Andrej Sali Lab

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

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

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