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1.
    
Molecular docking falls into the general category of global optimization problems because its main purpose is to find the most stable complex consisting of a receptor and its ligand. Conformational space annealing (CSA), a powerful global optimization method, is incorporated with the Tinker molecular modeling package to perform molecular docking simulations of six receptor-ligand complexes (3PTB, 1ULB, 2CPP, 1STP, 3CPA, and 1PPH) from the Protein Data Bank. In parallel, Monte Carlo with the minimization (MCM) method is also incorporated into the Tinker package for comparison. The energy function, consisting of electrostatic interactions, van der Waals interactions, and torsional energy terms, is calculated using the AMBER94 all-atom empirical force field. Rigid docking simulations for all six complexes and flexible docking simulations for three complexes (1STP, 3CPA, and 1PPH) are carried out using the CSA and the MCM methods. The simulation results show that the docking procedures using the CSA method generally find the most stable complexes as well as the native-like complexes more efficiently and accurately than those using the MCM, demonstrating that CSA is a promising search method for molecular docking problems.  相似文献   

2.
    
We consider the problem of loop closure, i.e., of finding the ensemble of possible backbone structures of a chain segment of a protein molecule that is geometrically consistent with preceding and following parts of the chain whose structures are given. We reduce this problem of determining the loop conformations of six torsions to finding the real roots of a 16th degree polynomial in one variable, based on the robotics literature on the kinematics of the equivalent rotator linkage in the most general case of oblique rotators. We provide a simple intuitive view and derivation of the polynomial for the case in which each of the three pair of torsional axes has a common point. Our method generalizes previous work on analytical loop closure in that the torsion angles need not be consecutive, and any rigid intervening segments are allowed between the free torsions. Our approach also allows for a small degree of flexibility in the bond angles and the peptide torsion angles; this substantially enlarges the space of solvable configurations as is demonstrated by an application of the method to the modeling of cyclic pentapeptides. We give further applications to two important problems. First, we show that this analytical loop closure algorithm can be efficiently combined with an existing loop-construction algorithm to sample loops longer than three residues. Second, we show that Monte Carlo minimization is made severalfold more efficient by employing the local moves generated by the loop closure algorithm, when applied to the global minimization of an eight-residue loop. Our loop closure algorithm is freely available at http://dillgroup. ucsf.edu/loop_closure/.  相似文献   

3.
    
Molecular Dynamics (MD) and Monte Carlo (MC) based simulation methods are widely used to investigate molecular and nanoscale structures and processes. While the investigation of systems in MD simulations is limited by very small time steps, MC methods are often stifled by low acceptance rates for moves that significantly perturb the system. In many Metropolis MC methods with hard potentials, the acceptance rate drops exponentially with the number of uncorrelated, simultaneously proposed moves. In this work, we discuss a multiparticle Acceptance Rate Optimized Monte Carlo approach (AROMoCa) to construct collective moves with near unit acceptance probability, while preserving detailed balance even for large step sizes. After an illustration of the protocol, we demonstrate that AROMoCa significantly accelerates MC simulations in four model systems in comparison to standard MC methods. AROMoCa can be applied to all MC simulations where a gradient of the potential is available and can help to significantly speed up molecular simulations. © 2015 Wiley Periodicals, Inc.  相似文献   

4.
    
We present a novel method for the local optimization of molecular complexes. This new approach is especially suited for usage in molecular docking. In molecular modeling, molecules are often described employing a compact representation to reduce the number of degrees of freedom. This compact representation is realized by fixing bond lengths and angles while permitting changes in translation, orientation, and selected dihedral angles. Gradient‐based energy minimization of molecular complexes using this representation suffers from well‐known singularities arising during the optimization process. We suggest an approach new in the field of structure optimization that allows to employ gradient‐based optimization algorithms for such a compact representation. We propose to use exponential mapping to define the molecular orientation which facilitates calculating the orientational gradient. To avoid singularities of this parametrization, the local minimization algorithm is modified to change efficiently the orientational parameters while preserving the molecular orientation, i.e. we perform well‐defined jumps on the objective function. Our approach is applicable to continuous, but not necessarily differentiable objective functions. We evaluated our new method by optimizing several ligands with an increasing number of internal degrees of freedom in the presence of large receptors. In comparison to the method of Solis and Wets in the challenging case of a non‐differentiable scoring function, our proposed method leads to substantially improved results in all test cases, i.e. we obtain better scores in fewer steps for all complexes. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009  相似文献   

5.
    
