2+) and Na+. The simulation set-up corresponds to an infinite array of parallel DNA mimicking the state in oriented DNA fibers or crystals. This work describes general properties of polyamine and Na+ binding to DNA. Simulated diffusion coefficients show satisfactory agreement with experimental NMR diffusion data of comparable systems. The interaction of the polyamines with DNA is dynamic in character and the cations mostly form short-lived contacts with the electronegative binding sites of DNA. Polyamines, Na+ and water interact most frequently with the charged phosphate atoms with preference for association from the minor groove side with O1P over O2P. There is a strong anti-correlation in the cation binding to the electronegative groups of DNA, i.e. the presence of a cation near one of the DNA sites repels other cations from binding to this and to the other sites separated by <7.5 A from each other. In contrast to the other polyamines, DAP2+ is able to form 'bridges' connecting neighboring phosphate groups along the DNA strand. A small fraction of DAP2+ and Put2+ can be found in the major grooves, while Spd3+ is absent there. The results of the MD simulations reveal principal differences in the polyamine-DNA interactions between the natural (Spd3+, Put2+ and spermine4+) and synthetic (DAP2+) polyamines.

Binding Sites↗
PubMed1994

Ligand-induced domain motion in the activation mechanism of a G-protein-coupled receptor.

Rapidly accumulating information about the structures and functions of transmembrane proteins in the class of G-protein-coupled receptors is facilitating the exploration of molecular details in the processes of cellular signal transduction. We have described recently a 3-D molecular model of the transmembrane portion of the 5-HT2A type of receptor of the neurotransmitter serotonin (5-hydroxytryptamine; 5-HT), constructed from such convergent empirical and theoretical considerations, and have used it for a computational simulation of the mechanisms of ligand-induced receptor activation and signal transduction. The molecular dynamics (MD) simulation of the interaction between the receptor model and ligands of different pharmacological efficacies pointed to a set of specific conformational changes propagated from the ligand binding site to a distal region of the receptor that is essential for signal transduction. The ligand-induced changes were found to correlate well with the known pharmacological properties, but it remained unclear how the binding of the small 5-HT2A receptor agonist molecules in the distal binding pocket could give rise to the specific conformational changes in a distant part of the receptor. As the MD simulations showed the secondary structure of the helical transmembrane domains of the receptor to be well maintained, and the conformational changes to involve mainly translations and rotations of the helices in the bundle relative to one another, an algorithm was developed to treat the ligand-induced conformational changes as rigid domain movements of transmembrane helices.(ABSTRACT TRUNCATED AT 250 WORDS)

Binding Sites↗
PubMed2007

Optical spectroscopic elucidation of beta-turns in disulfide bridged cyclic tetrapeptides.

Vibrational circular dichroism (VCD) spectroscopic features of type II beta-turns were characterized previously, but, criteria for differentiation between beta-turn types had not been established yet. Model tetrapeptides, cyclized through a disulfide bridge, were designed on the basis of previous experimental results and the observed incidence of amino acid residues in the i + 1 and i + 2 positions in beta-turns, to determine the features of VCD spectra of type I and II beta-turns. The results were correlated with electronic circular dichroism (ECD) spectra and VCD spectra calculated from conformational data obtained by molecular dynamics (MD) simulations. All cyclic tetrapeptides yielded VCD signals with a higher frequency negative and a lower frequency positive couplet with negative lobes overlapping. MD simulations confirmed the conformational homogeneity of these peptides in solution. Comparison with ECD spectroscopy, MD, and quantum chemical calculation results suggested that the low frequency component of VCD spectra originating from the tertiary amide vibrations could be used to distinguish between types of beta-turn structures. On the basis of this observation, VCD spectroscopic features of type II and VIII beta-turns and ECD spectroscopic properties of a type VIII beta-turn were suggested. The need for independent experimental as well as theoretical investigations to obtain decisive conformational information was recognized.

Amino Acid Sequence↗
PubMed2006

Molecular dynamics simulations of DNA with polarizable force fields: convergence of an ideal B-DNA structure to the crystallographic structure.

We have investigated to what extent molecular dynamics (MD) simulations can reproduce DNA sequence-specific features, given different electrostatic descriptions and different cell environments. For this purpose, we have carried out multiple unrestrained MD simulations of the DNA duplex d(CCAACGTTGG)2. With respect to the electrostatic descriptions, two different force fields are studied: a traditional description based on atomic point charges and a polarizable force field. With respect to the cell environment, the difference between crystal and solution environments is emphasized, as well as the structural importance of divalent ions. By imposing the correct experimental unit cell environment, an initial configuration with two ideal B-DNA duplexes in the unit cell is shown to converge to the crystallographic structure. This convergence is measured by the appearance of sequence-dependent features that very closely resemble the crystallographic ones as well as by the decay of the all-atom root-mean-squared coordinates deviations (RMSD) with respect to the crystallographic structure. Given the appropriate crystallographic constraints, this is the first example of multiple nanosecond molecular dynamics trajectory that shows an ideal B-DNA model converging to an experimental structure, with a significant decay of RMSD.

Base Sequence↗
PubMed2000

Developing a dynamic pharmacophore model for HIV-1 integrase.

We present the first receptor-based pharmacophore model for HIV-1 integrase. The development of "dynamic" pharmacophore models is a new method that accounts for the inherent flexibility of the active site and aims to reduce the entropic penalties associated with binding a ligand. Furthermore, this new drug discovery method overcomes the limitation of an incomplete crystal structure of the target protein. A molecular dynamics (MD) simulation describes the flexibility of the uncomplexed protein. Many conformational models of the protein are saved from the MD simulations and used in a series of multi-unit search for interacting conformers (MUSIC) simulations. MUSIC is a multiple-copy minimization method, available in the BOSS program; it is used to determine binding regions for probe molecules containing functional groups that complement the active site. All protein conformations from the MD are overlaid, and conserved binding regions for the probe molecules are identified. Those conserved binding regions define the dynamic pharmacophore model. Here, the dynamic model is compared to known inhibitors of the integrase as well as a three-point, ligand-based pharmacophore model from the literature. Also, a "static" pharmacophore model was determined in the standard fashion, using a single crystal structure. Inhibitors thought to bind in the active site of HIV-1 integrase fit the dynamic model but not the static model. Finally, we have identified a set of compounds from the Available Chemicals Directory that fit the dynamic pharmacophore model, and experimental testing of the compounds has confirmed several new inhibitors.

Computer Simulation↗