TMCrys: predict propensity of success for transmembrane protein crystallization

Prediction poverty levels of needy college students using RF-PCA model

Nowadays, poverty-stricken college students have become a special group among college students and occupied a higher proportion in it. How to accurately identify poverty levels of college students and provide funding is a new problem for universities. In this study, a novel model, which incorporated Random Forest with Principle Components Analysis (RF-PCA), is proposed to predict poverty levels of college students. To establish this model, we collect some useful information is to construct the datasets which include 4 classes of poverty levels and 21 features of poverty-stricken college students. Furthermore, the feature dimension reduction consists of two steps: the first step is to select the top 16 features with the ranking of feature, according to the Gini importance and Shapley Additive explanations (SHAP) values of features based on Random Forest (RF) model; the second step is to extract 11 dimensions by means of Principle Components Analysis (PCA). Subsequently, confusion metrics and receiver operating characteristic (ROC) curves are utilized to evaluate the promising performance of the proposed model. Especially the accuracy of the model achieves 78.61% . Finally, compared with seven states of the art classification algorithms, the proposed model achieves a higher prediction accuracy, which indicates that the results provide great potential to identify the poverty levels of college students.

Sequence-Based Prediction of Transmembrane Protein Crystallization Propensity

Transmembrane proteins play a vital role in cell life activities. There are several techniques to determine transmembrane protein structures and X-ray crystallography is the primary methodology. However, due to the special properties of transmembrane proteins, it is still hard to determine their structures by X-ray crystallography technique. To reduce experimental consumption and improve experimental efficiency, it is of great significance to develop computational methods for predicting the crystallization propensity of transmembrane proteins. In this work, we proposed a sequence-based machine learning method, namely Prediction of TransMembrane protein Crystallization propensity (PTMC), to predict the propensity of transmembrane protein crystallization. First, we obtained several general sequence features and the specific encoded features of relative solvent accessibility and hydrophobicity. Second, feature selection was employed to filter out redundant and irrelevant features, and the optimal feature subset is composed of hydrophobicity, amino acid composition and relative solvent accessibility. Finally, we chose extreme gradient boosting by comparing with other several machine learning methods. Comparative results on the independent test set indicate that PTMC outperforms state-of-the-art sequence-based methods in terms of sensitivity, specificity, accuracy, Matthew's Correlation Coefficient (MCC) and Area Under the receiver operating characteristic Curve (AUC). In comparison with two competitors, Bcrystal and TMCrys, PTMC achieves an improvement by 0.132 and 0.179 for sensitivity, 0.014 and 0.127 for specificity, 0.037 and 0.192 for accuracy, 0.128 and 0.362 for MCC, and 0.027 and 0.125 for AUC, respectively.

BCrystal: an interpretable sequence-based protein crystallization predictor

MOTIVATION

X-ray crystallography has facilitated the majority of protein structures determined to date. Sequence-based predictors that can accurately estimate protein crystallization propensities would be highly beneficial to overcome the high expenditure, large attrition rate, and to reduce the trial-and-error settings required for crystallization.

RESULTS

In this study, we present a novel model, BCrystal, which uses an optimized gradient boosting machine (XGBoost) on sequence, structural and physio-chemical features extracted from the proteins of interest. BCrystal also provides explanations, highlighting the most important features for the predicted crystallization propensity of an individual protein using the SHAP algorithm. On three independent test sets, BCrystal outperforms state-of-the-art sequence-based methods by more than 12.5% in accuracy, 18% in recall and 0.253 in Matthew's correlation coefficient, with an average accuracy of 93.7%, recall of 96.63% and Matthew's correlation coefficient of 0.868. For relative solvent accessibility of exposed residues, we observed higher values to associate positively with protein crystallizability and the number of disordered regions, fraction of coils and tripeptide stretches that contain multiple histidines associate negatively with crystallizability. The higher accuracy of BCrystal enables it to accurately screen for sequence variants with enhanced crystallizability.

AVAILABILITY AND IMPLEMENTATION

Our BCrystal webserver is at https://machinelearning-protein.qcri.org/ and source code is available at https://github.com/raghvendra5688/BCrystal.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Accurate multistage prediction of protein crystallization propensity using deep-cascade forest with sequence-based features

X-ray crystallography is the major approach for determining atomic-level protein structures. Because not all proteins can be easily crystallized, accurate prediction of protein crystallization propensity provides critical help in guiding experimental design and improving the success rate of X-ray crystallography experiments. This study has developed a new machine-learning-based pipeline that uses a newly developed deep-cascade forest (DCF) model with multiple types of sequence-based features to predict protein crystallization propensity. Based on the developed pipeline, two new protein crystallization propensity predictors, denoted as DCFCrystal and MDCFCrystal, have been implemented. DCFCrystal is a multistage predictor that can estimate the success propensities of the three individual steps (production of protein material, purification and production of crystals) in the protein crystallization process. MDCFCrystal is a single-stage predictor that aims to estimate the probability that a protein will pass through the entire crystallization process. Moreover, DCFCrystal is designed for general proteins, whereas MDCFCrystal is specially designed for membrane proteins, which are notoriously difficult to crystalize. DCFCrystal and MDCFCrystal were separately tested on two benchmark datasets consisting of 12 289 and 950 proteins, respectively, with known crystallization results from various experimental records. The experimental results demonstrated that DCFCrystal and MDCFCrystal increased the value of Matthew's correlation coefficient by 199.7% and 77.8%, respectively, compared to the best of other state-of-the-art protein crystallization propensity predictors. Detailed analyses show that the major advantages of DCFCrystal and MDCFCrystal lie in the efficiency of the DCF model and the sensitivity of the sequence-based features used, especially the newly designed pseudo-predicted hybrid solvent accessibility (PsePHSA) feature, which improves crystallization recognition by incorporating sequence-order information with solvent accessibility of residues. Meanwhile, the new crystal-dataset constructions help to train the models with more comprehensive crystallization knowledge.

The TMCrys server for supporting crystallization of transmembrane proteins

MOTIVATION

Due to their special properties, the structures of transmembrane proteins are extremely hard to determine. Several methods exist to predict the propensity of successful completion of the structure determination process. However, available predictors incorporate data of any kind of proteins, hence they can hardly differentiate between crystallizable and non-crystallizable membrane proteins.

RESULTS

We implemented a web server to simplify running TMCrys prediction method that was developed specifically to separate crystallizable and non-crystallizable membrane proteins.

AVAILABILITY AND IMPLEMENTATION

http://tmcrys.enzim.ttk.mta.hu.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.