http://bioinformatics.ca/links_directory/category/protein/3-d-structural-featuresThis section includes tools for searching for structural motifs, biochemical features found in protein structures, and functional sub-structures such as binding sites.http://bioinformatics.ca/links_directory/category/protein/3-d-structural-features/feed en http://3d-partner.life.nctu.edu.tw/3D-partner is a tool to predict interacting partners and binding models of a query protein sequence through the analysis of structural complexes.9207Mon, 20 May 2013 02:40:36 -0400 http://www.sbg.bio.ic.ac.uk/3dligandsite3DLigandSite is a web server for the prediction of ligand binding sites. Ligands bound to similar protein structures as the query structure are used to predict the binding site.9208Tue, 21 May 2013 03:30:16 -0400 http://3dlogo.uniroma2.it/3dLOGO/home.html3dLOGO is a server for the identification and analysis of conserved protein three-dimensional (3D) substructures.9209Tue, 21 May 2013 05:50:23 -0400 http://cogangs.biobase.de/3dtf/3D Transcription Factor (3DTF) is a web-server for the analysis of protein-DNA binding sites. It calculates the positional weight matrix (PWM), representing the DNA-binding specifity of the protein. 13810Sat, 18 May 2013 12:50:26 -0400 http://3vee.molmovdb.orgThe 3V web server extracts and analyzes all of the internal volumes from input RNA and protein structures. Output is volumetric representations in images and downloadable files.9213Mon, 20 May 2013 14:20:30 -0400 http://aladyn.escience-lab.orgThe ALADYN web server aligns pairs of protein structures by comparing their internal dynamics and detecting regions that sustain similar large-scale movements. Input is the structure files of two proteins.9220Mon, 20 May 2013 18:20:21 -0400 http://bioinformatics.univ-reunion.fr/analycys/AnalyCys is database for the analysis of conservation and conformation of disulphide bonds in SCOP structural families. This database has a wide range of applications including mapping of disulphide bond mutation patterns, identification of cysteine residues and disulphide bonds important for folding and stabilization, modeling of protein structures and in protein engineering.9231Thu, 31 May 2012 06:37:30 -0400 http://structure.pitt.edu/anchorANCHOR is a web-based tool for the analysis of protein-protein interfaces. ANCHOR indicates possible druggable pockets within the protein using anhor residues.10694Tue, 21 May 2013 10:10:23 -0400 http://salilab.org/our_resources.shtmlThis page contains various resources for comparative protein structure modelling and analysis from the Sali Lab at University of California at San Francisco (UCSF).11316Mon, 20 May 2013 15:30:14 -0400 http://manaslu.aecom.yu.edu/loopred/ArchPRED predicts the structure of loop regions in protein structures based on a fragment-search based method. Given a query loop of unknown structure, ArchPRED identifies which loops of know structures are likely to share conformational similarity with the query loop.9236Tue, 21 May 2013 00:10:40 -0400 http://www.imtech.res.in/raghava/bhairpred/BhairPred is a tool for predicting beta-hairpins in protein sequences using a support vector machine.9266Mon, 20 May 2013 16:40:20 -0400 http://bioinfo3d.cs.tau.ac.il/BioInfo3D is a collection of tools for the structural analysis of proteins, including tools for structural alignments and prediction of protein interactions.9276Sat, 11 May 2013 01:00:31 -0400 http://metals.zesoi.fer.hrBiologically Relevant Metals (BioMe) is a web based platform for calculation of various statistical properties of metal binding sites including distribution of coordinate geometry and other descriptive statistics for a metal ion. The underlying database contains for each metal ion: PDB code, structure determination method, types of metal binding chains and names and coordinates of bound ligands, among other details.13795Mon, 20 May 2013 00:10:39 -0400 http://iris.physics.iisc.ernet.in/bsdd/BSDD (Biomolecules Segment Display Device) searches for and displays user defined sequence motifs in known protein structures. This web based tool incorporates the graphics package of RASMOL for visualization.9314Sat, 18 May 2013 02:00:34 -0400 http://www.bioinsilico.org/cgi-bin/CAPSDB/staticHTML/homeCAPS-DB is a structural classification of helix-cappings or caps compiled from protein structures. Caps