Database

WWW-Address

Descriptions

EMBL

Http://www.ebi.ac.uk/embl/

European Molecular Biology Laboratory nucleotide sequence database at EBI, Hinxton, UK

GenBank

Http://www.ncbi.nlm.nih.gov/Genbank/GenbankOverview.html

DNA Genome Sequence Database at National Center for Biotechnology information, NCBI, Bethesda, MD, USA

DDBJ

Http://www.ddbj.nig.ac.jp/

DNA Data Bank Japan at CIB , Mishima, Japan

SWISS-PROT/TrEMBL

Http://www.expasy.ch/

Protein Sequence Database (Swiss Institute of Bioinformatics, SIB, Geneva, CH

PIR-PSD

Http://pir.georgetown.edu/pirwww/search/textpsd.shtml

PIR-International Protein Sequence Database, annotated protein database by PIR, MIPS and JIPID at NBRF, Georgetown University, USA

SRS

Http://srs.ebi.ac.uk/

Sequence Retrieval System

Database

WWW-Address

Descriptions

DbEST

Http://www.ncbi.nlm.nih.gov/dbEST/index.html

Database of Expressed Sequence Tags at NCBI, USA

TIGR

Http://www.tigr.org/tdb/tgi.shtml

TIGR Genome Indices, integrated analysis of public EST data, TIGR, USA

DbSNP

Http://www.ncbi.nlm.nih.gov/SNP/

Database of Single Nucleotide Polymorphism at NCBI, USA

CluSTr

Http://www.ebi.ac.uk/clustr/

Clusters of SWISS-PROT and TrEMBL proteins at EBI, UK

ProtoMap

Http://www.protomap.cs.huji.ac.il/

Hierarchical classification of all Swiss-Prot proteins

PROSITE

Http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_prosite.html

Prosite Protein functional pattern database

PRODOM

Http://prodes.toulouse.inra.fr/prodom/doc/prodom.html

The Protein Domain Database

PFAM

Http://www.sanger.ac.uk/Pfam/

 Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many

 common protein domains and families

Database

WWW-Address

Descriptions

PDB

Http://www.rcsb.org/pdb/index.html

Protein structural Data Bank cured by Research Collaboratory of Structural Bioinformatics By Rutgers, SDSC and NIST, USA

NDB

Http://ndbserver.rutgers.edu/NDB/ndb.html

Nucleic Acid structure Datatabase at Rutgers University , USA

EBI-MSD

Http://msd.ebi.ac.uk/

Macromolecular Structure Database at EBI, UK

CSD

Http://cds3.dl.ac.uk/cds/crystal.html

The Cambridge Structural Database of small-molecule crystal structures

Database

WWW-Address

Descriptions

SCOP  

Http://scop.mrc-lmb.cam.ac.uk/scop/

Structural Classification of Proteins

CATH  

Http://www.biochem.ucl.ac.uk/bsm/cath_new/index.html

Protein Structure Classification (Class Architecture Topology and Homologous superfamily)

3Dee  

Http://circinus.ebi.ac.uk:8080/3Dee/help/help_intro.html

A Database of Protein Domain Definitions

FSSP  

Http://www2.ebi.ac.uk/dali/fssp/

Fold Classification based on Structure-Structure alignment of Proteins

TOPS

Http://bioinformatics.leeds.ac.uk/~tops/

Protein structural topology and protein topology Cartoons

HOMSTRAD  

Http://www-cryst.bioc.cam.ac.uk/~homstrad/

Homologous Structure Alignment Database

PASS2

Http://www.ncbs.res.in/%7Efaculty/mini/campass/pass.html

Semi-Automated database of Protein Alignments organised as Structural Superfamilies

DIP

Http://dip.doe-mbi.ucla.edu/

Database of Interacting Proteins

Program

WWW – Address

Program Name

Fasta3

Http://www.ebi.ac.uk/fasta3/

Sequence similarity and homology searching against nucleotide and protein database using Fasta3 (Global Alignment)

BLAST2

Http://www.ebi.ac.uk/blastall/

NCBI blast2 (blastall) program (Local Alignment)

Blitz (bic_sw)

