Ab initio prediction

This section briefly reviews prediction of the native structure of a protein from its sequence of amino acid residues alone. These methods can be contrasted to the threading methods for fold assignment [Section II.A] [39-47,147], which detect remote relationships between sequences and folds of known structure, and to comparative modeling methods discussed in this review, which build a complete all-atom 3D model based on a related known structure. The methods for ab initio prediction include those that focus on the broad physical principles of the folding process [148-152] and the methods that focus on predicting the actual native structures of specific proteins [44,153,154,240]. The former frequently rely on extremely simplified generic models of proteins, generally do not aim to predict native structures of specific proteins, and are not reviewed here. 

Although comparative modeling is the most accurate modeling approach, it is limited by its absolute need for a related template structure. For more than half of the proteins and two-thirds of domains, a suitable template structure cannot be detected or is not yet known [9,11]. In those cases where no useful template is available, the ab initio methods are the only alternative. These methods are currently limited to small proteins and at best result only in coarse models with an RMSD error for the atoms that is greater than 4 A. However, one of the most impressive recent improvements in the field of protein structure modeling has occurred in ab initio prediction [155-157]. 

In the following we review very briefly applications of VASP to alloys and inter-metallic compounds illustrating the potential in making ab-initio predictions of materials properties, in characterizing solid surfaces, and in studying the structure and properties of complex melts. For a more extensive list of applications, see Refs. [10, 17]. 

Callis PR, Petrenko A, Muino PL, Tusell JR (2007) Ab initio prediction of tryptophan fluorescence quenching by protein electric field enabled electron transfer. J Phys Chem B 111(35) 10335-10339... 

Since the first theoretical ab-initio prediction of the existence of a stable gaseous complex between HC1 and NH3, NH3 + HC1 NH4CI [56], the interest has been focused on the nature of the stabilization. A number of theoretical and experimental studies have been carried out in order to establish the geometry of the equilibrium structure (or structures) of the complex and hence to define the character of the interaction as either ion-pair-like or H-bonded-like [56-65],... 

Hu, W.-P. and Truhlar, D. G. Modeling transition state solvation at the single-molecule level test of correlated ab initio predictions against experiment for the gas-phase SN2 reaction of microhydrated fluoride with methyl chloride, J.Am.Chem.Soc., 116 (1994), 7797-7800... 

Another computational approach for detecting /1-solenoid sequences is implemented in a program called BETAWRAP (Bradley et al., 2001). This approach aims to identify /1-solenoid sequences by using hydrophobic-residue sequence patterns of strand-turn-strand regions that were learned from non-/l-solenoid structures. This method also takes into consideration the repetitive character of these patterns in /1-solenoids. Unlike the sequence profile approaches, BETAWRAP can make ab initio predictions of /1-solenoid domains. However, it is less sensitive than the profile search and, sometimes, cannot distinguish /1-solenoids from other solenoids (A. V. K, unpublished observation) such as, for example, LRR proteins (Kobe and Deisenhofer, 1994 Kobe and Kajava, 2001). The latest modification of BETAWRAP algorithm, which is called BETAWRAPPRO (McDonnell et al., 2006), employs additional data provided by sequence profiles and this improves the results of /1-solenoid predictions. 

Lesk, A. M. (1997). CASP2 report on ab initio predictions. Proteins Suppl. 1, 151-166. 

Pugh WJ, Hadgraft J (1994) Ab initio prediction of human skin permeability coefficients. Int J Pharm 103 163-178. 

Totrov, M. and Abagyan, R. Detailed ab initio prediction oflysozym-antibody complex with 1.6 A accuracy. Struct. 

This impasse was eventually resolved by taking into consideration the calculated elastic constants of metastable structiu-es in addition to their energy difference at 0 K. Craievich et al. (1994), Craievich and Sanchez (1995) and Guillermet et al. (1995), using independent calculations, have suggested that the difference between TC and ab initio predictions may be associated with mechanical instabilities in the metastable phase. This point had been raised earlier by Pettifor (1988) and has the following consequence as reported by Saunders et al. (1988) ... 

Stimulated emission pumping spectra of HCP X1 have been recorded via the A lA" [12] and C lA states [5]. These 0.05-cm-1 resolution spectra sample eigenstates rather than feature states, extending to Vib - 25,315 cm-1, above the X state zero-point level, about 1300 cm-1 above the ab initio predicted linear HPC saddle point [5, 13]. 

The performance of the semiempirical methods for the calculation of thermochemical data depends on the extent to which the physics is included in the model and how well the neglected features can be accounted for by the parameterization. These methods can be assessed by validation against accurate experimental data or high level ab initio predictions. A summary of results for four semiempirical methods (MINDO/3, MNDO, AMI, and PM3) for the neutral enthalpies of formation in the G2/97 test set is given in Table 13. Overall, the newest method, PM3, does the best with an average absolute deviation of 7.02 kcal/mol. It has average absolute deviations of 3.91 and 4.27 kcal/mol for the subgroups of hydrocarbons and substituted hydrocarbons, respectively. 

The IR spectra of selenoketene and selenoketene- i, which were prepared by flow thermolysis of the 1,2,3-selenadiazoles 1 and 1-5d at 600°C, were investigated (Equation 4) <1995CPL211>. With the aid of ab initio predictions of vibrational frequencies and intensities, the spectra were assigned in detail. 

Ab initio ( predicting from the beginning ) methods. This method is aimed at identifying folds for which there is a complete lack of sequence... 

Energy-based calculations through theoretical models and energy minimization, such as, ab initio prediction (Bonneau and Baker, 2001). 

STRUCTURE PREDICTION AND MOLECULAR DOCKING 15.2.1. Ab initio Prediction of Protein Structure... 

P.J. Stephens et al., Ab initio prediction of optical rotation A comparison of density functional theory and Hartree-Fock methods for three 2,7,8-trioxabicyclo[3.2.1] octanes. Chirality 14, 288-296 (2002)... 

The first experimental determination of the activation energy Ea was done in 1949 by Robertson [24], His studies of liquid RDX yielded a value of 47.5 kcal/mol for Ea. Subsequent experiments seem to confirm that the Ea value is in the range 47 to 48 kcal/mol. Cosgrove and Owen [25] concluded that the decomposition occurs in the vapor phase based on experiments carried out near the melting point. In 1969 Rauch and Fanelli [26] reported that the liquid- and gas-phase reactions yield different products. They found that the gas-phase reaction produced N02 and the liquid-phase reaction N20 and C02. It has been widely accepted that N-N bond fission to yield N02 is the initial step in the decomposition. However, it has been difficult to firmly establish that as fact because of the difficulties in making kinetics measurements and the unreliability of ab initio predictions for molecules of this size. 

They determined the branching ratio of reaction I to reaction II to be 0.6 0.2. By modeling the reactions with RRKM theory they estimated the barrier to the nitro-nitrite rearrangement to be 55.5 1.5 kcal/mol, which is about 4 kcal/mol lower than that for C-N bond rupture. Previously, there had been ab initio predictions of the energy barrier to nitro-nitrite isomerization [89-91], but the values were significantly higher (by 20-30 kcal/mol) than that estimated by Wodtke et al. based on their data, as were the values published subsequently [92, 93]. 

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