UCSF Laboratory of Andrej Sali QB3

Databases

Protein Sequence DatabasesMore on Wikipedia

UniprotKB Comprehensive protein knowledgebase, includes manually curated SwissProt and automatically annotated TrEMBL
Protein Information ResourceIntegrated public bioinformatics resource to support genomic, proteomic and systems biology research and scientific studies
GenPeptCollection 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
ENSEMBLGenome databases for vertebrates and other eukaryotic species

Domains and Superfamilies

CATH/Gene3D 16 million protein domains classified into 2,626 superfamilies
InterProClassification 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)
ProDomComprehensive set of Protein Domain Families
ProSiteDatabase of Protein Families and Domains
SCOP Structural Classification of Proteins and Astral
SFLDStructure-Function Linkage Database: hierarchical classification of enzyme superfamilies.
SUPERFAMILYDatabase of structural and functional annotation for all proteins and genomes
SMARTAllows the identification and annotation of genetically mobile domains and the analysis of domain architectures
MEMEMotif-based sequence analysis tools
PRINTSCompendium 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
Protein Model Portal Gives access to various models computed by comparative modeling methods provided by different partner sites, and provides access to various interactive services for model building, and quality assessment
ModBase Database of comparative protein structure models generated by the ModPipe comparative modeling pipeline
SwissModel RepositoryDatabase of annotated three-dimensional comparative protein structure models generated by the fully automated homology-modelling pipeline SWISS-MODEL

Miscellaneous

PubMedEntry page to the NIH databases and tools
Stanford Genomic Resource Stanford resources maintained by the Saccharomyces Genome Database
PharmGKBPharmacogenomics Knowledgebase
DBALI Database of structure alignments
GENECENSUS A hierachical system for comparative genomics study
Structural Biology KnowledgebaseIntegrates a wide variety of structural biology and structural genomics resources

Alignment programs

Sequence and structure based sequence alignments More on Wikipedia

AlignMeAlignment of membrane proteins
ClustalWProgressive alignment
COMPASSMultiple Protein sequence alignments with assessment of statistical significance
EXPRESSOMultiple sequence alignment of sequences and structures
FFASSensitive profile-profile alignment tool
GenTHREADERSequence profile and predicted secondary structure
HHBlits/HHSearchHomology detection by iterative HMM-HMM comparison
MUSCLEProgressive/iterative alignment
MUSTERprofile-profile alignment
Promals3DMultiple protein sequence/structure alignments using secondary structure prediction, available homologs with 3D structures and user-defined constraints.
PSI-BlastPosition-specific iterative BLAST
SalignMultiple protein sequence/structure alignment
StaccatoConstructs multiple sequence alignment of sets of sequences and structures which is consistent with a structural alignment of the structure set.
T-CoffeeSensitive progressive alignment
MAFFTRapid multiple sequence alignment based on fast Fourier transform

Structure More on Wikipedia

CEA method for comparing and aligning protein structures
HHSearchSensitive pairwise comparison of profile Hidden Markov models
MammuthSequence-independent protein structural alignment method
Mammuth-multMultiple alignment version of MAMOTH
MultiprotMultiple structural alignments of protein structures by detecting the common geometrical cores between the input molecules
SalignMultiple protein sequence/structure alignment
TM-alignHighly optimized algorithm for protein structure comparison and alignment
GANGSTA+Protein structure alignment tool and database
MASSEfficient method for multiple alignment of protein structures and detection of structural motifs.
MUSTANGMultiple structural alignment algorithm
PDBeFold3D alignment of protein structures

Alignment modules in Molecular Graphics Programs

PyMOLMolecular graphics program with many features; use "super" command for sequence-independent alignment
UCSF ChimeraComplex molecular graphics program; for alignments: use MatchMaker tool and command
Accelrys Discovery Studio VisualizationDS Visualization for Windows and Linux
Swiss-PDB ViewerUser friendly interface allowing to analyze several proteins at the same time

