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1.Collecting 10 good starting sentences in introdection section. (1) The protein encoded by the rat neu proto-oncogene is a membrane-spanning receptor tyrosine kinase, homologous to the ErbB2

protein in humans, which plays a key role in cell division and cell growth. Biochemisty 51(12):2558-2568

(2) The mechanism via which this single-point mutation leads to cancer has been the subject of many studies, as summarized in our recent report, because insight into the molecular basis of the oncogenic effects of this mutation is key to understanding signal transduction for this RTKs. Biochemisty 51(12):2558-2568 (3) The adsorption of proteins can either be beneficial or detrimental dependign on the type of protein and the biological system in question. In the biomedical sciences, preventing adsorption of proteins or removing adsorbed proteins from surgical instruments has become an important issue, particularly with the advent of prion deseases. Biomacromolecules 9(5):1443-1453 (4) The first important step in drug absorption from oral solid dosage forms is dissolution, a process by which the drug molecules detach from the solid particles and enter into the surrounding gastrointestinal milieu. Thus dissolution rate is of fundamental importance in pharmaceutical dosage form design. Molecular Pharmaceutics 10(3):905-917

(5) In this context, somputational methods. Molecular dynamics

simulation in particular, are a powerful tool that has the potential to help discern patterns and add insights that are otherwise difficult to gain. Molecular Pharmaceutics 10(3):905-917 (6) Nitromethane has attracted lots of attention because it is the prototypical explosive, and its study can help us understand the reaction mechanism or initiation mechanism of more complex energetic materials such as RDX and HMX. 116(14):3514-3520 (7) Although extensive studies have been done on allostery in proteins or enzymes, less is known for that through DNA, which is normally considered as a mere template provinding binding sites. 339(6121):816-819 (8) Despite the interest in supported lipid bilayers, both as a research tool and as a technological development, few detailed molecular models of the systems have been developed. Langmuir 24(21):12469-12473 Science The Journal of Physical Chemistry A

(9) G-protein-coupled receptors are eukaryotic integral membrane proteins that modulate biological function by initiating cellular signalling in response to chemically diverse agonists. 469(7329):236-240 (10) Membrane fouling is still a major problem that hinders MBR’s more widespread and large-scale application, which is strongly affected by the characeristics of the mixed liquor. Comprehension of the inherent Nature

mechanisms and subsequent integrated modeling of the process seems greatly helpful for optimizaion of the MBR behavior. Engineering Chemisty Research 50(2):1127-1137 2.Collecting 10 good sentences in abstract section. (1) Results are interpreted in terms of the pressure dependence of both deformation mechanisms active at these grain sizes. 2005,309(5742):1838-1841 (2) These simulations, together with new shock experments on nanocrystalline nickel, raise the possibility of achieving ultrahard materials during and after shock loading. Science Science Industrial &

2005,309(5742):1838-1841 (3) Graphene-based nanomaterials have been recognized as potential candidates for various biomedical applications ranging from biosensing platform to cellular delivery of proteins and peptides. 29(46):14230-14238 (4) They are also implicated in the development of many types of cancer. Biochemisty 51(12):2558-2568 (5) Adsorption at both surfaces is driven by displacement of water molecules from the interfacial region. 9(5):1443-1453 (6) LTP adsorbed at the decane surface exhibits significant changes in its tertiary structure, and penetrates a considerable distance into the Biomacromolecules Langmuir

decane phase.