Http://www.ebi.ac.uk/bic_sw/

Compugen´s Bic2´s Smith & Waterman algorithm Implementation for protein database searches

(Local Alignment)

MPsrch

Http://www.ebi.ac.uk/MPsrch/

Edinburgh University´s new implementation of the Smith and Waterman algorithm (Local Alignment)

Scanps2.3

Http://www.ebi.ac.uk/scanps/

Fast implementation of the true Smith & Waterman algorithm for protein database searches

(Local Alignment)

PSI/PHI-BLAST

Http://www.ncbi.nlm.nih.gov/BLAST/

(Position Specific/Pattern Hit)Iterated BLAST (Local Alignment)

Dotlet

Http://www.isrec.isb-sib.ch/java/dotlet/Dotlet.html

A Java applet for sequence comparisons using the dot matrix method

REP

Http://www.embl-heidelberg.de/~andrade/papers/rep/search.html

Searches a protein sequence for a repeats

Program

WWW-Address

Program Description

SMART

http://smart.embl-heidelberg.de/

Domain Assignment (Oxford/EMBL)

PFAM

http://www.sanger.ac.uk/Software/Pfam/

(Sanger Centre/Wash-U/Karolinska Institute)

COGs

http://www.ncbi.nlm.nih.gov/COG/

Phylogenetic classification of proteins encoded in complete genomes

PRINTS

http://www.bioinf.man.ac.uk/dbbrowser/PRINTS/

PRINTS is a compendium of protein fingerprints

PRODOM

http://prodes.toulouse.inra.fr/prodom/doc/form.html

Protein Domain families.

BLOCKS

http://blocks.fhcrc.org/blocks/blocks_search.html

Multiply aligned ungapped segments corresponding to the most highly conserved regions of proteins

InterPro

http://www.ebi.ac.uk/interpro/

Integrated documentation resource for protein families, domains and functional sites.

SWISPROT

http://us.expasy.org/sprot/

Domain description in the annotations.

CD-Search

http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi

Search for Conserved Domains

Program

WWW- Address

Program Description

DAS

Http://www.sbc.su.se/~miklos/DAS/

Prediction of transmembrane regions in prokaryotes using the Dense Alignment Surface method (Stockholm University)

HMMTOP

Http://www.enzim.hu/hmmtop/

Prediction of transmembrane helices and topology of proteins (Hungarian Academy of Sciences)

PredictProtein

Http://dodo.cpmc.columbia.edu/predictprotein/

Prediction of transmembrane helix location and topology (Columbia University)

SOSUI

Http://sosui.proteome.bio.tuat.ac.jp/sosuiframe0.html

SOSUI - Prediction of transmembrane regions (TUAT; Tokyo Univ. of Agriculture & Technology)

TMAP

Http://www.mbb.ki.se/tmap/

Transmembrane detection based on multiple sequence alignment (Karolinska Institut; Sweden)

TMHMM

Http://www.cbs.dtu.dk/services/TMHMM-2.0/

Prediction of transmembrane helices in proteins (CBS; Denmark)

Program

WWW- Address

Program Description

Coils

Http://www.ch.embnet.org/software/COILS_form.html

Prediction of coiled coil regions in proteins. (Lupa’s method)

Paircoil

Http://nightingale.lcs.mit.edu/cgi-bin/score

Paircoil - Prediction of coiled coil regions in proteins (Berger's method)

Multicoil

Http://nightingale.lcs.mit.edu/cgi-bin/multicoil

Prediction of two- and three-stranded coiled coils

Program

WWW –Address

Program Description

ProtParam

Http://us.expasy.org/tools/protparam.html

Physico-chemical parameters of a protein sequence (amino-acid and atomic compositions, pI, extinction coefficient, etc.)