extracted from protein structures have been structurally classified based on geometry and conformation and organized in a tree-like hierarchical classification where the different levels correspond to different properties of the caps. CASP-DB is fully browsable and searchable and is regularly updated.13484Thu, 16 May 2013 23:30:21 -0400 http://sts.bioengr.uic.edu/castp/Computed Atlas of Surface Topography of proteins (CASTp) locates and measures concave surface regions on 3D protein structures. This tool can be used to study surface features, binding sites, and functional regions of proteins.9326Thu, 16 May 2013 03:00:43 -0400 http://ccrxp.netasa.orgA tool for the detection of conserved residue clusters from an input PDB file. Structural properties of each residue, such as solvent accessibility (ASA), secondary structure, conservation score etc. and the conserved residue clusters are also computed.9331Mon, 20 May 2013 16:10:28 -0400 http://schubert.bio.uniroma1.it/CHC_FIND/index.htmlCHC_FIND is a tool to analyze conserved hydrophobic contacts (CHC) from multiple structural alignments. In addition to a multiple sequence alignment, a structural alignment which provides the superposition of structurally conserved regions (SCRs) (i.e., results from SCR_FIND) needs to be provided.9340Tue, 21 May 2013 09:20:26 -0400 http://www.moseslab.csb.utoronto.ca/alan/cis_reg_test.htmlStatistical tests for natural selection on regulatory regions based on the strength of transcription factor binding sites.13380Fri, 17 May 2013 06:30:11 -0400 http://cmweb.enzim.huContact Map Web Viewer (CMWeb) is an online tool for studying basic properties of residue-residue contact formation and contact clusters. CMWeb can used to visualize contact maps, link contacts and display them in 3D or multiple sequence alignments, predict residue contacts, or calculate various contact statistics.13774Sun, 19 May 2013 14:10:26 -0400 http://zhanglab.ccmb.med.umich.edu/COFACTORCOFACTOR is a structure based method for annotating the biological function of proteins. Users input a 3D structure of their protein of interest and COFACTOR threads the structure through functional libraries to identify functional site homology. The COFACTOR algorithm ranked in the CASP9 experiments (2010) for function prediction.13756Sun, 19 May 2013 03:30:37 -0400 http://asia.genesilico.pl/colorado3d/COLORADO-3D allows you to color your protein structures to indicate the presence of potential errors in protein structure (detected by ANOLEA, PROSAII, PROVE or VERIFY3D), buried residues, and sequence conservation. The server returns a PDB-formatted file which can be displayed in RASMOL.9365Mon, 20 May 2013 07:10:24 -0400 http://conseq.bioinfo.tau.ac.il/ConSeq is a tool for predicting functionally and structurally important amino acid residues in protein sequences. The predictions are based on the assumptions that residues of functional importance are often conserved and solvent-accessible, and those of structural importance are often conserved and located in the protein core. A multiple sequence alignment is used to predict the relative solvent accessibility state and the evolutionary rate at each residue. ConSeq has been integrated into ConSurf (2010).9800Wed, 15 May 2013 00:20:24 -0400 http://consurf.tau.ac.il/The ConSurf server allows one to map levels of amino acid conservation to known protein structures in order to study areas of potential functional importance on the surface of the protein. A PDB file is required as input, and a multiple sequence alignment is optional. If an alignment is not provided, ConSurf will build one by performing a search for homologous sequences and then aligning them. ConSurf 2010 combines ConSurf and ConSeq for an easier, more intuitive interface.9374Sat, 18 May 2013 17:30:27 -0400 http://sarst.life.nthu.edu.tw/CPredCPred is a prediction tool for circular permutations (CP) in proteins.13797Tue, 21 May 2013 11:50:15 -0400 http://protein.bio.unipd.it/cspritz/CSpritz is a web server for the prediction of intrinsic protein disorder segments with annotation for homology, secondary structure and linear motifs.12142Tue, 21 May 2013 15:00:28 -0400 http://120.107.8.16/dbcpThe Disulfide Bonding Connectivity Pattern (DBCP) web server tool provides prediction of disulphide bonding connectivity patterns without the prior knowledge of the bonding states of cysteines. Useful in locating disulphide bridges and helping to solve protein folding.10705Tue, 21 May 2013 12:50:47 -0400 http://dnasite.limlab.ibms.sinica.edu.twDR.Bind webserver predicts the DNA-binding residues from the protein sequence or 3D structure. 