Biomacromolecules 9(5):1443-1453 Molecular

(7) Further analyses identified the underlying mechanism. Pharmaceutics 10(3):905-917

(8) It has been demonstrated that the available X-ray crystal structure of PDE2A was in the unbound state, explaining why it is not suitable for molecular docking studies on the enzyme-inhibitor binding. Journal of Physical Chemistry B 113(9):2896-2908 (9) The protein flexibility is incorporated in docking the ligands to the ensemble of representative structures extracted from a clustering analysis of the molecular dynamics simulation in explicit aqueous solution. Journal of Chemical Information and Modeling The

50(1):136-145 (10) Application of a specific stimulus opens the intracellular gate of a K+ channel, yielding a trasient period of ion conduction until the selectivity filter spontaneously undergoes a conformational change towards a non-conductive state. Nature 501(7456):121-124

3.Collecting 10 good sentences in introduction section. (1) If these softening effects could be suppressed, harder materials could be created, with potential applications to extreme environments as target capsules for the National Ignition Facility. 2005,309(5742):1838-1841 (2) Under those conditions, a regime is entered where plasticity is Science

controlled by both high strain rate and high pressure. 2005,309(5742):1838-1841


(3) These interactions play a decisive role in determining the toxicity/fate of GBNMs in biological systems. Langmuir 29(46):14230-14238

(4) Although a number of experimental and computational studies have elucidated the effect of carbon nanotubes and fullerenes on the conformation of proteins, there is a lack of information regarding the interaction of proteins with GBNMs. Langmuir 29(46):14230-14238

(5) Therefore, a thorough understanding is required on how GBNMs interact with proteins to avoid their adverse effect on cellular systems. Langmuir 29(46):14230-14238 (6) It is this effect of the V664E mutation that has been most frequently studied. Biochemisty 51(12):2558-2568

(7) Mutation of either motif had only a weak effect on self-association, presumably because the other motif remained available for interaction. Biochemisty 51(12):2558-2568 (8) MD simulations were performed in a single rigid unit cell using the NVT ensemble. 3(7):930-933 (9) Appllication of MD simulation in other aspects of pharmaceutical sciences is also emerging although publications are limited to date. Molecular Pharmaceutics 10(3):905-917 The Journal of Physical Chemistry Letters

(10) Fueled by the dramatic increases in computing power in recent years, the use of computational methods in pharmaceutical sciences has showed a growing trend. Molecular Pharmaceutics 10(3):905-917

4.Collecting 10 good sentences in experimental section. (1) Using molecular dynamics simulations, we verified that a nanocrystalline metal deforming plastically by GB accommodation gets harder as hydrostatic pressure is increased. Science

2005,309(5742):1838-1841 (2) Our experiments also indicate an increase in hardness in the samples recovered after shock loading, as expected from the measured residual dislocation densities. Science 2005,309(5742):1838-1841

(3) Four peptides were prepared, containing sequences derived from the transmembrand domains of the wild-type rat Neu protein.

Biochemisty 51(12):2558-2568 (4) In each case, the native Pro655 residue was mutated to Trp to yield significant absorbance at 280 nm, which in turn used to determine protein concentration and monitor protein sedimentation using AUC. Biochemisty 51(12):2558-2568 (5) We interpreted this to mean that the results from the adsorption simulations were relatively independent of force field type and that the similarity of the two sets of results from different initial random velocities in the starting conformation meant that our results are a good

estimate of the global behavior of the systems. 9(5):1443-1453


(6) It is widely accepted that surfaces are the places that have hot spots where chemical reactions occur more easily, because molecules in the surface are loosened and have more freedom. Chemistry A 116(14):3514-3520 (7) To validate the stability of the PDE2A structural model and to further test whether the PDE2AHomology structure modeled based on the high-resolution X-ray structure of human PDE5 is reasonable, we carried out a fully relaxed MD simulation on the PDE2AHomology structure in water. The Journal of Physical Chemistry B 113(9):2896-2908 (8) To sum up, the quality of the PDE2AHomology has been checked using four different types of criteria. 113(9):2896-2908 (9) The topolgy-dependent Gasteiger charge was used to assign charges to the protein and ligands for convenience to take into account the flexibility of the protein and ligand. and Modeling 50(1):136-145 (10) Afterward, the resultant sequence alignment was adjusted manually using the software BIOEDIT. Modeling 51(3):635-646 5.Collecting 10 good sentences in results and discussion section. Journal of Chemical Information and Journal of Chemical Information The Journal of Physical Chemistry B The Journal of Physical

