Databases

Protein Sequence DatabasesMore on Wikipedia

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

Domains and Superfamilies

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

Protein Structures and ModelsMore on Wikipedia

PDB	Contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies
ModBase	Database of comparative protein structure models generated by the ModPipe comparative modeling pipeline
PDB-Dev	Prototype database of structural models generated by integrative or hybrid methods, such as with our own IMP software
SwissModel Repository	Database of annotated three-dimensional comparative protein structure models generated by the fully automated homology-modelling pipeline SWISS-MODEL

Miscellaneous

PubMed	Entry page to the NIH databases and tools
Stanford Genomic Resource	Stanford resources maintained by the Saccharomyces Genome Database
PharmGKB	Pharmacogenomics Knowledgebase
GENECENSUS	A hierachical system for comparative genomics study
Structural Biology Knowledgebase	Integrates a wide variety of structural biology and structural genomics resources

Alignment programs

Sequence and structure based sequence alignments More on Wikipedia

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

Structure More on Wikipedia

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

Alignment modules in Molecular Graphics Programs

PyMOL	Molecular graphics program with many features; use "super" command for sequence-independent alignment
UCSF Chimera	Complex molecular graphics program; for alignments: use MatchMaker tool and command
Accelrys Discovery Studio Visualization	DS Visualization for Windows and Linux
Swiss-PDB Viewer	User friendly interface allowing to analyze several proteins at the same time

Comparative Modeling and Threading

Web-servers More on Wikipedia

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

ProgramsMore on Wikipedia

HHSuite	HHSearch, HHBlits, and pre-compiled databases
Modeller	Comparative modeling by satisfaction of spacial restraints
Rosetta@home	Distributed-computing implementation of Rosetta algorithm
RosettaCM	Molecular modeling softward
MolIDE	Open-source cross-platform graphical environment for homology modeling

Miscellaneous

Evaluation

Quality Estimation

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

Methods evaluation

CASP	Critical Assessment of protein Structure Prediction for Template-based modeling and free modeling, bi-annual
CAMEO	Continuous automated model evaluation of accuracy and reliability of various protein structure prediction services in a fully automated manner

Protein-protein Complexes

Protein-Ligand Resources

Comparative Genomics and Interaction Networks

Miscellaneous