We address a major obstacle to macromolecular docking algorithms by presenting a new method that takes into account the induced conformational adjustment of flexible loops situated at a protein/macromolecule interface. The method, MC2, is based on a multiple copy representation of the loops, coupled with a Monte Carlo conformational search of the relative position of the macromolecules and their side chain conformations. The selection of optimal loop conformations takes place during Monte Carlo cycling by the iterative adjustment of the weight of each copy. We describe here the parameterization of the method and trials on a protein-DNA complex of known 3-D structure, involving the Drosophila prd paired domain protein and its target oligonucleotide Wenqing, X. et al., Cell 1995, 80, 639. We demonstrate that our algorithm can correctly configure and position this protein, despite its relatively complex interactions with both grooves of DNA.  相似文献   

6.
    
An approach has been devised and tested for preserving the molecular dynamics molecular geometry taking into account energetic considerations during Reverse Monte Carlo (RMC) modeling. Instead of the commonly used fixed neighbor constraints, where molecules are held together by constraining distance ranges available for the specified atom pairs, here molecules are kept together via bond, angle, and dihedral potential energies. The scaled total potential energy contributes to the measure of the goodness‐of‐fit, thus, the atoms can be prevented from drifting apart. In some of the calculations (Lennard‐Jones and Coulombic) nonbonding potentials were also applied. The algorithm was successfully tested for the X‐ray structure factor‐based structure study of liquid dimethyl trisulfide, for which material now significantly more sensible results have been obtained than during previous attempts via any earlier version of RMC modeling. It is envisaged that structural modeling of a large class of materials, primarily liquids and amorphous solids containing molecules of up to about 100 atoms, will make use of the new code in the near future. © 2012 Wiley Periodicals, Inc.  相似文献   

7.
Although most ABA triblock copolymers are molecularly symmetric (i.e., the terminal blocks possess the same mass), molecularly asymmetric A1BA2 triblock copolymers are of greater fundamental interest in that they can be used to explore the transition from diblock to triblock copolymer in systematic fashion. In this study, we use a lattice Monte Carlo method known as the cooperative motion algorithm to simulate molten ABA triblock copolymers possessing a short terminal block to explore the effect of molecular asymmetry on the copolymer order–disorder transition (ODT). Reduced ODT temperatures, discerned by simultaneously analyzing several features of the simulation results, are found to compare favorably with experimental data. Of particular interest here is the initial depression in the ODT temperature for A1BA2 copolymers possessing a relatively short terminal (A2) block. This signature feature is successfully captured by the simulations and is found to be strongly dependent on composition, but weakly dependent on copolymer chain length. © 2012 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2013  相似文献   

8.
The condensed phase of the alternating copolyester of p-hydroxybenzoic acid (HBA) and 2-hydroxy-6-naphthoic acid (HNA) is investigated by studying the room temperature packing arrangement of the copolymer chains. A molecular modeling methodology is employed with a Monte Carlo sampling of the configurational phase space. Realistic poly(HBA-alt-HNA) polymer chains are represented by an explicit atom representation of the HBA/HNA dimers. States are sampled from the NVT ensemble using a sampling scheme consisting of (1) valence and torsional variations, (2) rigid body rotations of the chain about the chain axis, and (3) rigid body translations of the chain. The effect of chain packing on the conformation of chains, as well as the relative intra- and intermolecular orientations of aromatic rings, is investigated. Correlation of chain positioning along the chain axis is dominated by aromatic rings maintaining a center-to-center plane of registry. These layers of aromatic units pack with a preference for edge-to-face orientations in a herringbone-type pattern and have an intermolecular ring angle between the pairs of aromatic rings in the unit cell that is ca. 68°. The aromatic rings, on average, are rotated 38° out from the b–c plane. The phenylene rings of these copolyesters are less restricted in their relative orientation in comparison to the naphthalene rings. Intramolecular orientational probability density distributions indicate a preference for staggering the successive aromatic rings along the chain, with a staggering angle of ca. 66°. © 1998 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 36: 727–741, 1998  相似文献   

9.
Simulations of polymer‐solvent and polymer‐polymer aggregates, in which the study of hydrogen bonding plays an important role, have been carried out with two blend systems. The aim was to examine the influence of the solvent on blend complexation and to compare the strength of different hydrogen bonds in a blend system. We quantified the strength of one hydrogen bond in the blend environments. For this we used the EVOCAP software, developed by our institute. It allows the building of large molecular aggregates with realistic and homogeneous densities, with an implemented positioning algorithm of the molecules under consideration and their excluded volume, and a charge equilibration method for the partial charge calculation. In the simulated aggregates the specific interaction energy of the hydrogen atom forming the hydrogen bond was a useful indicator for our studies. Through a direct correlation of this specific‐interaction energy with the strength of the hydrogen bond, we supported the experimental result that, in toluene, complex formation between poly(methyl methacrylate) (PMMA) and PSOH, a hydroxyl‐modified polystyrene, is possible, but not in tetrahydrofuran. Varying the proton‐donor polymer, also a hydroxyl‐modified polystyrene, in blends of poly(vinyl methyl ether) (PVME) with groups of different donor strength, we reconstructed the experimental row of increasing hydrogen‐bond strengths.  相似文献   

10.
    