(1) The results obtained from the present study revealed differential adsoption patterns of the protein on GBNMs. 29(46):14230-14238 (2) These interactions could be resposible for the stability of GO-protein complex as suggested by the dominant role of electrostatic interaction observed during adsorption onGO. Langmuir 29(46):14230-14238 Langmuir

(3) In the case of graphene, the trend of COM distance highly correlated with the trend of van der Waals energy. 29(46):14230-14238 (4) Both sedimentation equilibrium and sedimentation velocity Biochemisty Langmuir

experiments were employed in 51(12):2558-2568

this study.

(5) These bands were assigned on the bases of data from previous studies. Biochemisty 51(12):2558-2568

(6) Here we provide strong evidence to support this hypothesis. Biochemisty 51(12):2558-2568 (7) We find that in the first 5 ns of the simulation the protein does not adsorb to the surface but undergoes both translational and rotational movement away from its starting conformation. 9(5):1443-1453 (8) Taking into account all of the above-discussed structures concerning the bound and unbound states of PDE2A and their binding with inhibitors, Biomacromolecules

we wanted to know whether we could also model the 3D structure of the inhibitor-bound state of PDE2A starting from the X-ray crystal structure. The Journal of Physical Chemistry B 113(9):2896-2908 (9) Like other typical kinases, the PI3K kinase domain consists of a mostly ?-helical carboxy-terminal lobe and an amino-terminal lobe between which the ATP binding pocket is located. Chemical Information and Modeling 50(1):136-145 (10) It is reasonable that both best docking experiments took place in the last cluster. 50(1):136-145 6.Collecting 10 good sentences in conclusion section. (1) The present study reveals that the difference in surface chemistries of NMs with same dimensions can lead to differential adsorption patterns and conformational changes in biomolecules. Langmuir Journal of Chemical Information and Modeling Journal of

29(46):14230-14238 (2) Although the LTP molecule does appear to spread at the interface, we see no evidence of unfolding of the secondary structure or surface denaturation to expose the hydrophobic core of the mollecule. Biomacromolecules 9(5):1443-1453 (3) Extensive molecular modeling, docking, and dynamics simulations have demonstrated that the strcture of PDE2A catalytic domain may exist in two different forms corresponding to the inhibitor-bound and

unbound states of the enzyme. 113(9):2896-2908

The Journal of Physical Chemistry B

(4) The ability of PDE2A to adopt different structural forms while maintaining the general structural feature of the catalytic site suggests that the binding pocket of PDE2A is very flexible and may accommodate a variety of ligands with distinctly different molecular structures, which leads us to better understand why PDE2 can catalyze the hydrolysis of both cAMP and cGMP whereas PDE4 and PDE5 can only respectively catalyze the hydrolysis of cAMP and cGMP. Chemistry B 113(9):2896-2908 (5) This work is likely to provide important insights into strategies for the discovery of more promising compounds to target PI3K?. (6) To address this problem, the initial MCH-R1 model was subjected to a strategic ligand supported refinement protocol using compounds of different chemotypes. Modeling 51(3):635-646 (7) This protocol allowed the explanation of several reported SAR data. Journal of Chemical Information and Modeling 51(3):635-646 (8) Our observations also highlight some of the complications that can arise in the interpretation of S2 values determined by NMR relaxation experiments. The Journal of Physical Chemistry B Journal of Chemical Information and The Journal of Physical


(9) To the extent that the results of MD simulations and NMR relaxation experiments can be reconciled within an analytical framework like that described in this paper, we expect that MD simulations will prove to be a valuable tool in the extraction of thermodynamic quantities from NMR experiments. The Journal of Physical Chemistry B

