DisCovER: distance- and orientation-based covariational threading for weakly homologous proteins

Single-sequence protein-RNA complex structure prediction by geometric attention-enabled pairing of biological language models

Ground-breaking progress has been made in structure prediction of biomolecular assemblies, including the recent breakthrough of AlphaFold 3. However, it remains challenging for AlphaFold 3 and other state-of-the-art deep learning-based methods to accurately predict protein-RNA complex structures, in part due to the limited availability of evolutionary and structural information related to protein-RNA interactions that are used as inputs to the existing approaches. Here, we introduce ProRNA3D-single, a new deep-learning framework for protein-RNA complex structure prediction with only single-sequence input. Using a novel geometric attention-enabled pairing of biological language models of protein and RNA, a previously unexplored avenue, ProRNA3D-single enables the prediction of interatomic protein-RNA interaction maps, which are then transformed into multi-scale geometric restraints for modeling 3D structures of protein-RNA complexes via geometry optimization. Benchmark tests show that ProRNA3D-single convincingly outperforms current state-of-the-art methods including AlphaFold 3, particularly when evolutionary information is limited; and exhibits remarkable robustness and performance resilience by attaining better accuracy with only single-sequence input than what most methods can achieve even with explicit evolutionary information. Freely available at https://github.com/Bhattacharya-Lab/ProRNA3D-single, ProRNA3D-single should be broadly useful for modeling 3D structures of protein-RNA complexes at scale, regardless of the availability of evolutionary information.

PLMSearch: Protein language model powers accurate and fast sequence search for remote homology

Homologous protein search is one of the most commonly used methods for protein annotation and analysis. Compared to structure search, detecting distant evolutionary relationships from sequences alone remains challenging. Here we propose PLMSearch (Protein Language Model), a homologous protein search method with only sequences as input. PLMSearch uses deep representations from a pre-trained protein language model and trains the similarity prediction model with a large number of real structure similarity. This enables PLMSearch to capture the remote homology information concealed behind the sequences. Extensive experimental results show that PLMSearch can search millions of query-target protein pairs in seconds like MMseqs2 while increasing the sensitivity by more than threefold, and is comparable to state-of-the-art structure search methods. In particular, unlike traditional sequence search methods, PLMSearch can recall most remote homology pairs with dissimilar sequences but similar structures. PLMSearch is freely available at https://dmiip.sjtu.edu.cn/PLMSearch .

An interactive visualization tool for educational outreach in protein contact map overlap analysis

Recent advancements in contact map-based protein three-dimensional (3D) structure prediction have been driven by the evolution of deep learning algorithms. However, the gap in accessible software tools for novices in this domain remains a significant challenge. This study introduces GoFold, a novel, standalone graphical user interface (GUI) designed for beginners to perform contact map overlap (CMO) problems for better template selection. Unlike existing tools that cater more to research needs or assume foundational knowledge, GoFold offers an intuitive, user-friendly platform with comprehensive tutorials. It stands out in its ability to visually represent the CMO problem, allowing users to input proteins in various formats and explore the CMO problem. The educational value of GoFold is demonstrated through benchmarking against the state-of-the-art contact map overlap method, map_align, using two datasets: PSICOV and CAMEO. GoFold exhibits superior performance in terms of TM-score and Z-score metrics across diverse qualities of contact maps and target difficulties. Notably, GoFold runs efficiently on personal computers without any third-party dependencies, thereby making it accessible to the general public for promoting citizen science. The tool is freely available for download for macOS, Linux, and Windows.

Recent Progress of Protein Tertiary Structure Prediction

The prediction of three-dimensional (3D) protein structure from amino acid sequences has stood as a significant challenge in computational and structural bioinformatics for decades. Recently, the widespread integration of artificial intelligence (AI) algorithms has substantially expedited advancements in protein structure prediction, yielding numerous significant milestones. In particular, the end-to-end deep learning method AlphaFold2 has facilitated the rise of structure prediction performance to new heights, regularly competitive with experimental structures in the 14th Critical Assessment of Protein Structure Prediction (CASP14). To provide a comprehensive understanding and guide future research in the field of protein structure prediction for researchers, this review describes various methodologies, assessments, and databases in protein structure prediction, including traditionally used protein structure prediction methods, such as template-based modeling (TBM) and template-free modeling (FM) approaches; recently developed deep learning-based methods, such as contact/distance-guided methods, end-to-end folding methods, and protein language model (PLM)-based methods; multi-domain protein structure prediction methods; the CASP experiments and related assessments; and the recently released AlphaFold Protein Structure Database (AlphaFold DB). We discuss their advantages, disadvantages, and application scopes, aiming to provide researchers with insights through which to understand the limitations, contexts, and effective selections of protein structure prediction methods in protein-related fields.

