Predicting Protein-Protein Interactions via Gated Graph Attention Signed Network

Leveraging Artificial Intelligence to Expedite Antibody Design and Enhance Antibody-Antigen Interactions

This perspective sheds light on the transformative impact of recent computational advancements in the field of protein therapeutics, with a particular focus on the design and development of antibodies. Cutting-edge computational methods have revolutionized our understanding of protein-protein interactions (PPIs), enhancing the efficacy of protein therapeutics in preclinical and clinical settings. Central to these advancements is the application of machine learning and deep learning, which offers unprecedented insights into the intricate mechanisms of PPIs and facilitates precise control over protein functions. Despite these advancements, the complex structural nuances of antibodies pose ongoing challenges in their design and optimization. Our review provides a comprehensive exploration of the latest deep learning approaches, including language models and diffusion techniques, and their role in surmounting these challenges. We also present a critical analysis of these methods, offering insights to drive further progress in this rapidly evolving field. The paper includes practical recommendations for the application of these computational techniques, supplemented with independent benchmark studies. These studies focus on key performance metrics such as accuracy and the ease of program execution, providing a valuable resource for researchers engaged in antibody design and development. Through this detailed perspective, we aim to contribute to the advancement of antibody design, equipping researchers with the tools and knowledge to navigate the complexities of this field.

State-of-the-art computational methods to predict protein-protein interactions with high accuracy and coverage

Prediction of protein-protein interactions (PPIs) commonly involves a significant computational component. Rapid recent advances in the power of computational methods for protein interaction prediction motivate a review of the state-of-the-art. We review the major approaches, organized according to the primary source of data utilized: protein sequence, protein structure, and protein co-abundance. The advent of deep learning (DL) has brought with it significant advances in interaction prediction, and we show how DL is used for each source data type. We review the literature taxonomically, present example case studies in each category, and conclude with observations about the strengths and weaknesses of machine learning methods in the context of the principal sources of data for protein interaction prediction.

Predicting Protein-Protein Interactions Using Sequence and Network Information via Variational Graph Autoencoder

Protein-protein interactions (PPIs) play a critical role in the proteomics study, and a variety of computational algorithms have been developed to predict PPIs. Though effective, their performance is constrained by high false-positive and false-negative rates observed in PPI data. To overcome this problem, a novel PPI prediction algorithm, namely PASNVGA, is proposed in this work by combining the sequence and network information of proteins via variational graph autoencoder. To do so, PASNVGA first applies different strategies to extract the features of proteins from their sequence and network information, and obtains a more compact form of these features using principal component analysis. In addition, PASNVGA designs a scoring function to measure the higher-order connectivity between proteins and so as to obtain a higher-order adjacency matrix. With all these features and adjacency matrices, PASNVGA trains a variational graph autoencoder model to further learn the integrated embeddings of proteins. The prediction task is then completed by using a simple feedforward neural network. Extensive experiments have been conducted on five PPI datasets collected from different species. Compared with several state-of-the-art algorithms, PASNVGA has been demonstrated as a promising PPI prediction algorithm.

Modeling multi-opinion propagation in complex systems with heterogeneous relationships via Potts model on signed networks

This paper investigates how the heterogenous relationships around us affect the spread of diverse opinions in the population. We apply the Potts model, derived from condensed matter physics on signed networks, to multi-opinion propagation in complex systems with logically contradictory interactions. Signed networks have received increasing attention due to their ability to portray both positive and negative associations simultaneously, while the Potts model depicts the coevolution of multiple states affected by interactions. Analyses and experiments on both synthetic and real signed networks reveal the impact of the topology structure on the emergence of consensus and the evolution of balance in a system. We find that, regardless of the initial opinion distribution, the proportion and location of negative edges in the signed network determine whether a consensus can be formed. The effect of topology on the critical ratio of negative edges reflects two distinct phenomena: consensus and the multiparty situation. Surprisingly, adding a small number of negative edges leads to a sharp breakdown in consensus under certain circumstances. The community structure contributes to the common view within camps and the confrontation (or alliance) between camps. The importance of inter- or intra-community negative relationships varies depending on the diversity of opinions. The results also show that the dynamic process causes an increase in network structural balance and the emergence of dominant high-order structures. Our findings demonstrate the strong effects of logically contradictory interactions on collective behaviors, and could help control multi-opinion propagation and enhance the system balance.

