SPServer: split-statistical potentials for the analysis of protein structures and protein-protein interactions.

BACKGROUND: Statistical potentials, also named knowledge-based potentials, are scoring functions derived from empirical data that can be used to evaluate the quality of protein folds and protein-protein interaction (PPI) structures. In previous works we decomposed the statistical potentials in different terms, named Split-Statistical Potentials, accounting for the type of amino acid pairs, their hydrophobicity, solvent accessibility and type of secondary structure. These potentials have been successfully used to identify near-native structures in protein structure prediction, rank protein docking poses, and predict PPI binding affinities. RESULTS: Here, we present the SPServer, a web server that applies the Split-Statistical Potentials to analyze protein folds and protein interfaces. SPServer provides global scores as well as residue/residue-pair profiles presented as score plots and maps. This level of detail allows users to: (1) identify potentially problematic regions on protein structures; (2) identify disrupting amino acid pairs in protein interfaces; and (3) compare and analyze the quality of tertiary and quaternary structural models. CONCLUSIONS: While there are many web servers that provide scoring functions to assess the quality of either protein folds or PPI structures, SPServer integrates both aspects in a unique easy-to-use web server. Moreover, the server permits to locally assess the quality of the structures and interfaces at a residue level and provides tools to compare the local assessment between structures. SERVER ADDRESS: https://sbi.upf.edu/spserver/ .

On the mechanisms of protein interactions: predicting their affinity from unbound tertiary structures.

Motivation: The characterization of the protein-protein association mechanisms is crucial to understanding how biological processes occur. It has been previously shown that the early formation of non-specific encounters enhances the realization of the stereospecific (i.e. native) complex by reducing the dimensionality of the search process. The association rate for the formation of such complex plays a crucial role in the cell biology and depends on how the partners diffuse to be close to each other. Predicting the binding free energy of proteins provides new opportunities to modulate and control protein-protein interactions. However, existing methods require the 3D structure of the complex to predict its affinity, severely limiting their application to interactions with known structures. Results: We present a new approach that relies on the unbound protein structures and protein docking to predict protein-protein binding affinities. Through the study of the docking space (i.e. decoys), the method predicts the binding affinity of the query proteins when the actual structure of the complex itself is unknown. We tested our approach on a set of globular and soluble proteins of the newest affinity benchmark, obtaining accuracy values comparable to other state-of-art methods: a 0.4 correlation coefficient between the experimental and predicted values of ΔG and an error < 3 Kcal/mol. Availability and implementation: The binding affinity predictor is implemented and available at http://sbi.upf.edu/BADock and https://github.com/badocksbi/BADock. Contact: j.planas-iglesias@warwick.ac.uk or baldo.oliva@upf.edu. Supplementary information: Supplementary data are available at Bioinformatics online.

InteractoMIX: a suite of computational tools to exploit interactomes in biological and clinical research.

Virtually all the biological processes that occur inside or outside cells are mediated by protein-protein interactions (PPIs). Hence, the charting and description of the PPI network, initially in organisms, the interactome, but more recently in specific tissues, is essential to fully understand cellular processes both in health and disease. The study of PPIs is also at the heart of renewed efforts in the medical and biotechnological arena in the quest of new therapeutic targets and drugs. Here, we present a mini review of 11 computational tools and resources tools developed by us to address different aspects of PPIs: from interactome level to their atomic 3D structural details. We provided details on each specific resource, aims and purpose and compare with equivalent tools in the literature. All the tools are presented in a centralized, one-stop, web site: InteractoMIX (http://interactomix.com).

External Validation of the Machine Learning-Based Thermographic Indices for Rheumatoid Arthritis: A Prospective Longitudinal Study.

External validation is crucial in developing reliable machine learning models. This study aimed to validate three novel indices-Thermographic Joint Inflammation Score (ThermoJIS), Thermographic Disease Activity Index (ThermoDAI), and Thermographic Disease Activity Index-C-reactive protein (ThermoDAI-CRP)-based on hand thermography and machine learning to assess joint inflammation and disease activity in rheumatoid arthritis (RA) patients. A 12-week prospective observational study was conducted with 77 RA patients recruited from rheumatology departments of three hospitals. During routine care visits, indices were obtained at baseline and week 12 visits using a pre-trained machine learning model. The performance of these indices was assessed cross-sectionally and longitudinally using correlation coefficients, the area under the receiver operating curve (AUROC), sensitivity, specificity, and positive and negative predictive values. ThermoDAI and ThermoDAI-CRP correlated with CDAI, SDAI, and DAS28-CRP cross-sectionally (ρ = 0.81; ρ = 0.83; ρ = 0.78) and longitudinally (ρ = 0.55; ρ = 0.61; ρ = 0.60), all p < 0.001. ThermoDAI and ThermoDAI-CRP also outperformed Patient Global Assessment (PGA) and PGA + C-reactive protein (CRP) in detecting changes in 28-swollen joint counts (SJC28). ThermoJIS had an AUROC of 0.67 (95% CI, 0.58 to 0.76) for detecting patients with swollen joints and effectively identified patients transitioning from SJC28 > 1 at baseline visit to SJC28 ≤ 1 at week 12 visit. These results support the effectiveness of ThermoJIS in assessing joint inflammation, as well as ThermoDAI and ThermoDAI-CRP in evaluating disease activity in RA patients.

