Protein Structure and Visualization
Protein Structure Prediction
Structural Alignments
Structural Analysis
Protein Stability and Mutation
Protein Structure/Function
Evolutionary Conservation
Molecular Simulation
Macromolecular Motion and Normal Mode Analysis
Electrostatics and pKa
Protein-Ligand Complexes
Drug Discovery and Small Molecules
Protein-Protein Interactions
Kinetic Models

Protein Structure and Visualization [top]

The RCSB, the source for protein structure (.pdb) files

PMDB, the Protein Model Database

PPG, protein pictures and animations online

MBT, the Molecular Biology Toolkit

WebFEATURE, a structural analysis tool for scanning queries for functional sites in proteins and nucleic acids

VMD, Visual Molecular Dynamics, the standard for molecular visualization

UCSF Chimera, molecular visualization with Python extensions

Jmol, a Java-based visualization program

PyMOL, a versatile visualization program

Protein Structure Prediction [top]

RPBS, a site for structural bioinformatics

PROTINFO, a server that predicts protein tertiary structure

SCRATCH, provides many predictions given an amino acid sequence

MODBASE, database of comparative protein structures based on sequence

AS2TS, protein structure comparison

University College London, various server-based tools

SPACE, analysis and prediction of biomolecule structures and complexes

Structure Prediction Meta Server, a collection of tools

Web-based threading, online sequence alignments

Bioinformatics Unit at University College London, a collection of tools including PSIPRED, DISOPRED, and DomPred

Structural Alignments [top]

SALIGN, a web interface to the multiple sequence alignment of Modeller

MISTRAL, multiple protein structural alignment

DBAli Database, protein structure alignments from SCOP

SuperPose, generates sequence alignments, structure alignments, PDB coordinates, and RMSD statistics

Structural Analysis [top]

Gaia, a web server for the assessment of homology models based on packing and covalent geometry

Prosa, analysis of protein folding

SCR_FIND, analysis of structurally conserved regions

CHC_FIND, analysis of conserved hydrophobic contacts

CAMPO, analysis of evolutionarily conserved residues

PAT, the Protein Analysis Toolkit

WebProAnalyst, analysis of structure-activity relationships

WWW servers, including CX, DPX, and PRIDE

MDDNA, a tool for analyzing MD trajectories of DNA

Protein Stability and Mutation [top]

FoldX, an empirical force field for evaluating the effects of protein mutations on stability

I-Mutant2.0, stability predictions based on mutation

PDB_Hydro, a tool to mutate and solvate proteins

Protein Structure/Function [top]

Diamond STING, analysis of sequence, structure, and function relationships

STING Millenium Suite, includes visualization and complex analysis tools

ProFunc, predicts function of proteins whose 3D structures are known

Gene3D, combined analysis of structure, function, and evolutionary relationships

SuMo, search for protein functional sites

Evolutionary Conservation [top]

ConSurf, scoring of residues in protein structures to calculate evolutionary conservation

ConSurf-HSSP, maps evolutionary conservation among homologs

PRIDE, fold recognition

Molecular Simulation [top]

GROMACS, Fast, Flexible, and Free MD

AMBER, Assisted Model Building with Energy Refinement

CHARMM, Chemistry at HARvard Molecular Mechanics

NAMD, "Not Another Molecular Dynamics"

Pymacs, a Python-based series of tools for interfacing with GROMACS

Theory of Molecular Dynamics Simulations, with a historical intorduction and practical considerations

Temperature Generator for REMD, a tool to predict the temperatures for Replica Exchange MD given the desired exchange probability

Free Energy Tutorial, written by David Mobley, illustrates the how to conduct free energy calculations in GROMACS

Free Energy Best Practices, practical considerations in conducting free energy calculations

Macromolecular Motion and Normal Mode Analysis [top]

MolMovDB, classification of molecular motions

MolMovDB, an alternate site

Normal Modes, assessment on the Web

MovieMaker, creates downloadable movies of protein motions

Normal Mode Analysis, Web-based normal mode calculations

Dynamite, an online processing tool to view large-scale motions and generate porcupine plots

elNémo, a web interface to an elastic network model server

Crystallography [top]

Crystallography, a guide to data interpretation

Crystallography Overview

Image Library of Biological Macromolecules

Electrostatics and pKa [top]

H++, Virginia Tech's automated system for pKa prediction

PCE, electrostatic computation tool based on MEAD

PPD v1.0, the Protein pKa Database

PDB2PQR, facilitates electrostatic calculations by converting .pdb files into .pqr input files

Protein-Ligand Complexes [top]

AffinDB, database of binding affinities

PEARLS, to compute interaction energies

Q-SiteFinder, an energy-based method for binding site prediction

PocketFinder, a geometry-based method for binding site prediction

MOAD, the Mother of All Databases (structure and binding data)

Ligand Depot, information about small molecules bound to DNA and proteins

PDB-Ligand, a ligand database for classification of ligand-binding structures

MSDsite, analysis of bound ligands and active sites

PRODRG, generates coordinate and topology files for ligands; especially useful in GROMACS

Drug Discovery and Small Molecules [top]

HIC-Up, the Hetero-compound Information Centre - Uppsala

DrugBank, combines drug information with information about targets

ZINC Database, an extensive database of ligands

Virtual Computational Chemistry Laboratory, molecular calculations

ChemDB, small molecule database

SuperDrug, 3D structures and conformers of drugs

PubChem, an Entrez database of small molecules

ChEBI, small molecule database

ChemIDplus, small molecule database from the National Library of Medicine (Bethesda, MD)

WebMolecules, database of 3D models for drugs

SuperLigands, ligand structures from the Protein Data Bank

ChemBank, US NCI database hosted at the Broad Institute

ChemID Plus, from the US National Library of Medicine

CHEMnetBASE, chemical names, properties, and references

eMolecules, a searchable database of small molecules

QueryChem, search tool using text and structure

Unleashed Informatics, host of BOND, BOND+, and SMID databases

OSIRIS Property Explorer, an interactive tool to determine the chemical characteristics of a given molecule

Protein-Protein Interactions [top]

BIND, the Biomolecular Interaction Network Database

ClusPro, an algorithm for protein-protein docking

iPfam, visualization of protein-protein interactions

PIBASE, a comprehensive database of interfaces between protein domains

Kinetic Models [top]

BioModels Database, database of kinetic models of biochemical systems

Cornell Theory Center, how biomolecules fold, move, and conform to each other

Bioinformatics [top]

Bioinformatics Databases, hosted by the University of Pittsburgh - a searchable list

2can, bioinformatics basics

The Bioinformatics Links Directory, a directory of freely-accessible tools

SChiSM2, for creating interactive web pages of molecular structures

Education [top]

Microarray MediaBook, an online animation of microarray technology

Intermediary Metabolism, a case study to explain metabolic disorders