• Modbase Search
• User Login
• Datasets
• Search Types
• Display Types
• Search Properties
• Advanced Search Properties
• Advanced Search Type
• Input Sequence
• FASTA Format
• Sequence Similarity Search (BLAST)
• Sequence Identity Search


• Linking to Modbase models from external Databases


• Retrieving coordinate files or alignment files in pdb/xml format


• Model Details page
• Model Details (Graphical)
• Model coverage sketch
• Model image
• Model Details (Schema)
• Filtered models


• Sequence/Model Overview
• Sequence Overview
• Model coverage sketch
• Model Overview
• Model/Fold Reliability


• Sequence Information
• Primary Sequence Database ID
• Original Sequence Database ID
• Original Sequence
• Organism information (Taxonomy)


• Model Information
• Alignment Significance
• E-Value
• Model Score
• ModPipe Protein Quality Score
• z-Dope
• Model Coverage
• Protein Length
• Target Region
• Template Region
• Template PDB
• Reliable Model
• Reliable Fold Assignment
• PSI-Blast Fold Assignment
• Sequence Identity
• ModPipe Version
• Coordinate (3D) File
• Modeller Error Profile
• PAP Alignment Format
• PIR Alignment Format
• Model Information


• LIGBASE
• Ligbase: Coverage Sketch
• Ligbase: Ligand binding sites
• Ligbase: Binding sites derived from the template
• Ligbase: Binding sites inherited from related pdb files


• SNP Information
• Action
• SNP: Coverage Sketch
• SNP Details
• SNP Stability


• MODWEB Modeling Server
• Modeller License Key
• ModWeb Calculations
• ModWeb Personal Information
• ModWeb Input Sequence
• ModWeb FASTA Format
• ModWeb Output
• ModWeb Advanced Modelling Options
• How to find ModWeb Models in Modbase?


• Predicted Protein Complexes

To access the User Login page, please go to the login page

There are several kinds of possible user logins:

• Public: no login necessary
• Academic: the academic agreement has to get accepted
• ModWeb created User Logins (Username/Password received from ModWeb)
• Private Datasets for specific User Groups (e.g. NYSGXRC)

For a ModWeb dataset, the user receives username/password by email after the modweb calculation has been finished and the data have been stored in ModBase.

During the login process, ModBase sets a cookie for each user login. These cookies are being checked at every ModBase query. Once a cookie is set, there is no need for subsequent logins for that user, unless the cookie gets deleted.

ModBase is organized into Datasets. The comprehensive Dataset (combination of all SP/TR datasets) comprises comparative models of all sequences in the SwissProt and TrEMBL databases that have detectable similarity to an experimental protein structure.
Additionally, there are datasets for specific projects (SNP-HUMAN, Plasmodium falciparum, etc), datasets for user groups (e.g. nysgxrc), and dataset created by ModWeb calculations.

While some datasets are accessible publically, the majority of models are only accessible for the academic community.

ModWeb calculations are generally only available to the user who initiated the ModWeb calculation, unless it is specifically requested to make a dataset available to other user groups.

To select a specific subset of the datasets available to you, please go to the search page, and click on "Select specific dataset(s)". This will open two boxes. The left box contains all datasets available to you. The right box contains a subset of those. You can either click on a dataset on the left, and then click the arrow, or double click a dataset on the left, to include it into the search. You can also double click a dataset on the right to exclude it from the search. If you don't use this menu (Collapse dataset selection), all available datasets are selected by default.

Different search options are available in ModBase.

• Model (Default)

  Search for MODBASE models.

• Sequence Similarity

  Blast search is performed against the comprehensive datasets.

• Ligand Binding

  Under Construction

• Interacting Proteins

  Under Construction

Depending on the chosen search mode, different display options are available in ModBase.

• Model Detail (graphical)

  Detailed view for models of one sequence. An image of the model with the highest sequence identity to its template is prominently displayed, all other models are available through their thumbprint images.

• Model Detail (schema)

  Schematic view for models of one sequence. A thumbprint of each model together with a schema of the sequence coverage are displayed.

• Sequence Overview

  Summary of sequence data for up to 500 models including the sequence coverage sketch. Click on the sketch to go to the Model Details (Graphical) page for this sequence.

• SNP View

  SNP related properties

• Interacting Proteins

  Predicted Interacting Proteins

• Ligand Binding

  A number of ligand binding properties from LIGBASE, ligand based or sequence based are displayed.

Search properties are dependent on the chosen search mode.
The most common are described here:

• Database Accession Number

  Any SwissProt, TrEMBL, GenPept or PIR accession number gets accepted and will be translated to an internal sequence id.

• Template PDB code

  Search for models calculated using the input template structure.

• Template or Homolog PDB code

  Search for models calculated using the input template structure or a homolog based on 95% identity.