Simulated annealing (SA) is a popular global minimizer that can conveniently be applied to complex macromolecular systems. Thus, a molecular dynamics or a Monte Carlo simulation starts at high temperature, which is decreased gradually, and the system is expected to reach the low-energy region on the potential energy surface of the molecule. However, in many cases this process is not efficient. Alternatively, the low-energy region can be reached more effectively by minimizing the energy of selected molecular structures generated along the simulation pathway. The efficiency of SA to locate energy-minimized structures within 5 kcal/mol above the global energy minimum is studied as applied to three peptide models with increasing geometrical restrictions: (1) The linear pentapeptide Leu-enkephalin described by the ECEPP potential, (2) a cyclic hexapeptide described by the GROMOS force field energy EGRO alone, and (3) the same cyclic peptide with EGRO combined with a restraining potential based on 31 proton–proton restraints obtained from nuclear magnetic resonance (NMR) experiments. The efficiency of SA is compared to that of the Monte Carlo minimization (MCM) method of Li and Scheraga, and to our local torsional deformations (LTD) method for the conformational search of cyclic molecules. The results for the linear peptide show that SA provides a relatively weak guidance towards the most stable energy region; as expected, this guidance increases for the cyclic peptide and the cyclic peptide with NMR restraints. However, in general, MCM and LTD are significantly more efficient than SA as generators of low-energy minimized structures. This suggests that LTD might provide a better search tool than SA in structure determination of protein regions for which a relatively small number of restraints are provided by NMR. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1659–1670, 1999  相似文献   

11.
    
In this study, we propose a novel optimization algorithm, with application to the refinement of molecular complexes. Particularly, we consider optimization problem as the calculation of quasi-static trajectories of rigid bodies influenced by the inverse-inertia-weighted energy gradient and introduce the concept of advancement region that guarantees displacement of a molecule strictly within a relevant region of conformational space. The advancement region helps to avoid typical energy minimization pitfalls, thus, the algorithm is suitable to work with arbitrary energy functions and arbitrary types of molecular complexes without necessary tuning of its hyper-parameters. Our method, called controlled-advancement rigid-body optimization of nanosystems (Carbon), is particularly useful for the large-scale molecular refinement, as for example, the putative binding candidates obtained with protein–protein docking pipelines. Implementation of Carbon with user-friendly interface is available in the SAMSON platform for molecular modeling at https://www.samson-connect.net . © 2019 Wiley Periodicals, Inc.  相似文献   

12.
    
The solubility of N2 in poly(α‐n‐hexyl‐β,L ‐aspartate), a stereoregular poly(β‐peptide), was investigated with atomistic Monte Carlo simulations. The structure of this material is intermediate between that of polymers able to form a three‐dimensional crystal lattice and that of liquid‐crystalline polymers with a biphasic distribution. The dependence of the calculated solubility coefficients on both the parameters of the force field and the temperature was examined. The results are compared with recently reported experimental data. Furthermore, the motion of the penetrant molecules within the polymer matrix was analyzed. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 2928–2936, 2003  相似文献   

13.
    
The Cavity Energetic Sizing Algorithm (CESA) method of in 't Veld (J Phys Chem B 2000, 104, 12028) is extended to characterize the nonspherical nature of free volume. The new technique is introduced with reference to simple model fluids (water, hard spheres, and a Lennard‐Jones fluid) and then applied to polymers of interest to membrane scientists. A set of shape parameters is introduced, characterizing nanopores in terms of surface area, volume, radius of gyration, and span. Results are presented for Lennard‐Jones fluid and hard sphere fluid, and for the high free volume polymers (poly‐trimethyl‐silyl‐propane) poly(1‐trimethylsilyl‐1‐propyne) (PTMSP) and a random copolymer of 2,2‐bis(trifluoromethyl)‐4,5‐difluoro‐1,3‐dioxole (TFE/BDD). PTMSP is observed to have an average free volume cluster span of 1.43 nm, compared to TFE/BDD with an average cluster span of 0.98 nm, consistent with the markedly higher permeability of CO2 observed in PTMSP. An additional method for measuring free volume is introduced, similar to a method introduced by Greenfield and Theodorou (Macromolecules 1993, 26, 5461; Mol Simul 1997, 19, 329; Macromolecules 1998, 31, 7068; 2001, 34, 8541), which measures free volume relative to a specific probe. The method captures 1–3 times the fractional cavity volume captured by CESA. Free volume measurements are presented for a set of polysulfones with respect to noble gas probes (J Chem Phys 2005, 122, 84906; J Mol Struct 2005, 739, 173). © 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44:1385–1393, 2006  相似文献   

14.
    