Compute pI/Mw

Http://us.expasy.org/tools/pi_tool.html

Compute the theoretical pI and Mw from a SWISS-PROT or TrEMBL entry or for a user sequence

MW,pI, Titration

Http://www.up.univ-mrs.fr/~wabim/d_abim/compo-p.html

Computes pI, composition and allows to see a titration curve

REP

Http://www.embl-heidelberg.de/~andrade/papers/rep/search.html

Searches a protein sequence for a repeats

SAPS

Http://www.isrec.isb-sib.ch/software/SAPS_form.html

Statistical analysis of protein sequences at EMBnet-CH

PEST

Http://www.icnet.uk/LRITu/projects/pest/

Identification of PEST regions

HLA Bind

Http://bimas.dcrt.nih.gov:80/molbio/hla_bind/

Prediction of MHC type I (HLA) peptide binding

SYFPEITHI

Http://syfpeithi.bmi-heidelberg.com/scripts/MHCServer.dll/home.htm

Prediction of MHC type I and II peptide binding

ProtScale

Http://us.expasy.org/cgi-bin/protscale.pl

Amino acid scale representation (Hydrophobicity, other conformational parameters, etc.)

Drawhca

Http://www.lmcp.jussieu.fr/~soyer/www-hca/hca-form.html

Draw an HCA (Hydrophobic Cluster Analysis) plot of a protein sequence

Protein Colourer

Http://www2.ebi.ac.uk/cgi-bin/translate/visprot.pl

Tool for colouring amino acid sequence

Colorseq

Http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_color.html

Tool to highlight (in red) a selected set of residues in a protein sequence

SMS

Http://www.sanbi.ac.za/~rmuller/SMS/index.html

Sequence Manipulation Suite is a collection of web-based programs for analyzing and formatting DNA and protein sequences

Program

WWW-Address

Program Description

SIM+ LALNVIEW

http://us.expasy.org/tools/sim-prot.html

Alignment of two protein sequences with SIM, results can be viewed with LALNVIEW

LALIGN

http://www.ch.embnet.org/software/LALIGN_form.html

Finds multiple matching subsegments in two sequences

CLUSTALW

http://www2.ebi.ac.uk/clustalw/

Multiple Sequence Alignment at EBI

T-Coffee

http://www.ch.embnet.org/software/Tcoffee.html

Multiple Sequence Alignment

At EMBnet

ALIGN

http://www2.igh.cnrs.fr/bin/align-guess.cgi

Multiple Sequence Alignment

at Genestream (IGH)

DIALIGN

http://bibiserv.techfak.uni-bielefeld.de/dialign/

Multiple sequence alignment based on segment-to-segment comparison, at University of Bielefeld, Germany

Match-Box

http://www.fundp.ac.be/sciences/biologie/bms/matchbox_submit.shtml

Print-out from multiple alignments University

of Namur, Belgium

MSA

http://stateslab.bioinformatics.med.umich.edu/ibc/msa.html

Multiple Sequence Alignment

at Washington University

Multalin

http://prodes.toulouse.inra.fr/multalin/multalin.html

Multiple sequence alignment by Florence Corpet

MUSCA

http://cbcsrv.watson.ibm.com/Tmsa.html

Multiple sequence alignment using pattern discovery, at IBM

AMAS

http://barton.ebi.ac.uk/servers/amas_server.html

Analyse Multiply Aligned Sequences

Bork's alignment tools

http://www.bork.embl-heidelberg.de:8080/Alignment/

Various tools to enhance the results of multiple alignments (including consensus building)

CINEMA

http://www.biochem.ucl.ac.uk/bsm/dbbrowser/CINEMA2.1/

Color Interactive Editor for Multiple Alignments

ESPript

http://prodes.toulouse.inra.fr/ESPript/cgi-bin/nph-ESPript_exe.cgi

Tool to print a multiple alignment

Plogo

http://www.cbs.dtu.dk/gorodkin/appl/plogo.html

Sequence logos at CBS/Denmark

JalView

http://www.sander.embl-ebi.ac.uk/Services/protein_profiles/ef-hand-fimb/align.html

Multiple Sequence Alignment Viewer/Editor

DbClustal

http://igbmc.u-strasbg.fr:8080/DbClustal/dbclustal.html

Rapid and reliable global multiple alignments of protein sequences detected by database searches