Prediction of Adverse Drug Reaction Linked to Protein Targets Using Network-Based Information and Machine Learning

Drug discovery attrition rates, particularly at advanced clinical trial stages, are high because of unexpected adverse drug reactions (ADR) elicited by novel drug candidates. Predicting undesirable ADRs produced by the modulation of certain protein targets would contribute to developing safer drugs, thereby reducing economic losses associated with high attrition rates. As opposed to the more traditional drug-centric approach, we propose a target-centric approach to predict associations between protein targets and ADRs. The implementation of the predictor is based on a machine learning classifier that integrates a set of eight independent network-based features. These include a network diffusion-based score, identification of protein modules based on network clustering algorithms, functional similarity among proteins, network distance to proteins that are part of safety panels used in preclinical drug development, set of network descriptors in the form of degree and betweenness centrality measurements, and conservation. This diverse set of descriptors were used to generate predictors based on different machine learning classifiers ranging from specific models for individual ADR to higher levels of abstraction as per MEDDRA hierarchy such as system organ class. The results obtained from the different machine-learning classifiers, namely, support vector machine, random forest, and neural network were further analyzed as a meta-predictor exploiting three different voting systems, namely, jury vote, consensus vote, and red flag, obtaining different models for each of the ADRs in analysis. The level of accuracy of the predictors justifies the identification of problematic protein targets both at the level of individual ADR as well as a set of related ADRs grouped in common system organ classes. As an example, the prediction of ventricular tachycardia achieved an accuracy and precision of 0.83 and 0.90, respectively, and a Matthew correlation coefficient of 0.70. We believe that this approach is a good complement to the existing methodologies devised to foresee potential liabilities in preclinical drug discovery. The method is available through the DocTOR utility at GitHub (https://github.com/cristian931/DocTOR).

Three-Dimensional Graph Matching to Identify Secondary Structure Correspondence of Medium-Resolution Cryo-EM Density Maps

Cryo-electron microscopy (cryo-EM) is a structural technique that has played a significant role in protein structure determination in recent years. Compared to the traditional methods of X-ray crystallography and NMR spectroscopy, cryo-EM is capable of producing images of much larger protein complexes. However, cryo-EM reconstructions are limited to medium-resolution (~4-10 Å) for some cases. At this resolution range, a cryo-EM density map can hardly be used to directly determine the structure of proteins at atomic level resolutions, or even at their amino acid residue backbones. At such a resolution, only the position and orientation of secondary structure elements (SSEs) such as α-helices and β-sheets are observable. Consequently, finding the mapping of the secondary structures of the modeled structure (SSEs-A) to the cryo-EM map (SSEs-C) is one of the primary concerns in cryo-EM modeling. To address this issue, this study proposes a novel automatic computational method to identify SSEs correspondence in three-dimensional (3D) space. Initially, through a modeling of the target sequence with the aid of extracting highly reliable features from a generated 3D model and map, the SSEs matching problem is formulated as a 3D vector matching problem. Afterward, the 3D vector matching problem is transformed into a 3D graph matching problem. Finally, a similarity-based voting algorithm combined with the principle of least conflict (PLC) concept is developed to obtain the SSEs correspondence. To evaluate the accuracy of the method, a testing set of 25 experimental and simulated maps with a maximum of 65 SSEs is selected. Comparative studies are also conducted to demonstrate the superiority of the proposed method over some state-of-the-art techniques. The results demonstrate that the method is efficient, robust, and works well in the presence of errors in the predicted secondary structures of the cryo-EM images.