13778Mon, 13 May 2013 13:20:30 -0400 http://ef-site.hgc.jp/eF-seek/index.jspeF-seek predicts protein functional sites by searching for similar electrostatic potential and molecular surface shapes against eF-site, a database of electrostatic surfaces for representative ligand binding sites.10359Mon, 20 May 2013 19:50:10 -0400 http://mammoth.bcm.tmc.edu/report_maker/Evolutionary trace (ET) report maker pools information from different sources including databases and on-the-fly multiple sequence analysis to produce a pdf formatted document as output. The emphasis is on prediction of functional sites of proteins.10326Tue, 21 May 2013 02:00:26 -0400 http://www.pdg.cnb.uam.es/eva/con/index.htmlEVAcon automates the continuous evaluation of inter-residue contact prediction servers. Results can be viewed statically or dynamically generated.9980Tue, 21 May 2013 16:40:29 -0400 http://www.cbs.dtu.dk/services/FeatureMap3D/FeatureMap3D is a tool to map protein features and sequence conservation onto homologous structures in PDB.10243Sun, 19 May 2013 04:10:10 -0400 http://cluster.physics.iisc.ernet.in/ff/FF (Fragment Finder) takes a PDB ID, a structure coordinate file or a list of phi and psi angles as input and searches for matches to a specified structural fragment. Users can tailor the search based on sequence similarity and vary the dataset searched against.10047Sun, 19 May 2013 19:40:21 -0400 http://foldminer.stanford.edu/FoldMiner aligns a user-supplied or identified query structure to a database of single domain targets to discover structural neighbours and characteristic motifs. Query structures can also be aligned to one or more user-specified structures using the LOCK 2 algorithm.9866Sat, 18 May 2013 00:20:30 -0400 http://bioserv.rpbs.univ-paris-diderot.fr/fpocketFpocket web server detects small molecule pockets by relying on the geometric alpha sphere theory. It also tracks pockets during molecular dynamics so to provide insight on pocket dynamics (mdpocket) and transposes mdpocket to the combined analysis of homologous structures (hpocket).10654Sat, 18 May 2013 19:40:28 -0400 http://gene3d.biochem.ucl.ac.uk/WebServices/The Gene3D web services provide programmatic access to the CATH-Gene3D annotation resources and in-house software tools. These services include Gene3DScan for identifying structural domains within protein sequences, access to pre-calculated annotations for the major sequence databases, and linked functional annotation from UniProt, GO and KEGG.12180Mon, 20 May 2013 20:50:26 -0400 http://globplot.embl.de/GlobPlot has the ability to plot the tendency towards globularity for a given protein sequence. Can also perform SMART/Pfam domain prediction.9732Fri, 17 May 2013 15:20:27 -0400 http://www.glycosciences.de/modeling/glyprot/php/main.phpGlyprot is a tool for predicting and modelling all potential N-glycosylation sites in a given 3D structure.9973Tue, 21 May 2013 15:10:11 -0400 http://biophysics.cs.vt.edu/H++H++ is an automated tool for computing pK values of ionizable groups in macromolecules and adding missing hydrogen atoms according to the specified pH of the environment. Given a (PDB) structure file on input, H++ outputs the completed structure in several common formats (PDB, PQR, AMBER inpcrd/prmtop) and provides a set of tools useful for analysis of electrostatic-related molecular properties.10048Tue, 21 May 2013 14:10:27 -0400 http://caps.ncbs.res.in/harmony/Harmony is a server to assess the compatibility of an amino acid sequence with a proposed three-dimensional structure.10287Fri, 17 May 2013 14:40:28 -0400 http://bioinfo3d.cs.tau.ac.il/I2I-SiteEngine/Interface-to-Interface (I2I)-SiteEngine compares pairs of interacting protein binding sites by recognizing similarity of physico-chemical properties and shapes in the protein-protein interfaces.10035Mon, 20 May 2013 07:00:29 -0400 http://www.icgeb.org/protein/ICGEBnet Protein Tools is a resource for analysis of 3D protein structures including domain predictors, a protein fold similiarity server (PRIDE), and tools for calculating atom protusion (CX) and/or