Consensus

http://www.bork.embl-heidelberg.de/Alignment/consensus.html

Calculates the consensus for the CLUSTAL or MSF multiple alignment

AliBee

http://www.genebee.msu.su/services/malign_reduced.html

Multiple Alignment

DiAlign

http://bibiserv.techfak.uni-bielefeld.de/cgi-bin/dialign_submit

Pairwise and multiple
alignments by comparing whole segments of the sequences

Multiple Align Show

http://www.bioinformatics.org/SMS/multi_align.html

Enhance the output of sequence
alignment programs

ESPrint

http://prodes.toulouse.inra.fr/ESPript/

Easy Sequencing in Postscript, is a utility to generate a pretty PostScript output from aligned sequences

Program

WWW-Address

Program Description

Phylip

Http://bioportal.bic.nus.edu.sg/phylip/index.html

Set of PHYLIP PROGRAMS FOR MOLECULAR SEQUENCE ANALYSIS

Phylodendron

Http://www.es.embnet.org/Doc/phylodendron/treeprint-form.html

Phylogenetic tree printer - very useful in visualizing *.dnd

TreeTop

Http://www.genebee.msu.su/services/phtree_reduced.html

Phylogenetic Tree Prediction

Program

WWW-Address

Program Description

ScanProsite

http://us.expasy.org/tools/scanprosite/

Scans a sequence against PROSITE or a pattern against SWISS-PROT and TrEMBL

InterPro Scan

http://www.ebi.ac.uk/interpro/scan.html

Integrated search in PROSITE, Pfam, PRINTS and other family and domain databases

Frame-ProfileScan

http://www.isrec.isb-sib.ch/software/PFRAMESCAN_form.html

Scans a short DNA sequence against protein profile databases (including PROSITE)

Pfam-HMM

http://pfam.wustl.edu/hmmsearch.shtml

Scans a sequence against the Pfam protein families db

PRATT

http://www2.ebi.ac.uk/pratt/

Interactively generates conserved patterns from a series of unaligned proteins

PPSEARCH

http://www2.ebi.ac.uk/ppsearch/

Scans a sequence against PROSITE (allows a graphical output); at EBI

PROSITE scan

http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_prosite.html

Scans a sequence against PROSITE (allows mismatches); at PBIL

PATTINPROT

http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_pattinprot.html

Scans a protein sequence or a protein database for one or several pattern(s); at PBIL

SMART

http://smart.embl-heidelberg.de/

Simple Modular Architecture Research Tool; at EMBL

TEIRESIAS

http://cbcsrv.watson.ibm.com/Tspd.html

Generate patterns from a collection of unaligned protein or DNA sequences; at IBM

Hits

http://hits.isb-sib.ch/

Relationships between protein sequences and motifs

Program

WWW – Address

Program Description

A  GADIR

Http://www.embl-heidelberg.de/Services/serrano/agadir/agadir-start.html

An algorithm to predict the helical content of peptides

BCM PSSP

Http://dot.imgen.bcm.tmc.edu:9331/pssprediction/pssp.html

BCM – Protein secondary structure prediction

Prof

Http://www.aber.ac.uk/~phiwww/prof/

Cascaded Mutiple Classifiers for Secondary Structure Prediction

GOR IV

Http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_gor4.html

GOR Secondary Structure Prediction (Garnier et.al.,1996)

HNN

Http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_nn.html

Hierarchical Neural Network method (Guermeur, 1997

Jpred

Http://jura.ebi.ac.uk:8888/

A consensus method for protein secondary structure prediction at EBI

nnPredict

Http://www.cmpharm.ucsf.edu/~nomi/nnpredict.html

University of California at San Francisco (UCSF)

PedictProtein

Http://cubic.bioc.columbia.edu/predictprotein/

PHDsec, PHDacc, PHDhtm, PHDtopology, PHDthreader, MaxHom, EvalSec from Columbia University

PREDATOR

Http://www.embl-heidelberg.de/cgi/predator_serv.pl

Protein secondary structure prediction from single or multiple sequences at EMBL (Argos' group)

ZPRED

Http://kestrel.ludwig.ucl.ac.uk/zpred.html

MultPredict Secondary Structure of Multiply Aligned Sequences

Program

WWW –Address

Program Description

SWISS-MODEL

Http://www.expasy.org/swissmod/SWISS-MODEL.html

An automated knowledge-based protein modelling server

Geno3d

Http://geno3d-pbil.ibcp.fr/cgi-bin/geno3d_automat.pl?page=/GENO3D/geno3d_home2.html

