1 Bioinformatics Tools for Protein Structure Analysis and Visualisation

1.1 Molecular Biology Databases

1.2 Primary DNA/Protein Sequence Databases

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

1.3 Secondary Protein/DNA Sequence Databases

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

1.4 Primary Protein/Ligand/DNA Structure Databases

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

1.5 Secondary Protein/DNA Structure Databases

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

2 Protein Structure and Function Prediction Methods

2.1 Sequence to Function: (protein Sequence Analysis)

2.1.1 Sequence Database (Similarity) Searching

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 Bic2 Smith & Waterman algorithm Implementation for protein database searches (Local Alignment)
MPsrch http://www.ebi.ac.uk/MPsrch/ Edinburgh University 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

2.1.2 Domain Analysis

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

2.1.3 Transmembrane Region Prediction/Analysis

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)

2.1.4 Coiled Coil Region Prediction Tools

Program WWW Address Program Description
Coils http://www.ch.embnet.org/software/COILS_form.html Prediction of coiled coil regions in proteins. (Lupa 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

2.1.5 Primary Structure Analysis

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

2.1.6 Mutiple Sequence Alignment methods/visualization and editing

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

2.1.7 Phylogentic Analysis of Protein, DNA 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

2.1.8 Pattern and Profile Searches Methods

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

2.2 Structure to Function:

2.2.1 Protein Secondary Structure Prediction

Program WWW Address Program Description
AGADIR 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

2.2.2 Protein 3D Structure Prediction Comparative (Homology) Modelling

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 Threading (fold-recognition)

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

3 Molecular Analysis and Visualisation Tools

3.1 Protein 3D Structure Analysis and Visualisation Tools

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

3.2 Modeling, Docking, Molecular Design, Drug Design Tools

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)