Comparative Modeling and Threading

Web-servers More on Wikipedia

3D-JIGSAWFragment assembly
FugueSequence-structure homology recognition
HHPredSensitive protein homology detection and structure prediction by HMM-HMM-comparison
i-TasserThreading fragment structure reassembly
IntFOLDIntegrated Protein Structure and Function Prediction Server
M4TComparative Modelling using a combination of multiple templates and iterative optimization of alternative alignments
ModWebComparative modeling server based on Modeller
Phyre2Protein homology/analogy recognition engine
RaptorXRemote homology detection, protein 3D modeling, binding site prediction
RobettaRosetta homology modeling and ab initio fragment assembly with Ginzu domain prediction
SwissModelLocal similarity/fragment assembly

ProgramsMore on Wikipedia

HHSuiteHHSearch, HHBlits, and pre-compiled databases
ModellerComparative modeling by satisfaction of spacial restraints
Rosetta@homeDistributed-computing implementation of Rosetta algorithm
RosettaCMMolecular modeling softward
MolIDEOpen-source cross-platform graphical environment for homology modeling

Miscellaneous

PredictProteinSecondary structure, families of related proteins, solvent accessibility, transmembrane helix prediction, non-regular secondary structure and intrinsically disordered regions, disulphide bridges and inter-residue contacts, trans-membrane beta barrels structures, and more.
MolSoftLarge repertoire of tools and databases

Evaluation

Quality Estimation

Cameo Quality EstimationParticipating Groups in the Cameo QE project
ModEvalEstimates model quality by estimating the native overlap, and by computing scores and profile based on statistical potentials: TSVMod, zDOPE, GA341, zDOPE-Profile
ProQ2Support Vector machine based predictor
Prosa 2003Knowledge-based potentials of mean force.
QMEAN LocalComposite scoring function describing five different structural descriptors
SwissModel WorkspaceSeveral assessment tools to estimate the quality and structural features of protein models and template structures: Dfire, Procheck, DSSP, Promotif, Anolea, Gromos, QMEANS6
Verify 3DMeasures the compatibility of a protein model with its sequence using a 3D profile.
What_CheckProtein verification tools
ModFoldModel Quality Assessment Server
ProSA-webProtein-Structure Analysis
Kinemage3D Macromolecule analysis, includes Kinemage 3D graphics, Rampage for Ramachandran plot generation, MolProbity structure validation, and more

Methods evaluation

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

Protein-protein Complexes

PatchDockMolecular docking algorith based on shape complementarity principles
FastContactFree energy scoring tool for protein-protein complex structures
FiberDockFlexible Induced-fit Backbone Refinement in Molecular Docking
MetaMQAPIIBioinformatics and protein engineering toolkit

Protein-Ligand Resources

DockBlasterA free virtual docking server
ZincA database of commercially-available compounds for virtual screening

Comparative Genomics and Interaction Networks

structureVizCytoscape plugin that links visualization of biological networks in Cytoscape with visualization and analysis of molecular structures in UCSF Chimera.
MicrobesOnlineComparative and functional genomics analysis
StringProtein function, and interaction network analysis

Miscellaneous

Pedant3Protein Extraction, Description and ANalysis Tool
Biology WorkbenchWeb-based tool for biologists
Andrej Sali, PhD, Professor, Department of Bioengineering and Therapeutic Sciences; Department of Pharmaceutical Chemistry; School of Pharmacy, University of California at San Francisco, UCSF MC 2552, Mission Bay, Byers Hall, 1700 4th Street, Suite 503B, San Francisco, CA 94158-2330, Tel +1 (415) 514-4227, Fax +1 (415) 514-4231, 4234, , Web http://www.salilab.org, Assistant: Ms. Hilary Mahon, Email: , Tel +1 (415) 514-4228, Lab +1 (415) 514-4258, 4233