Automatic modelling of protein three-dimensional structure

CPHmodels

Http://www.cbs.dtu.dk/services/CPHmodels/

Automated neural-network based protein modelling server

SWEET

Http://www.dkfz-heidelberg.de/spec/sweet2/doc/index.html

Constructing 3D models of saccharids from their sequences

Mod Web

Http://pipe.rockefeller.edu/mwtest-cgi/main.cgi

Server for Comparative Protein Structure Modelling

InsightII

Http://www.accelrys.com/about/msi.html

Molecular Modelling/Dynamics Tools

Sybyl

Http://www.tripos.com/software/index.html

Molecular Modelling/Dynamics Tools

Modeller

Http://guitar.rockefeller.edu/modeller/modeller.html

A program for automated protein homology modeling

GROMACS

Http://rugmd4.chem.rug.nl/~gmx/

Complete modelling package for proteins, membrane systems

Program

WWW –Address

Program Description

UCLA-DOE

Http://fold.doe-mbi.ucla.edu/

Protein 3D-Structre Prediction Server

TOPITS

Http://www.embl-heidelberg.de/predictprotein/predictprotein.html

Topology of protein 3D- structure prediction method.

3D-PSSM

Http://www.bmm.icnet.uk/~3dpssm/

Protein fold recognition using 1D and 3D sequence profiles coupled with secondary structure information (Foldfit)

123D

Http://123d.ncifcrf.gov/123D+.html

combines sequence profiles, secondary structure prediction, and contact capacity potentials to thread a protein sequence through the set of structures

UCSC HMM Applications

Http://www.cse.ucsc.edu/research/compbio/HMM-apps/

SAM HMM construction and remote homology detection and protein structure prediction

FFAS

Http://bioinformatics.burnham-inst.org/pages/servers/index.html

Fold assignment method is based on the profile-profile matching algorithm

Program

WWW –Address

Program Description

Swiss-PdbViewer

Http://us.expasy.org/spdbv/

A program to display, analyse and superimpose protein 3D structures

Mod View

Http://guitar.rockefeller.edu/modview/news.shtml

Graphical application for analysis of multiple sequences and structures of biomolecules

Rasmol

http://www.umass.edu/microbio/rasmol/

Molecular Visualization Freeware

PREPI

http://www.bmm.icnet.uk/people/suhail/prepi.html

Molecular Graphics Program

SURFNET

http://www.biochem.ucl.ac.uk/~roman/surfnet/surfnet.html

Generates surfaces and void regions between surfaces from coordinate data supplied in a PDB file

Raster3D

http://www.bmsc.washington.edu/raster3d/raster3d.html

Set of tools for generating high quality raster images of proteins or other molecules

WHAT_

CHECK

http://www.cmbi.kun.nl/swift/whatcheck/

The protein verification tools from the WHAT IF program

Procheck

http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html

A program that checks the stereo-chemical quality of a protein structure

WebMol

http://www.cmpharm.ucsf.edu/~walther/webmol.html

A Java Protein Structure  Viewer

VMD

http://www.ks.uiuc.edu/Research/vmd/

VMD (Visual Molecular Dynamics)

WinMGM

http://www.ibanez.li/~mr/index.html

A molecular graphics program for PDB files that runs on Linux intel and solaris intel platforms

Swiss-PDB Viewer

http://www.expasy.ch/spdbv/

A 3D graphics and molecular modeling program for the

simultaneous analysis

PyMOL

http://pymol.sourceforge.net/

A free and open-source molecular graphics system for visualization

MolScript

http://www.avatar.se/molscript/

A program for displaying structures in both detailed and schematic formats and writing images in various formats

PyMOL

http://pymol.sourceforge.net/

A free and open-source molecular graphics system for visualization, animation, editing, and publication-quality imagery.

Qmol

http://lancelot.bio.cornell.edu/jason/qmol.html

A lightweight OpenGL based molecular viewer for Windows95/NT/00 and X Windows

MidasPlus

http://www.cgl.ucsf.edu/Outreach/midasplus/

A program for displaying, manipulating and analysing    macromolecules

GRASS

http://trantor.bioc.columbia.edu/GRASS/surfserv_enter.cgi

Graphical Representation and Analysis of Structure Server

Program

WWW-Address

Description

 AbM

http://www.accelrys.com/about/oxmol.html

Antibody Structure Modeling  - Oxford Molecular Group, Inc.

