Annotated Links for Homology Course

General-useful and interesting links related to homlogy modeling


Molecular Modeling Laboratory  Homepage for our computer center describing our software with links to manuals.

Protein Science Authors Instructions Details instructions for submissions to the journal Protein Science

York Lab    Extensive tools for protein sequence analysis

BCM   Single point of entry for molecular biology related searchs

CMSMBR   Extensive tools for protein sequence analysis

Protein Structure Prediction Center(CASP1-7)   Provides the means of objectivly testing protein structure prediction methods via the process of blind prediction
    CASP6 evaluation- Issue of Proteins dedicated to evaluation of  CASP5 results

BOXSHADE    Pretty Printing and Shading of Multiple-Alignment files

JOY   A program to annotate protein sequence alignments with three-dimensional (3D) structural features


 

Databases- searchable collections of data related to protein structure
 

Protein Data Bank (PDB)    A repository for the processing and distribution of 3-D macromolecular structure data primarily determined experimentally by X-ray crystallography and NMR

PDB_SUM     A database of the known 3D structures with links to well formated  analysis data

SWISS-PROT   An annotated protein sequence database

GenBank   The NIH genetic sequence database, an annotated collection of all publicly available DNA sequences

Protein Information Resource (PIR) A comprehensive, non-redundant, annotated, fully classified and extensively cross-referenced protein sequence database

Owl A non-redundant composite of 4 publicly-available primary sources

RESID    A database of protein post-translational modifications with descriptive, chemical, structural and bibliographic information

MRS   Searches multiple databases including DSSP-A database of secondary structure assignments and HSSP-A database of homology-derived secondary structure of proteins

HOMSTRAD    An homologous structure alignment database

CATH    A novel hierarchical classification of protein domain struct,Class(C), Architecture(A), Topology(T) and Homologous superfamily (H)

Entrez    An NIH retrieval system for searching several linked databases including PubMed

ModBase   A database of three-dimensional protein models calculated by comparative modeling

Structural Application of Proteins (SCOP)   Aims to provide a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known

Database of Macromolecular Movements   This describes the motions that occur in proteins and other macromolecules, particularly using movies.  Associated with it are a variety of free software tools and servers for structural analysis

DBGET/LinkDB Integrated Database Retrieval System   A simple database retrieval system for finding and obtaining specific entries of diverse databases

CLUSPROT   A service that delineates spatial clusters in protein structures on the basis of atomic contacts between residues

AllAll   Determines the relationship of each peptide sequence versus the others and constructs phylogenetic trees, 2D optimal placements, multiple alignments, probabilistic ancestral sequences, variation indices and predictions of surface, interior and active site positions in the 3D fold

ProDom The protein domain database

Template Search-servers available to find homologous sequences
 

BLAST A set of similarity search programs designed to explore all of the available sequence databases

MPsrch  Smith & Waterman algorithm implementation for protein database searches

Fasta    Scans a protein or DNA sequence library for similar sequences

Beauty(BLAST Enhanced Alignment Utility)   incorporates information on sequence family membership, the location of the conserved domains, and the locations of any annotated domains and sites directly into BLAST search results

Sequence Alignment-servers which perform stepwise and multiple sequence alignments
 

Scoring Matrix Paper   

BCM Matrix PowerPoint Presentation   

BCM Search Launcher    Pairwise or multiple alignments using various other web servers

BATON   Creates an alignment output file in the JOY format

DALI   A multiple alignment of structural neighbours

ClustalW An improved progressive multiple sequence alignment method

Block Maker   finds conserved blocks in a group of two or more unaligned protein sequences, which are assumed to be related, using two different algorithms

MULTALIN   Multiple sequence alignment with hierarchical clustering

AMAS(Analyse Multiply Aligned Sequences)    Performs a systematic characterisation of the physico- chemical properties seen at each position in a multiple protein sequence alignment

Modeling- programs used to help construct propossed protein structures
 

WhatIF   A protein structure analysis program that can be used for mutant prediction, structure verification, molecular graphics, etc.

SCWRL ( Sidechain placement With a Rotamer Library)   A program for adding sidechains to a protein backbone based on the backbone-dependent rotamer library

Insight II    A 3D graphical environment for molecular modeling

Automated Structure Predition- servers which return a propossed protein structure for a submitted sequence
 

MatchMaker    Prediction of Protein structure from sequence using threading

LIBRA 1   A computer application for analyzing protein structures and sequence

SWISS-MODEL   An Automated Comparative Protein Modelling Server

CPHmodels    predicts protein structure using comparative (homology) modelling

UCSC   Iterative SAM HMM construction and remote homology detection and protein structure prediction

UCLA-DOE   A Fold-Recognition server aimed to help in the computational analysis and prediction of structure from amino acid sequences

PredictProtein   Retrieves similar sequences in the database and predicts aspects of protein structure

Congen   CONformation GENerator program

MODELLER   A program for homology protein structure modelling by satisfaction of spatial restraints

Consensus Secondary Structure Prediction

Alternate :  Consensus Secondary Structure Prediction

Model Evaluation and Analysis- programs and servers used to verify the consistancy of propossed structures with specific theoretical constraints,to compare one structure with another, or analyze various interactions within the model

 

ADIT!  allows the user to check the format of coordinate and structure factor files and to perform a variety of validation tests on a structure prior to deposition in the PDB

SQUID   A program to display/analysis/validate molecular structures, carry out MD analysis, draw 2D/3D/4D grapical representation of data

SAVES: Structure Analysis and Verification Server   Performs structure validation calculations using PROCHECK, PROVE, Verify3D,ERRAT and WHAT_IF programs

Verify3D   Structure Evaluation server is a tool designed to help in the refinement of crystallographic structures

PROCHECK  Checks the stereochemical quality of a protein structure, producing a number of PostScript plots analysing its overall and residue-by-residue geometry

Errat   A protein structure verification algorithm that is especially well-suited for evaluating the progress of crystallographic model building and refinement

ProFit    A protein least squares fitting program