UCSF Laboratory of Andrej Sali QB3

Our Resources

DBAli Database of sequence and structure alignments generated by different alignment methods
IceDB Integrated database for New York Structural Genomics Research Consortium
Integral Membrane Database Integral membrane database for 34 genomes.
LigBase Database of structurally defined ligand binding sites in PDB
Membrane Protein counts Counts of membrane protein families represented in 34 genomes.
ModBase Comprehensive database of annotated comparative protein structure models
PiBase Comprehensive database of structurally defined interfaces in proteins
ALBASE-3 Database of multiple protein structure alignments used to derive MODELLER restraints
Structural decoys Series of structural decoys used in the Sali Lab.
Includes the MOULDER, MODPIPE and MODEM sets.
Models and Alignments in our publications Links to models and alignments in our publications
Web Services
AllosMod Modeling of Ligand-induced Protein Dynamics and Beyond
AllosMod-FoXS Structure Generation and SAXS Profile Calculations
EVA Server for continuous, automatic, and statistically significant assessment of protein structure prediction servers
FoXS Fast SAXS profile computation with Debye formula
FoXSDock Macromolecular docking restrained by a small angle X-ray scattering profile
LigScore Pose & Rank - a web server for scoring protein-ligand complexes
ModEval Web server to model evaluation using TSVMod, DOPE and GA341
ModLoop Server for modeling of loops in protein structures
ModWeb Server for automated comparative protein structure modeling
PCSS Predicts peptide recognition specificity based on sequence and structure features
SAXS Merge An automated statistical method to merge SAXS profiles from different concentrations and exposure times
pG server Program for model assessment based on the ProsaII Z-score
Programs and Methods
Flex-EM A method for fitting and refining a component structure within its map at intermediate resolution
IMP Integrative Modeling Platform
iDOCK The integrative docking method uses atomistic models of two interacting proteins and one or more datasets from experimental techniques (SAXS, EM, NMR and MS)
MODELLER Program for comparative protein structure modelling by satisfaction of spatial restraints
MDT MDT prepares a raw frequency table, given information from MODELLER alignments and/or PDB files
ModTie MODTIE makes structure-based predictions of binary and higher-order protein complexes utilizing ModBase and PiBASE.
SOAP Statistically optimized atomic statistical potentials for ranking loops and protein-protein interfaces.
ModView Web plugin for visualization and analysis of multiple protein sequences and structures
ASGL Program for preparing simple PostScript plots
Miscellaneous programs PSA (surface accessibility), ELLIPSOID (antigenicity index)
Patcher Program for localizing binding sites in protein structures based on a patch optimization scheme and a composite scoring function
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 94143, Tel +1 (415) 514-4227, Fax +1 (415) 514-4231, 4234, , Web http://www.salilab.org