Assessment of inflammation in patients with rheumatoid arthritis using thermography and machine learning: a fast and automated technique.

OBJECTIVES: Sensitive detection of joint inflammation in rheumatoid arthritis (RA) is crucial to the success of the treat-to-target strategy. In this study, we characterise a novel machine learning-based computational method to automatically assess joint inflammation in RA using thermography of the hands, a fast and non-invasive imaging technique. METHODS: We recruited 595 patients with arthritis and osteoarthritis, as well as healthy subjects at two hospitals over 4 years. Machine learning was used to assess joint inflammation from the thermal images of the hands using ultrasound as the reference standard, obtaining a Thermographic Joint Inflammation Score (ThermoJIS). The machine learning model was trained and tuned using data from 449 participants with different types of arthritis, osteoarthritis or without rheumatic disease (development set). The performance of the method was evaluated based on 146 patients with RA (validation set) using Spearman's rank correlation coefficient, area under the receiver-operating curve (AUROC), average precision, sensitivity, specificity, positive and negative predictive value and F1-score. RESULTS: ThermoJIS correlated moderately with ultrasound scores (grey-scale synovial hypertrophy=0.49, p<0.001; and power Doppler=0.51, p<0.001). The AUROC for ThermoJIS for detecting active synovitis was 0.78 (95% CI, 0.71 to 0.86; p<0.001). In patients with RA in clinical remission, ThermoJIS values were significantly higher when active synovitis was detected by ultrasound. CONCLUSIONS: ThermoJIS was able to detect joint inflammation in patients with RA, even in those in clinical remission. These results open an opportunity to develop new tools for routine detection of joint inflammation.

A Thermographic Disease Activity Index for remote assessment of rheumatoid arthritis.

OBJECTIVES: Remote assessment of patients with rheumatoid arthritis (RA) has increased during recent years. However, telematic consultations preclude the possibility of carrying out a physical examination and obtaining objective inflammation. In this study, we developed and validated two novel composite disease activity indexes (Thermographic Disease Activity Index (ThermoDAI) and ThermoDAI-CRP) based on thermography of hands and machine learning, in order to assess disease activity easily, rapidly and without formal joint counts. METHODS: ThermoDAI was developed as the sum of Thermographic Joint Inflammation Score (ThermoJIS), a novel joint inflammation score based on the analysis of thermal images of the hands by machine learning, the Patient Global Assessment (PGA) and, for ThermoDAI-CRP, the C reactive protein (CRP). Construct validity was tested in 146 patients with RA by using Spearman's correlation with ultrasound-determined grey-scale synovial hypertrophy (GS) and power Doppler (PD) scores, CDAI, SDAI and DAS28-CRP. RESULTS: Correlations of ultrasound scores with ThermoDAI (GS=0.52; PD=0.56) and ThermoDAI-CRP (GS=0.58; PD=0.61) were moderate to strong, while the correlations of ultrasound scores with PGA (GS=0.35; PD=0.39) and PGA+CRP (GS=0.44; PD=0.46) were weak to moderate. ThermoDAI and ThermoDAI-CRP also showed strong correlations with Clinical Disease Activity Index (ρ>0.83), Simplified Disease Activity Index (ρ>0.85) and Disease Activity Score with 28-Joint Counts-CRP (ρ>0.81) and high sensitivity for detecting active synovitis using remission criteria. CONCLUSIONS: ThermoDAI and ThermoDAI-CRP showed stronger correlations with ultrasound-determined synovitis than PGA and PGA + CRP, thus presenting an opportunity to improve remote consultations with patients with RA.

VORFFIP-driven dock: V-D2OCK, a fast and accurate protein docking strategy.

The experimental determination of the structure of protein complexes cannot keep pace with the generation of interactomic data, hence resulting in an ever-expanding gap. As the structural details of protein complexes are central to a full understanding of the function and dynamics of the cell machinery, alternative strategies are needed to circumvent the bottleneck in structure determination. Computational protein docking is a valid and valuable approach to model the structure of protein complexes. In this work, we describe a novel computational strategy to predict the structure of protein complexes based on data-driven docking: VORFFIP-driven dock (V-D2OCK). This new approach makes use of our newly described method to predict functional sites in protein structures, VORFFIP, to define the region to be sampled during docking and structural clustering to reduce the number of models to be examined by users. V-D2OCK has been benchmarked using a validated and diverse set of protein complexes and compared to a state-of-art docking method. The speed and accuracy compared to contemporary tools justifies the potential use of VD2OCK for high-throughput, genome-wide, protein docking. Finally, we have developed a web interface that allows users to browser and visualize V-D2OCK predictions from the convenience of their web-browsers.