UniprotKB | Comprehensive protein knowledgebase, includes manually curated SwissProt and automatically annotated TrEMBL ![](//salilab.org/img/pubmed_light.png) |
Protein Information Resource | Integrated public bioinformatics resource to support genomic, proteomic and systems biology research and scientific studies ![](//salilab.org/img/pubmed_light.png) |
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 ![](//salilab.org/img/pubmed_light.png) |
ENSEMBL | Genome databases for vertebrates and other eukaryotic species ![](//salilab.org/img/pubmed_light.png) |
CATH/Gene3D | 16 million protein domains classified into 2,626 superfamilies ![](//salilab.org/img/pubmed_light.png) |
InterPro | Classification of proteins into families and prediction of domains and sites. ![](//salilab.org/img/pubmed_light.png) |
PFAM | Collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs) ![](//salilab.org/img/pubmed_light.png) |
ProDom | Comprehensive set of Protein Domain Families ![](//salilab.org/img/pubmed_light.png) |
ProSite | Database of Protein Families and Domains ![](//salilab.org/img/pubmed_light.png) |
SCOP | Structural Classification of Proteins and Astral ![](//salilab.org/img/pubmed_light.png) |
SFLD | Structure-Function Linkage Database: hierarchical classification of enzyme superfamilies. ![](//salilab.org/img/pubmed_light.png) |
SUPERFAMILY | Database of structural and functional annotation for all proteins and genomes ![](//salilab.org/img/pubmed_light.png) |
SMART | Allows the identification and annotation of genetically mobile domains and the analysis of domain architectures ![](//salilab.org/img/pubmed_light.png) |
MEME | Motif-based sequence analysis tools ![](//salilab.org/img/pubmed_light.png) |
PRINTS | Compendium of protein fingerprints/conserved motifs used to characterize a protein family ![](//salilab.org/img/pubmed_light.png) |
GeneCensus | Gerstein Lab Resources |
AlignMe | Alignment of membrane proteins ![](//salilab.org/img/pubmed_light.png) |
ClustalW | Progressive alignment ![](//salilab.org/img/pubmed_light.png) |
COMPASS | Multiple Protein sequence alignments with assessment of statistical significance ![](//salilab.org/img/pubmed_light.png) |
EXPRESSO | Multiple sequence alignment of sequences and structures ![](//salilab.org/img/pubmed_light.png) |
FFAS | Sensitive profile-profile alignment tool ![](//salilab.org/img/pubmed_light.png) |
GenTHREADER | Sequence profile and predicted secondary structure ![](//salilab.org/img/pubmed_light.png) |
HHBlits/HHSearch | Homology detection by iterative HMM-HMM comparison ![](//salilab.org/img/pubmed_light.png) |
MUSCLE | Progressive/iterative alignment ![](//salilab.org/img/pubmed_light.png) |
MUSTER | profile-profile alignment ![](//salilab.org/img/pubmed_light.png) |
Promals3D | Multiple protein sequence/structure alignments using secondary structure prediction, available homologs with 3D structures and user-defined constraints. ![](//salilab.org/img/pubmed_light.png) |
PSI-Blast | Position-specific iterative BLAST ![](//salilab.org/img/pubmed_light.png) |
Salign | Multiple protein sequence/structure alignment ![](//salilab.org/img/pubmed_light.png) |
Staccato | Constructs multiple sequence alignment of sets of sequences and structures which is consistent with a structural alignment of the structure set. ![](//salilab.org/img/pubmed_light.png) |
T-Coffee | Sensitive progressive alignment ![](//salilab.org/img/pubmed_light.png) |
MAFFT | Rapid multiple sequence alignment based on fast Fourier transform ![](//salilab.org/img/pubmed_light.png) |
CE | A method for comparing and aligning protein structures ![](//salilab.org/img/pubmed_light.png) |
HHSearch | Sensitive pairwise comparison of profile Hidden Markov models ![](//salilab.org/img/pubmed_light.png) |
Mammuth | Sequence-independent protein structural alignment method ![](//salilab.org/img/pubmed_light.png) |
Mammuth-mult | Multiple alignment version of MAMOTH ![](//salilab.org/img/pubmed_light.png) |
Multiprot | Multiple structural alignments of protein structures by detecting the common geometrical cores between the input molecules ![](//salilab.org/img/pubmed_light.png) |
Salign | Multiple protein sequence/structure alignment ![](//salilab.org/img/pubmed_light.png) |
TM-align | Highly optimized algorithm for protein structure comparison and alignment ![](//salilab.org/img/pubmed_light.png) |
GANGSTA+ | Protein structure alignment tool and database ![](//salilab.org/img/pubmed_light.png) |
MASS | Efficient method for multiple alignment of protein structures and detection of structural motifs. ![](//salilab.org/img/pubmed_light.png) |
MUSTANG | Multiple structural alignment algorithm ![](//salilab.org/img/pubmed_light.png) |
PDBeFold | 3D alignment of protein structures |
3D-JIGSAW | Fragment assembly ![](//salilab.org/img/pubmed_light.png) |
Fugue | Sequence-structure homology recognition ![](//salilab.org/img/pubmed_light.png) |
HHPred | Sensitive protein homology detection and structure prediction by HMM-HMM-comparison ![](//salilab.org/img/pubmed_light.png) |
i-Tasser | Threading fragment structure reassembly ![](//salilab.org/img/pubmed_light.png) |
IntFOLD | Integrated Protein Structure and Function Prediction Server ![](//salilab.org/img/pubmed_light.png) |
M4T | Comparative Modelling using a combination of multiple templates and iterative optimization of alternative alignments ![](//salilab.org/img/pubmed_light.png) |
ModWeb | Comparative modeling server based on Modeller ![](//salilab.org/img/pubmed_light.png) |
Phyre2 | Protein homology/analogy recognition engine ![](//salilab.org/img/pubmed_light.png) |
RaptorX | Remote homology detection, protein 3D modeling, binding site prediction ![](//salilab.org/img/pubmed_light.png) |
Robetta | Rosetta homology modeling and ab initio fragment assembly with Ginzu domain prediction ![](//salilab.org/img/pubmed_light.png) |
SwissModel | Local similarity/fragment assembly ![](//salilab.org/img/pubmed_light.png) |
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 ![](//salilab.org/img/pubmed_light.png) |
ProQ2 | Support Vector machine based predictor ![](//salilab.org/img/pubmed_light.png) |
Prosa 2003 | Knowledge-based potentials of mean force. ![](//salilab.org/img/pubmed_light.png) |
QMEAN Local | Composite scoring function describing five different structural descriptors ![](//salilab.org/img/pubmed_light.png) |
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 ![](//salilab.org/img/pubmed_light.png) |
Verify 3D | Measures the compatibility of a protein model with its sequence using a 3D profile. ![](//salilab.org/img/pubmed_light.png) |
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 |