• Annotation Keyword

  Search for modeled sequences who's annotation contains the search keyword. This search is currently very computationally expensive, and therefore slow.

• Internal ID

  Search using our internal sequence/alignment/model id, based on the MD5 digest of the searched entity.

Often, Modbase returns several models for one sequence. If you check:
Apply to all models of a sequence
the advanced search criteria will be applied to all models for the query sequence(s).
If you check:
some models of a sequence.
the advanced search criteria will apply to some of the models for the query sequence(s).

Search options for model properties are available:
Model Score
Evalue
Sequence Identity
Protein Size
Model Size

Those properties can get combined using boolean operators.

ModPipe, the software that calculates the ModBase models, modifies the original protein sequences to replace non-standard amino acid residues. The Original Sequence represents the un-modified version, gets only displayed if a modification has taken place.

Enter a sequences in either FAST format or just the amino acid residues. Non-standard residues are being ignored.

Search by sequence similarity using BLAST.

The Action Pulldown Menues give the users the option to:

• Jump to different Modbase pages:
  Ligand Binding
  SNP View
  Model Overview or Details pages
  
  
• Retrieve Files for the current or the checked Models:
  Alignment files
  Coordinate Files
  
  
• Launch Chimera:
  
  Chimera is an interactive molecular graphics program developed by the Computer Graphics Lab at UCSF. It can be used as a helper application for several types of files linked to web pages. If Chimera is installed on the user's computer, the Modbase-Chimera action will launch Chimera, retrieve template and alignment information about the current model, and display them in Chimera.
  Chimera Installation Instructions

To link from outside pages to specific Modbase Sequences/Models, please use the following link construction:

Link to specific Database ID (SwissProt,TrEMBL,GI):
http://salilab.org/modbase/searchbyid?databaseID=P04848

Link to the SNP dataset:
All SNPs for the sequence:
http://salilab.org/modbase/searchbyid? databaseID=P43632&displaymode=snpview

Specific dbSnp ID:
http://salilab.org/modbase/searchbyid?databaseID=P43632&dbsnpID=rs1143507

Link to specific dataset:
http://salilab.org/modbase/searchbyDATASET?datasetNAME=nysgxrc_1jd1_06-04f

If you link to Modbase, please drop me a note (), just for information. Thanks!

This is the default MODBASE page for models for one sequence. Sequence information, model/sequence coverage and model information are displayed. Two version of this page are available: Graphical and schematic

The graphical Model Details page gives access to all available information for the models of one sequence: Sequence information, model information, database crosslinks. If there are several models for the current sequence, the model with the highest sequence identity to its template is displayed, and thumbprints of the other models are show as well. Mouseover the thumbprint to get information about that model.

This image indicates the modeled area of the query sequence. The red and green areas show that models are available for those stretches of the sequence.

The colors signify the quality of the best model for this area:
Top line: Sequence Identity to template structure: green: >=30%, red: <30%
Middle line: Template/Target Evalue: green: <=0.0001, red: >0.0001
Third line: Model Score: green: >=0.7, red: <0.7
The bottom line (only present on model details page) indicates the modeled area of the current model.

If (a) specific dataset(s) have been selected, and the query sequence has been modeled in other available datasets as well, the darker colors indicate the selected dataset(s) and the light colors the others.

The model images are created on the fly using MolScript and raster 3d.

The schematic model details page shows a thumbprint of each model and a sketch of the model/sequence coverage.

Modbase contains many models for some sequences. This might be due to a very long sequence, or because this sequence has been processed in several datasets. To avoid confusion, a "filtered" subset of the models are displayed on the model details pages, if there are more than 5 models for the current sequence. The filtering is done very crude, to span the whole length of the sequence. Please click on "all models" if you are not satisfied with the displayed models, a better one might be hiding. On the schematic page, a mouseover the thumbprint gives more information about that model.

This is the default page when the search results in more than one sequences. There are two models: Sequence Overview and Model Overview.

The Sequence Overview page summarizes the search results for many sequences. The sequence coverage Sketch indicates the modeled area(s) for the given sequence. Click on the sketch to go to the "Model Details" page.

Similar as the Model Details Sketch, but smaller and with less complexity.

The Model Overview page displays the search results as one line for each model. Details about modeling quality and templates are being displayed. Click on the thumbprint on the left to get to the "Model Details" page for that model.

Please click on the Thumbnail to go the the Model Details (graphical) page for this model.

The Sequence Database ID displayed on the "Sequence Information" section is chosen according to the following order of availability:
1. SwissProt ID
2. TrEMBL Accession Number
3. GenPept GI ID
4. The ID provided in the dataset at time of processing
The Annotation line comes with the chosen ID.
The Organism information has been obtained from the NCBI Taxonomy database, and links to it.