depth (DPX) indexes in 3D models.9955Mon, 20 May 2013 07:40:22 -0400 http://caps.ncbs.res.in/imot/iMOTserver.htmliMOT (interacting MOTif) server is designed to search for spatially interacting motifs among proteins sharing similar 3-dimensional structures.9890Thu, 16 May 2013 23:00:14 -0400 http://www.reading.ac.uk/bioinf/IntFOLD/The IntFOLD web server is an integrated web resource for protein folding recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction.12129Thu, 16 May 2013 04:10:36 -0400 http://www.mitchell-lab.org/kfcThe KFC Server is a web-based implementation of the Knowledge-based FADE and Contacts (KFC) model. KFC predicts the subset of residues responsible for the majority of a protein interface's binding free energy. Users input protein-protein or protein-DNA information for visualization of binding hot spots within the protein structure.10469Thu, 16 May 2013 22:00:21 -0400 http://kinari.cs.umass.edu/KINARI-Web is a web server for performing rigidity analysis and visually exploring rigidity properties of proteins. It also provides tools for pre-processing the input data, such as selecting relevant chains from PDB files, adding hydrogen atoms and identifying stabilizing interactions.12212Sun, 19 May 2013 18:30:25 -0400 http://abcis.cbs.cnrs.fr/kindock/KinDOCK is a tool for the analysis of ATP-binding sites of protein kinases based on a structural library of protein kinase-ligand complexes extracted from the Protein Data Bank (PDB).10240Sat, 18 May 2013 10:30:42 -0400 http://knots.mit.edu/KNOTS is a web server that detects knots in protein structures.10408Mon, 20 May 2013 21:50:23 -0400 http://bioinfo3d.cs.tau.ac.il/MAPPISMultiple Alignment of Protein-Protein Interfaces (MAPPIS) is a tool for the recognition of spatially conserved chemical interactions shared by a set of protein-protein interfaces or regions of protein interaction. Users input a set of protein-protein complexes and MAPPIS returns a list of shared interaction properties of the interfaces.10487Sun, 19 May 2013 14:30:20 -0400 http://bental.tau.ac.il/MCPep/MCPep webserver performs Monte Carlo simulations of helical peptides in association with lipid membranes. Aqueous phase simulations are also computed. MCPep reports the main determinants of peptide-membrane interactions (e.g. average location and orientation in the membrane, free energy of membrane association).13831Tue, 21 May 2013 08:20:20 -0400 http://bioinfo3d.cs.tau.ac.il/MolAxisThe MolAxis web server allows users to identify transmembrane channels in proteins and channels in macromolecules that connect buried cavities to the external surface. Gating residues, channel lining residues and a 3D graphical representation of the channel surface are output.10456Sun, 19 May 2013 09:20:20 -0400 http://mole.upol.cz/MOLEonline 2.0 is a tool for the analysis of access/egress paths to biomolecular channels. A 3D graphical representation of the channel is displayed along with a list of lining residues and biochemical properties.13725Mon, 20 May 2013 07:40:11 -0400 http://bcb.dei.unipd.it/MolLocMolecular Local surface comparison (MolLoc) is a web server for the structural comparison of molecular surfaces. Users input two structures in PDB format for comparison of binding sites, cavities or other residues.10592Fri, 17 May 2013 04:30:06 -0400 http://projects.villa-bosch.de/dbase/molsurfer/Molsurfer is a graphical tool that links a 2D projection of a macromolecular interface to a 3D view of the macromolecular structures. It can be used to study protein-protein and protein-DNA/RNA interfaces.10107Sun, 19 May 2013 00:30:27 -0400 http://proteinformatics.charite.de/mplot/MPlot is a web server for the analysis, visualization and plotting of the tertiary structure contacts and geometrical features of helical membrane proteins.10671Mon, 20 May 2013 19:50:18 -0400 http://bioinfo3d.cs.tau.ac.il/MultiBindMultiple Alignment of Protein Binding Sites (MultiBind) is a prediction tool for protein binding sites. Users input a set of protein-small molecule complexes and MultiBind predicts the common physio-chemical patterns responsible for protein binding.10486Fri, 17 May 2013 17:50:25 -0400 http://casp.rnet.missouri.edu/nncon.htmlUsing 2D-recursive neural networks, NNcon is a web server for predicting protein contact maps.10548Sat, 18 May 2013 01:50:19 -0400 http://www.receptors.org/NR/servers/html/Nuclear