| UniprotKB | Comprehensive protein knowledgebase, includes manually curated SwissProt and automatically annotated TrEMBL  |
| Protein Information Resource | Integrated public bioinformatics resource to support genomic, proteomic and systems biology research and scientific studies |
| GenPept | Collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB |
| ENSEMBL | Genome databases for vertebrates and other eukaryotic species |
| CATH/Gene3D | 16 million protein domains classified into 2,626 superfamilies |
| InterPro | Classification of proteins into families and prediction of domains and sites. |
| PFAM | Collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs) |
| ProDom | Comprehensive set of Protein Domain Families |
| ProSite | Database of Protein Families and Domains |
| SCOP | Structural Classification of Proteins and Astral |
| SFLD | Structure-Function Linkage Database: hierarchical classification of enzyme superfamilies. |
| SUPERFAMILY | Database of structural and functional annotation for all proteins and genomes |
| SMART | Allows the identification and annotation of genetically mobile domains and the analysis of domain architectures |
| MEME | Motif-based sequence analysis tools |
| PRINTS | Compendium of protein fingerprints/conserved motifs used to characterize a protein family |
| GeneCensus | Gerstein Lab Resources |
| AlignMe | Alignment of membrane proteins |
| ClustalW | Progressive alignment |
| COMPASS | Multiple Protein sequence alignments with assessment of statistical significance |
| EXPRESSO | Multiple sequence alignment of sequences and structures |
| FFAS | Sensitive profile-profile alignment tool |
| GenTHREADER | Sequence profile and predicted secondary structure |
| HHBlits/HHSearch | Homology detection by iterative HMM-HMM comparison |
| MUSCLE | Progressive/iterative alignment |
| MUSTER | profile-profile alignment |
| Promals3D | Multiple protein sequence/structure alignments using secondary structure prediction, available homologs with 3D structures and user-defined constraints. |
| PSI-Blast | Position-specific iterative BLAST |
| Salign | Multiple protein sequence/structure alignment |
| Staccato | Constructs multiple sequence alignment of sets of sequences and structures which is consistent with a structural alignment of the structure set. |
| T-Coffee | Sensitive progressive alignment |
| MAFFT | Rapid multiple sequence alignment based on fast Fourier transform |
| CE | A method for comparing and aligning protein structures |
| HHSearch | Sensitive pairwise comparison of profile Hidden Markov models |
| Mammuth | Sequence-independent protein structural alignment method |
| Mammuth-mult | Multiple alignment version of MAMOTH |
| Multiprot | Multiple structural alignments of protein structures by detecting the common geometrical cores between the input molecules |
| Salign | Multiple protein sequence/structure alignment |
| TM-align | Highly optimized algorithm for protein structure comparison and alignment |
| GANGSTA+ | Protein structure alignment tool and database |
| MASS | Efficient method for multiple alignment of protein structures and detection of structural motifs. |
| MUSTANG | Multiple structural alignment algorithm |
| PDBeFold | 3D alignment of protein structures |
| 3D-JIGSAW | Fragment assembly |
| Fugue | Sequence-structure homology recognition |
| HHPred | Sensitive protein homology detection and structure prediction by HMM-HMM-comparison |
| i-Tasser | Threading fragment structure reassembly |
| IntFOLD | Integrated Protein Structure and Function Prediction Server |
| M4T | Comparative Modelling using a combination of multiple templates and iterative optimization of alternative alignments |
| ModWeb | Comparative modeling server based on Modeller |
| Phyre2 | Protein homology/analogy recognition engine |
| RaptorX | Remote homology detection, protein 3D modeling, binding site prediction |
| Robetta | Rosetta homology modeling and ab initio fragment assembly with Ginzu domain prediction |
| SwissModel | Local similarity/fragment assembly |
| Cameo Quality Estimation | Participating Groups in the Cameo QE project |
| ModEval | Estimates model quality by estimating the native overlap, and by computing scores and profile based on statistical potentials: TSVMod, zDOPE, GA341, zDOPE-Profile |
| ProQ2 | Support Vector machine based predictor |
| Prosa 2003 | Knowledge-based potentials of mean force. |
| QMEAN Local | Composite scoring function describing five different structural descriptors |
| SwissModel Workspace | Several assessment tools to estimate the quality and structural features of protein models and template structures: Dfire, Procheck, DSSP, Promotif, Anolea, Gromos, QMEANS6 |
| Verify 3D | Measures the compatibility of a protein model with its sequence using a 3D profile. |
| What_Check | Protein verification tools |
| ModFold | Model Quality Assessment Server |
| ProSA-web | Protein-Structure Analysis |
| Kinemage | 3D Macromolecule analysis, includes Kinemage 3D graphics, Rampage for Ramachandran plot generation, MolProbity structure validation, and more |