The original Sequence Database ID from the fasta file that was used for the modeling calculation. The prefix "CU" indicates a custom database ID. This ID can be useful to identity sequences from modweb calculations.

MODBASE currently contains 16 datasets of complete genomes. These are included in the pull-down menu.

Since MODBASE also contains the comprehensive datasets of sequences in UNIPROT, virtually all organisms are represented. However, when searching for other organisms than found in the pull-down menu, please restrict your search further, by choosing a property from the "Search by Properties" pull-down menu, and entering an appropriate search-term, or by choosing a specific dataset (excluding the comprehensive datasets).

The Organism information has been obtained from the NCBI Taxonomy database, and links to it.

Significance of the alignment between the target and the template as reported by NCBI's PSI-BLAST program (Nucl. Acids Res. 25, 3389-3402, 1997). This is the significance reported during the template (PDB) database search. It is not the significance of the modeling alignment produced by MODELLER.

ModPipe1.0: Significance of the alignment between the target and the template as reported by NCBI's PSI-BLAST program (Nucl. Acids Res. 25, 3389-3402, 1997). This is the significance reported during the template (PDB) database search. It is not the significance of the modeling alignment produced by MODELLER. ModPipe2 and later:Similar significance value, but calculated by MODELLER using the Built-Profile routine.

Score for the reliability of a Model, derived from statistical potentials (F. Melo, R. Sanchez, A. Sali,2001 PDF). A model is predicted to be good when the model score is higher than a pre-specified cutoff (0.7). A reliable model has a probability of the correct fold that is larger than 95%. A fold is correct when at least 30% of its Calpha atoms superpose within 3.5A of their correct positions.

Length of the modeled sequences (original sequence, not the modeled part).

Length of the model;

A reliable model is a model that is evaluated as good by a new model evaluation procedure (F. Melo, R. Sanchez, A. Sali,2001 PDF). A model is predicted to be good when the model score is higher than a pre-specified cutoff (0.7). A reliable model has a probability of the correct fold that is larger than 95%. A fold is correct when at least 30% of its Calpha atoms superpose within 3.5A of their correct positions.

A reliable fold assignment is a fold assignment that corresponds to a significant PSI-BLAST hit or to a reliable model. A PSI-BLAST hit is significant when it is obtained in a filtered search and its E-value is smaller than 0.0001. Thus, a reliable fold assignment can correspond to an unreliable model if the PSI-BLAST score is significant.

A PSI-BLAST fold assignment is a fold assignment that corresponds to a significant PSI-BLAST hit. A PSI-BLAST hit is significant when it is obtained in a filtered search and its E-value is smaller than 0.0001. Thus, a PSI-BLAST fold assignment can correspond to an unreliable model.

Percentage of identical residues in the alignment between the target and the template as reported during the template search.

The ModPipe Protein Quality Score is a composite score comprising sequence identity to the template, coverage, and the three individual scores evalue, z-Dope and GA341.

The region of the protein sequence that is modeled.

The length of the original protein sequence.

The PDB code of the template the model is based on.

The region of the pdb structure that was used as a template.

ModPipe is the underlying software pipeline that is used to build all ModBase models. ModPipe1.0 relies on PSI-Blast and Impala for template selection and fold assignment. ModPipe2 is additionally using the Built-Profile method in Modeller. ModPipe2 models are also scored with the MPQS and z-Dope.

Coordinate file for the model in the PDB format. The "fifth column" (which normally contains B-factors or order parameters) contains the MODELLER error profile.

The 'PAP' format is nicer to look at than the 'PIR' format, but not as computer friendly. The WRITE_ALIGNMENT command description in the MODELLER manual contains more detailed information about this format.

The 'PIR' format resembles that of the PIR sequence database. It is described in the MODELLER manual and is used for comparative modeling with MODELLER because it can contain all the information useful for modeling.

Ligbase is a structural database of ligand binding sites. The ligbase database tables contain all amino acid residues that are within 5 Angstroems from a small molecul ligand in a given pdb file. The current version of ligbase contains ligand binding information from 16629 pdb files.

ModBase queries the Ligbase tables to derive ligand binding information for protein structure models. For additional Ligbase functionality, please see http://salilab.org/ligbase.

Putative ligand binding sites of MODBASE models are derived from the template on the fly by parsing the MODBASE alignment file. The native ligand binding residues of the template (TEMPL) and the derived ligand binding sites of the model (MODEL) are shown. Additionally, the putative binding residues of the model are colored in its image. If a gap is found in the alignment at a ligand binding residue, a "-" is displayed instead of the model residue.

If atoms from different hetero groups are less than 1.8 A apart, they are considered "one ligand", and all residues codes are show for that ligand.

