Volume 7, Issue 1

Quality Assessment (QA) plays an important role in protein structure prediction. Traditional multimodel QA method usually suffer from searching databases or comparing with other models for making predictions, which usually fail when the poor quality models dominate the model pool. We propose a novel protein single-model QA method which is built on a new representation that converts raw atom information into a series of carbon-alpha (Cα) atoms with side-chain information, defined by their dihedral angles and bond lengths to the prior residue. An LSTM network is used to predict the quality by treating each amino acid as a time-step and consider the final value returned by the LSTM cells. To the best of our knowledge, this is the first time anyone has attempted to use an LSTM model on the QA problem; furthermore, we use a new representation which has not been studied for QA. In addition to angles, we make use of sequence properties like secondary structure parsed from protein structure at each time-step without using any database, which is different than all existed QA methods. Our model achieves an overall correlation of 0.651 on the CASP12 testing dataset. Our experiment points out new directions for QA problem and our method could be widely used for protein structure prediction problem. The software is freely available at GitHub: https://github.com/caorenzhi/AngularQA

We study the discrete and discrete fractional representation of a pharmacokinetics - pharmacodynamics (PK-PD) model describing tumor growth and anti-cancer effects in continuous time considering a time scale hℕ0h$h\mathbb{N}_0^h$, where h > 0. Since the measurements of the tumor volume in mice were taken daily, we consider h = 1 and obtain the model in discrete time (i.e. daily). We then continue with fractionalizing the discrete nabla operator to obtain the model as a system of nabla fractional difference equations. The nabla fractional difference operator is considered in the sense of Riemann-Liouville definition of the fractional derivative. In order to solve the fractional discrete system analytically we state and prove some theorems in the theory of discrete fractional calculus. For the data fitting purpose, we use a new developed method which is known as an improved version of the partial sum method to estimate the parameters for discrete and discrete fractional models. Sensitivity analysis is conducted to incorporate uncertainty/noise into the model. We employ both frequentist approach and Bayesian method to construct 90 percent confidence intervals for the parameters. Lastly, for the purpose of practicality, we test the discrete models for their efficiency and illustrate their current limitations for application.

We develop a computational method for simulating the nonlinear dynamics of an elastic tumor-host interface. This work is motivated by the recent linear stability analysis of a two-phase tumor model with an elastic membrane interface in 2D [47]. Unlike the classic tumor model with surface tension, the elastic interface condition is numerically challenging due to the 4th order derivative from the Helfrich bending energy. Here we are interested in exploring the nonlinear interface dynamics in a sharp interface framework. We consider a curvature dependent bending rigidity (curvature weakening [22]) to investigate metastasis patterns such as chains or fingers that invade the host environment. We solve the nutrient field and the Stokes flow field using a spectrally accurate boundary integral method, and update the interface using a nonstiff semi-implicit approach. Numerical results suggest curvature weakening promotes the development of branching patterns instead of encapsulated morphologies in a long period of time. For non-weakened bending rigidity, we are able to find self-similar shrinking morphologies based on marginally stable value of the apoptosis rate.

A riboswitch is a type of RNA molecule that regulates important biological functions by changing structure, typically under ligand-binding. We assess the extent that these ligand-bound structural alternatives are present in the Boltzmann sample, a standard RNA secondary structure prediction method, for three riboswitch test cases. We use the cluster analysis tool RNAStructProfiling to characterize the different modalities present among the suboptimal structures sampled. We compare these modalities to the putative base pairing models obtained from independent experiments using NMR or fluorescence spectroscopy. We find, somewhat unexpectedly, that profiling the Boltzmann sample captures evidence of ligand-bound conformations for two of three riboswitches studied. Moreover, this agreement between predicted modalities and experimental models is consistent with the classification of riboswitches into thermodynamic versus kinetic regulatory mechanisms. Our results support cluster analysis of Boltzmann samples by RNAStructProfiling as a possible basis for de novo identification of thermodynamic riboswitches, while highlighting the challenges for kinetic ones.