112(19):6155-6158 (10) For the bidisperse case, the values of the particle Knudsen number indicate that momentum transport is not dominated by collisions, justifying the adoption of high-order moment methods, not constrained by the hydrodynamic limit assumption, also for this case. & Engineering Chemistry Research 52(1):187-198 7.Collecting 10 good sentences containing good usage of prepositions. (1) In this work, the self-diffusion of hydrocarbons in IRMOF-1 was studied as a function of chain length with a combination of molecular dynamics simulations and pulsed field gradient NMR experiments. The Journal of Physical Chemistry Letters 3(7):930-933 (2) Metal-organic frameworks and related materials formed by the self-assembly of organic linkers via coordinating nodes are an exciting new development in the field of porous materials. Physical Chemistry Letters 3(7):930-933 (3) As the loading is increased, some hexane molecules are forced into less favorable locations, and more low-barrier hops betwwen sites occur. The Journal of Industrial

The Journal of Physical Chemistry Letters 3(7):930-933 (4) The molecules located on corners and edges of the parallelepiped crystal are not as tightly bound to their surrounding neighbors as those located in other positions. Molecular Pharmaceutics 10(3):905-917

(5) These enzymes are essential for cyclic nucleotide signaling since they represent, at least for eukaryotic cells, esentially the only way for a cell to terminate a cyclic nucleotide signal. Chemistry B 113(9):2896-2908 (6) In addition, PDEs are largely responsible for confining a cyclic nucleotide signal to particular locations and to prevent its diffusion throughout the cell. 113(9):2896-2908 (7) Using the developed 3D structural model, we were able to carry out molecular docking, molecular dynamics simulations, and binding free energy calculations to explore possible binding modes of the potent PDE2A inhibitors and to identify key amino acids involved in the PDE2-inhibitor binding. 113(9):2896-2908 (8) The computational experiment was designed to give an indication on the actual binding modes of PDE2A with Bay60-7550 and ND7001. The Journal of Physical Chemistry B 113(9):2896-2908 (9) We first inserted the inhibitor into the binding cavity and oriented in a The Journal of Physical Chemistry B The Journal of Physical Chemistry B The Journal of Physical

favorable position by slightly rotating Phb830 and Y827 side chains. The Journal of Physical Chemistry B 113(9):2896-2908 (10) Moreover, it reveals new insights into the critical recognition sites within the receptor. 51(3):635-646 8.Collecting 10 good sentences containing good usage of phrases. (1) This was in contrast to graphene,where majority of the amino acid residues lost their conformation and underwent α to turn and 310 helical transitions. Langmuir 29(46):14230-14238 Journal of Chemical Information and Modeling

(2) The results are in line with the snapshots taken at the end of the simulation. Langmuir 29(46):14230-14238

(3) However, the protein formed a higer number of contacts with graphene compared to GO and rGO that may be attributed to the different surface chemistries of GBNMs. Langmuir

29(46):14230-14238 (4) Because of the presence of electronegative functional groups on the surface of GO and rGO, the negatively charged amino acid residues in the protein may experience repulsion from the surface of GO and rGO and the positively charged amino acid residues attracted favorably toward them as suggested. Langmuir 29(46):14230-14238

(5) The results were in conflict with results obtained in bacterial membranes. Biochemisty 51(12):2558-2568

(6) The significantly lower Ds from simulation for methane is consistent with the idea that the experimental results for methane are not a measure of pure intracrystalline self-diffusion. Chemistry Letters 3(7):930-933 (7) These observations are in accordance with detailed X-ray diffraction and Monte Carlo studies performed for Ar and N2 in IRMOF-1. Journal of Physical Chemistry Letters 3(7):930-933 (8) It should be noted that this strategy of using the TraPPE force field for the guest molecules and DREIDING for the MOF has also yielded good predictions of adsorption isotherms for small molecules in a variety of MOFs. The Journal of Physical Chemistry Letters 3(7):930-933 The The Journal of Physical

(9) Dissolution of the molecules from the crystal surface is far from a random process. Molecular Pharmaceutics 10(3):905-917

(10) However, it is unclear how these important ligands bind with PDE2 in the active site and, to the best of our knowledge. Physical Chemistry B 113(9):2896-2908 The Journal of



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