The article introduces RaptorX, a web-based server for protein structure modeling that focuses on template-based tertiary structure prediction, secondary structure prediction, alignment quality assessment, and probabilistic alignment sampling. RaptorX stands out from other servers by its ability to handle distant homologs and sparse sequence profiles through a profile-entropy scoring method, conditional random fields (CRFs), and multiple-template threading (MTT). These features enable RaptorX to deliver high-quality structural models for targets with only remote templates. The server also provides domain parsing, disorder prediction, and functional annotation, making it a comprehensive tool for protein structure prediction and analysis. Since its release in August 2011, RaptorX has processed over 6,000 sequences from approximately 1,600 users worldwide, demonstrating its effectiveness and utility in the field of structural biology.The article introduces RaptorX, a web-based server for protein structure modeling that focuses on template-based tertiary structure prediction, secondary structure prediction, alignment quality assessment, and probabilistic alignment sampling. RaptorX stands out from other servers by its ability to handle distant homologs and sparse sequence profiles through a profile-entropy scoring method, conditional random fields (CRFs), and multiple-template threading (MTT). These features enable RaptorX to deliver high-quality structural models for targets with only remote templates. The server also provides domain parsing, disorder prediction, and functional annotation, making it a comprehensive tool for protein structure prediction and analysis. Since its release in August 2011, RaptorX has processed over 6,000 sequences from approximately 1,600 users worldwide, demonstrating its effectiveness and utility in the field of structural biology.