Dengue viral capsid plays a significant role in viral life cycle of dengue, especially in vial genome protection and virus-cell fusion. Revealing mechanisms of the viral capsid protein assembly may lead to the discovery of anti-viral drugs that inhibit the assembly of the viral capsid. The E and M-proteins are arranged into heterotetramers, which consists of two copies of E and M-protein. The heterotetramers are assembled into a highly ordered capsid. While many investigations of the interactions between E and M-proteins have been performed, there are very few studies on the interactions between the heterotetramers and their roles in capsid assembly. Utilizing a series of computational approaches, this study focuses on the assembly mechanism of the heterotetramers. Our electrostatic analyses lead to the identification of four binding modes between each two dengue heterotetramers that repeat periodically throughout the virus capsid. Among these four binding modes, heterotetramers in binding modes I, II and IV are attractive. But in the binding mode III the heterotetramers repel each other, making mode III a suitable target for drug design. Furthermore, MD simulations were performed following by salt bridges analysis. This study demonstrates that using computational approaches is a promising direction to study the dengue virus.

The structural details of cellulose I β were discussed according to molecular dynamics simulations with the GLYCAM-06 force field. The simulation outcomes were in agreement with previous experimental data, including structural parameters and hydrogen bond pattern at 298 K. We found a new conformation of cellulose I β existed at the intermediate temperature that is between the low and high temperatures. Partial chain rotations along the backbone direction were found and conformations of hydroxymethyl groups that alternated from tg to either gt or gg were observed when the temperature increased from 298 K to 400 K. In addition, the gg conformation is preferred than gt . For the structure adopted at high temperature of 500 K, major chains were twisted and two chains detached from each plain. In contrast to the observation under intermediate temperature, the population of hydroxymethyl groups in gt exceeded that in gg conformation at high temperature. In addition, three patterns of hydrogen bonding were identified at low, intermediate and high temperatures in the simulations. The provided structural information indicated the transitions occurred around 350 K and 450 K, considered as the transitional temperatures of cellulose I β in this work.

The Illumina Infinium HumanMethylation27 (Illumina 27K) BeadChip assay is a relatively recent high-throughput technology that allows over 27,000 CpGs to be assayed. The Illumina 27K methylation data is less commonly used in comparison to gene expression in bioinformatics. It provides a critical need to find the optimal feature ranking (FR) method for handling the high dimensional data. The optimal FR method on the classifier is not well known, and choosing the best performing FR method becomes more challenging in high dimensional data setting. Therefore, identifying the statistical methods which boost the inference is of crucial importance in this context. This paper describes the detailed performances of FR methods such as fisher score, information gain, chi-square, and minimum redundancy and maximum relevance on different classification methods such as Adaboost, Random Forest, Naive Bayes, and Support Vector Machines. Through simulation study and real data applications, we show that the fisher score as an FR method, when applied on all the classifiers, achieved best prediction accuracy with significantly small number of ranked features.

A new CBSF empirical scoring function for the estimation of binding energies between proteins and small molecules is proposed in this report. The final score is obtained as a sum of three energy terms calculated using descriptors based on a simple counting of the interacting protein-ligand atomic pairs. All the required weighting coefficients for this method were derived from a pretrained neural network. The proposed method demonstrates a high accuracy and reproduces binding energies of protein-ligand complexes from the CASF-2016 test set with a standard deviation of 2.063 kcal/mol (1.511 log units) and an average error of 1.682 kcal/mol (1.232 log units). Thus, CBSF has a significant potential for the development of rapid and accurate estimates of the protein-ligand interaction energies.

A particle-cluster treecode based on barycentric Hermite interpolation is presented for fast summation of electrostatic particle interactions in 3D. The interpolation nodes are Chebyshev points of the 2nd kind in each cluster. It is noted that barycentric Hermite interpolation is scale-invariant in a certain sense that promotes the treecode’s efficiency. Numerical results for the Coulomb and screened Coulomb potentials show that the treecode run time scales like O ( N log N ), where N is the number of particles in the system. The advantage of the barycentric Hermite treecode is demonstrated in comparison with treecodes based on Taylor approximation and barycentric Lagrange interpolation.