Integrating deep learning, threading alignments, and a multi-MSA strategy for high-quality protein monomer and complex structure prediction in CASP15

We report the results of the "UM-TBM" and "Zheng" groups in CASP15 for protein monomer and complex structure prediction. These prediction sets were obtained using the D-I-TASSER and DMFold-Multimer algorithms, respectively. For monomer structure prediction, D-I-TASSER introduced four new features during CASP15: (i) a multiple sequence alignment (MSA) generation protocol that combines multi-source MSA searching and a structural modeling-based MSA ranker; (ii) attention-network based spatial restraints; (iii) a multi-domain module containing domain partition and arrangement for domain-level templates and spatial restraints; (iv) an optimized I-TASSER-based folding simulation system for full-length model creation guided by a combination of deep learning restraints, threading alignments, and knowledge-based potentials. For 47 free modeling targets in CASP15, the final models predicted by D-I-TASSER showed average TM-score 19% higher than the standard AlphaFold2 program. We thus showed that traditional Monte Carlo-based folding simulations, when appropriately coupled with deep learning algorithms, can generate models with improved accuracy over end-to-end deep learning methods alone. For protein complex structure prediction, DMFold-Multimer generated models by integrating a new MSA generation algorithm (DeepMSA2) with the end-to-end modeling module from AlphaFold2-Multimer. For the 38 complex targets, DMFold-Multimer generated models with an average TM-score of 0.83 and Interface Contact Score of 0.60, both significantly higher than those of competing complex prediction tools. Our analyses on complexes highlighted the critical role played by MSA generating, ranking, and pairing in protein complex structure prediction. We also discuss future room for improvement in the areas of viral protein modeling and complex model ranking.

rrQNet: Protein contact map quality estimation by deep evolutionary reconciliation

Protein contact maps have proven to be a valuable tool in the deep learning revolution of protein structure prediction, ushering in the recent breakthrough by AlphaFold2. However, self-assessment of the quality of predicted structures are typically performed at the granularity of three-dimensional coordinates as opposed to directly exploiting the rotation- and translation-invariant two-dimensional (2D) contact maps. Here, we present rrQNet, a deep learning method for self-assessment in 2D by contact map quality estimation. Our approach is based on the intuition that for a contact map to be of high quality, the residue pairs predicted to be in contact should be mutually consistent with the evolutionary context of the protein. The deep neural network architecture of rrQNet implements this intuition by cascading two deep modules-one encoding the evolutionary context and the other performing evolutionary reconciliation. The penultimate stage of rrQNet estimates the quality scores at the interacting residue-pair level, which are then aggregated for estimating the quality of a contact map. This design choice offers versatility at varied resolutions from individual residue pairs to full-fledged contact maps. Trained on multiple complementary sources of contact predictors, rrQNet facilitates generalizability across various contact maps. By rigorously testing using publicly available datasets and comparing against several in-house baseline approaches, we show that rrQNet accurately reproduces the true quality score of a predicted contact map and successfully distinguishes between accurate and inaccurate contact maps predicted by a wide variety of contact predictors. The open-source rrQNet software package is freely available at https://github.com/Bhattacharya-Lab/rrQNet.

LOMETS3: integrating deep learning and profile alignment for advanced protein template recognition and function annotation

Deep learning techniques have significantly advanced the field of protein structure prediction. LOMETS3 (https://zhanglab.ccmb.med.umich.edu/LOMETS/) is a new generation meta-server approach to template-based protein structure prediction and function annotation, which integrates newly developed deep learning threading methods. For the first time, we have extended LOMETS3 to handle multi-domain proteins and to construct full-length models with gradient-based optimizations. Starting from a FASTA-formatted sequence, LOMETS3 performs four steps of domain boundary prediction, domain-level template identification, full-length template/model assembly and structure-based function prediction. The output of LOMETS3 contains (i) top-ranked templates from LOMETS3 and its component threading programs, (ii) up to 5 full-length structure models constructed by L-BFGS (limited-memory Broyden–Fletcher–Goldfarb–Shanno algorithm) optimization, (iii) the 10 closest Protein Data Bank (PDB) structures to the target, (iv) structure-based functional predictions, (v) domain partition and assembly results, and (vi) the domain-level threading results, including items (i)–(iii) for each identified domain. LOMETS3 was tested in large-scale benchmarks and the blind CASP14 (14th Critical Assessment of Structure Prediction) experiment, where the overall template recognition and function prediction accuracy is significantly beyond its predecessors and other state-of-the-art threading approaches, especially for hard targets without homologous templates in the PDB. Based on the improved developments, LOMETS3 should help significantly advance the capability of broader biomedical community for template-based protein structure and function modelling.