AMBER

http://www.amber.ucsf.edu/amber/amber.html

AMBER - Oxford Molecular Group, Inc.

AMPAC

http://www.semichem.com/ampac.html

Graphical User Interface

AutoDock

http://www.scripps.edu/pub/olson-web/doc/autodock/

Automated Docking of Flexible Ligands to Macromolecules - Scripps Research Inst

CAChe

http://www.accelrys.com/about/oxmol.html

Oxford Molecular Group, Inc.

CAVEAT

http://www.cchem.berkeley.edu/~pabgrp/Data/caveat.html

Design of Organic Molecules

Cerius2 Visualizer

http://www.accelrys.com/about/msi.html

Molecular Simulations, Inc.

CHIME

http://www.mdlchime.com/chime/

CHIME - MDL Information Systems, Inc.

GLOCP

http://clogp.pomona.edu/chem/biobyte/manuals/ClogP_Formatted.html

Quantitative Structure Activity Relationships (QSAR)

CloneMap

http://www.cgcsci.com/#CloneMap

Plasmid map drawing, restriction site mapping, and virtual cloning -CGC Scientific, Inc.

Cobra

http://www.accelrys.com/about/oxmol.html

Oxford Molecular Group, Inc.

Composer

http://www.tripos.com/software/composer.html

Complete, Accurate Protein Homology Models-Tripos, Inc.

CONCORD

http://www.tripos.com/software/concord.html

Fast, High Quality 3D Structures from 2D Input -Tripos, Inc.

DISCO

http://www.tripos.com/software/disco.html

Rapid, Intelligent Pharmacophore Generation -Tripos, Inc.

DIVA

http://www.accelrys.com/about/oxmol.html

Oxford Molecular

AutoDock3.0

http://www.scripps.edu/pub/olson-web/dock/autodock/

A suite of automated docking tools.

DOCK

http://www.cmpharm.ucsf.edu/kuntz/dock.html

Docking Program

FlexiDock

http://www.tripos.com/software/fdock.html

Drug Design Tripos, Inc.

GASP

http://www.tripos.com/software/gasp.html

Automatic pharmacophore elucidation with full

Conformational flexibility

GRAMM

http://reco3.ams.sunysb.edu/gramm/

Protein Docking

QUANTA

http://www.accelrys.com/about/msi.html

Molecular Simulations Inc., (Burlington, MA, USA)

FTDOCK

http://www.bmm.icnet.uk/docking/

A program for carrying out rigid-body docking between biomolecules

ECEPPAK

http://www.tc.cornell.edu/reports/NIH/resource/CompBiologyTools/

Cornell Theory Center package to carry out global conformational searches using the ECEPP/3 force field

CHARMM

http://yuri.harvard.edu/

 (Chemistry at HARvard Molecular Mechanics) is

a molecular dynamics and energy minimization program

ICM

http://www.molsoft.com/icmpages/icmcore.htm

MolSoft ICM programs and modules for applications including for structure analysis, modeling, docking, homology modeling and virtual ligand screening

LOOPP

http://www.tc.cornell.edu/reports/NIH/resource/CompBiologyTools/

Linear Optimization of Protein Potentials. Cornell Theory Center program for potential optimization and alignments of sequences and structures

MOIL

http://www.tc.cornell.edu/reports/NIH/resource/CompBiologyTools/

Cornell Theory Center package for molecular dynamics simulation of biological molecules

NAMD

http://www.ks.uiuc.edu/Research/namd/

A parallel object-oriented molecular dynamics simulation program

WAM - Web

http://antibody.bath.ac.uk/

Antibody Modelling

CastP

http://cast.engr.uic.edu/cast/

Server that calculates measurements of structural pockets and cavities of proteins and nucleic acids

Efsite

http://pi.protein.osaka-u.ac.jp/eF-site/

eFsite (electrostatic-surface of Functional site)

PASS

http://www.delanet.com/~bradygp/pass/

Putative Active Site with Spheres (Freeware)