Many pdb files used as templates don't include a ligand, but closely related pdb files might have one or more ligands bound. Using DBALI , a database of structural alignments, and using the information in the PDB-Ligbase tables, the INHERITOR table of Ligbase contains the amino acid residues of pdb files with ligands and the equivalent residues of related pdb files. Additionally, the sequence identity and coverage between those pdb files and between the respective binding sites are stored. Once the INHERITOR information is retrieved, putative ligand binding sites from related pdb files are determined similar to the binding sites derived from the templates. The inherited residues are shown (INHER) together with the equivalent model residues (MODEL).

The ligbase coverage sketch displays the same information as the general model coverage sketch. Additionally, it displays the position of the amino acid residues which are putative ligand binding residues.

ModWeb is a comparative modeling server.

When a MODWEB job is finished (with the option of depositing the models into MODBASE), the user gets an email including the dataset name, and the username/password for MODBASE to access that particular dataset.
Access the MODWEB dataset:

http://salilab.org/modbase/search?dataset=ModWebEnterYourDatasetIDHere&username=YourUserName&password=YourPassWord

Alternatively, please do the following:

1. go to http://salilab.org/modbase
2. click "User Login"
3. choose "Individual User" and click "Select Mode"
4. Enter Username/Password from the MODWEB email and click "submit query"
5. This should have brought you back to the Search Page. Mouse-over the "Current Logins" field, to see whether the login was successful (cookie has been set).

There are three ModWeb input options:

• Single Sequence:
  Paste a single sequence to be modeled into the text field or upload FASTA file of that sequence.
  
• Multiple Sequences:
  Multiple Sequences (up to 50) can be pasted into the textfield or a FASTA file can be uploaded. Please note the header specifications for easier viewing of the results.


• Template PDB file:
  When a PDB file is submitted to ModWeb, it is used as a template to calculate models of all sequences in SwissProt/TrEMBL that are related to this template structure.

Personal information for modweb calculations are solely collected for dataset identification, when the models are displayed in ModBase.

Enter a sequences in either FAST format or just the amino acid residues. Non-standard residues are being ignored.

If non-standard sequences (i.e. a sequence that is not 100% identical to a sequence in SwissProt, TrEMBL or Genpept) gets submitted in ModWeb, it is advisable to create the following header line for each sequence

>CU|information about sequence CU stands for "Custom", in this case, ModBase will display everything following the | in the results table. This makes the identification of input sequences in the ModBase output much easier.

When only one sequences is submitted to ModWeb, the user has the option of:

• Depositing the Results in ModBase
• Receiving the Results by Email

For all other requests, the results will be deposited in ModBase. The user will receive an email about the access information (dataset name, username, password) and a short summary of the results.

! This functionality is not completely mature.
The file formats might be changing in the next few months.
If you have suggestions for different formats, please email .

Retrieval of Modbase Models and Alignments is possible using wget:
Example:
wget 'http://salilab.org/modbase/retrieve/modbase/?databaseID=P21812'

Non Academic Users:
Please add '&dataset=public' to the retrieve url like:
wget 'http://salilab.org/modbase/retrieve/modbase/?databaseID=P21812&dataset=public'

Options:
One of more of the following Parameters:

databaseID=P21812
dataset=SP/TR2004
modelID=P21812
seqID=P21812
dataset=ModWeb0-xxx (your ModWeb Job Identifier)
type=model (default, alternatively: alignment)
You can search for databaseID, OR seqID, OR modelID, OR alignID, OR modweb dataset.
You can combine each with dataset and/or type parameter.

About the cookies.txt file:
in order to set you access permissions when using wget, you have to transfer the modbase cookies
to a cookies file. Example:
cat cookies.txt
modbase.compbio.ucsf.edu FALSE / FALSE 2116975226 modbase-academic modbase_user&anonymous&modbase_passwd&anonymous

You can use this link also to retrieve coordinate files directly through a web-browser:
http://salilab.or/modbase/retrieve/modbase?databaseID=P21812

For all other requests, the results will be deposited in ModBase. The user will receive an email about the access information (dataset name, username, password) and a short summary of the results.

MODBASE contains structure-based predictions of 3,213 binary and 1,234 higher order protein complexes in Saccharomyces cerevisiae involving 750 and 195 proteins, respectively. To generte candidate complexes, comparative models of individual proteins were built and combined together using complexes of known structure as templates. These candidate complexes were then assessed using a statistical potential, derived from binary domain interfaces in PIBASE (http://salilab.org/pibase). A benchmark indicates a false positive rate of 3% and a true positive rate of 97%. Moreover, the predicted complexes are also filtered using functional annotation (http://yeastgenome.org) and sub-cellular localization (http://yeastgfp.ucsf.edu) data.