A comprehensive mathematical model was developed using Monte Carlo simulation to describe the mechanism of ethylene and α-olefin copolymerization. The model studies the polymerization mechanism using coordination catalysts and is able to predict molecular weight and detailed chemical composition distributions. This work is considered to be a useful tool that enables us to understand and described the monomer sequence distribution as a function of chain length in semi-batch polymerization reactors.  相似文献   

15.
    
Obesity is one of the most provoking health burdens in the developed countries. One of the strategies to prevent obesity is the inhibition of pancreatic lipase enzyme. The aim of this study was to build QSAR models for natural lipase inhibitors by using the Monte Carlo method. The molecular structures were represented by the simplified molecular input line entry system (SMILES) notation and molecular graphs. Three sets – training, calibration and test set of three splits – were examined and validated. Statistical quality of all the described models was very good. The best QSAR model showed the following statistical parameters: r2 = 0.864 and Q2 = 0.836 for the test set and r2 = 0.824 and Q2 = 0.819 for the validation set. Structural attributes for increasing and decreasing the activity (expressed as pIC50) were also defined. Using defined structural attributes, the design of new potential lipase inhibitors is also presented. Additionally, a molecular docking study was performed for the determination of binding modes of designed molecules.  相似文献   

16.
    
Parameterization of a molecular dynamics force field is essential in realistically modeling the physicochemical processes involved in a molecular system. This step is often challenging when the equations involved in describing the force field are complicated as well as when the parameters are mostly empirical. ReaxFF is one such reactive force field which uses hundreds of parameters to describe the interactions between atoms. The optimization of the parameters in ReaxFF is done such that the properties predicted by ReaxFF matches with a set of quantum chemical or experimental data. Usually, the optimization of the parameters is done by an inefficient single‐parameter parabolic‐search algorithm. In this study, we use a robust metropolis Monte‐Carlo algorithm with simulated annealing to search for the optimum parameters for the ReaxFF force field in a high‐dimensional parameter space. The optimization is done against a set of quantum chemical data for MgSO4 hydrates. The optimized force field reproduced the chemical structures, the equations of state, and the water binding curves of MgSO4 hydrates. The transferability test of the ReaxFF force field shows the extend of transferability for a particular molecular system. This study points out that the ReaxFF force field is not indefinitely transferable. © 2013 Wiley Periodicals, Inc.  相似文献   

17.
    
Cassandra is an open source atomistic Monte Carlo software package that is effective in simulating the thermodynamic properties of fluids and solids. The different features and algorithms used in Cassandra are described, along with implementation details and theoretical underpinnings to various methods used. Benchmark and example calculations are shown, and information on how users can obtain the package and contribute to it are provided. © 2017 Wiley Periodicals, Inc.  相似文献   

18.
    
This article presents effects of polydispersity in polymers grafted on spherical surfaces on grafted polymer chain conformations, grafted layer thickness, and free‐end monomer distribution within the grafted layer. At brush‐like grafting densities, as polydispersity index (PDI) increases, the scaling exponent of radius of gyration of grafted chains approaches that of a single chain grafted on the same nanoparticle, because polydispersity alleviates monomer crowding within the brush. At high PDI, the chains shorter than the number average chain length, Nn, have more compressed conformations, and the chains longer than Nn overall stretch less than in the monodisperse case. As seen in polydisperse flat brushes at high grafting densities, the grafted layer thickness on spherical nanoparticle increases with PDI. Polydispersity eliminates the region near the surface devoid of free‐end monomers seen in monodisperse cases, and it reduces the width of free‐end monomer distribution and shifts the free‐end monomer distribution close to the surface. © 2012 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2012  相似文献   

19.
    
A computer simulation model was used to study the polymerization behavior of multifunctional, vegetable‐oil‐derived macromonomers. Mixtures of olefins (A) and acrylates (B) were initially randomly dispersed on a cubic lattice of size L3. Interactions between A, B, and the solvent sites were considered with respect to their relative proximity, mobility and some kinetics. The Metropolis algorithm was used to move each functional group (A and B). Stirred and equilibrated samples were prepared before reaction initiation. Reactions between the functional groups were implemented with a bonding probability kαβ, which was subject to the availability of unsaturated bonds. The conversion factor, that is, the growth of A–B bonds, was analyzed for a range of polymer concentrations (p = 0.2–0.8) with different reaction probabilities (i.e., kαβ). A stirred (nonequilibrium) sample did not allow sufficient time for the functional groups to arrange according to the interaction parameters. Therefore, the simulations were rerun with equilibrated samples and were found to be consistent with experimental observations. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 1164–1172, 2004  相似文献   

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