Receptor Structure Analysis Server (NRSAS) is a multi-purpose collection of tools for the analyses of nuclear hormone receptors.10132Sun, 19 May 2013 13:40:11 -0400 http://opm.phar.umich.edu/Orientations of Proteins in Membranes (OPM) database: curated resource, provides spatial positions of membrane-bound peptides and proteins of known 3D structure, together with their structural classification, topology and intracellular localization. Data can be searched and retrieved, database offers downloadable coordinates. Protein images and visualization tools provided.13471Tue, 21 May 2013 16:50:07 -0400 http://www.ofranlab.org/paratome/Paratome is a web tool for the identification of Antigen Binding Regions (ABRs) in antibodies. It accepts as an input the sequences or 3D structures (in PDB format) of antibodies.13784Sat, 18 May 2013 07:20:23 -0400 http://past.in.tum.de/Polypeptide Angles Suffix Tree (PAST) provides methods for searching three-dimensional protein structures and identifying frequent common substructures (structural motifs) using an approach independent of the sequence of amino acids.10270Sun, 19 May 2013 16:00:09 -0400 http://pbs.rnet.missouri.eduPBSword is a web server designed for efficient and accurate comparisons and searches of geometrically similar protein-protein binding sites from a large-scale database. 13798Tue, 21 May 2013 05:00:07 -0400 http://pcfamily.life.nctu.edu.twThe PCFamily server identifies template-based homologous protein complexes or families, and infers functional modules for query proteins. Useful for binding model visualizations and annotating query proteins.10669Mon, 20 May 2013 19:30:19 -0400 http://pdb2pqr.sourceforge.net/Server that allows users to convert PDB files into PQR files by adding missing atoms, optimizing hydrogen bonding and assigning atomic charge and radius parameters. The resulting PQR file can be used for electrostatic calculations which can give insight into the influence of electrostatics on biomolecular structures.9853Tue, 21 May 2013 19:30:08 -0400 http://pdbfun.uniroma2.it/pdbFun allows the user to search the PDB as a database of annotated residues. One can limit the search by annotations such as domains, binding sites, active sites, solvent exposure and residue type.10060Mon, 20 May 2013 16:30:26 -0400 http://wwwmgs.bionet.nsc.ru/mgs/systems/fastprot/pdbsitescan.htmlPDBSiteScan takes a PDB file as input, and searches for stuctural matches with the PDBSite set of known functional sites.9869Tue, 21 May 2013 13:30:34 -0400 http://lorentz.immstr.pasteur.fr/solvate_mutate.phpPDB_Hydro provides tools for mutating and solvating structures of biological macromolecules like proteins or DNA. It identifies strongly and poorly solvated exposed surfaces of structures in an effort to help identify potential interaction zones.10217Mon, 20 May 2013 15:00:14 -0400 http://pfp.technion.ac.il/PFP (Patch Finder Plus) is a tool for extracting and displaying positive electrostatic patches on protein surfaces which can be indicative of nucleic acid binding interfaces.10425Mon, 20 May 2013 15:30:24 -0400 http://phemto.orgchm.bas.bg/Protein pH-dependent Electric Moment Tools (PHEMTO) is a web server for evaluating protein electrostatic characteristics relative to their molecular interactions. Input is the atomic coordinate file in PDB format; output is electric/dipole moments and interactive visualization as well as the full electrostatic characteristics.10258Mon, 20 May 2013 09:40:29 -0400 http://pheps.orgchm.bas.bg/home.htmlpH-dependent Protein Electrostatics Server (PHEPS) performs global and local pH-dependent electrostatic analysis of protein structures. The user can supply a PDB ID or upload a coordinate file.10229Tue, 21 May 2013 09:00:22 -0400 http://phosfinder.bio.uniroma2.itPhosfinder uses a structural comparison algorithm to identify phosphate binding sites in protein structures. It scans a query structure in PDB format against a set of known 3D phosphate binding motifs and outputs a visual display of the predicted binding sites on the query protein structure.12119Tue, 21 May 2013 17:40:09 -0400 http://pipe.scs.fsu.edu/PI2PE (Protein Interface/Interior Prediction Engine) consists of three predictors (WESA, cons-PPISP, and DISPLAR) for predicting solvent accessibility and interface residues from the structure of a protein-binding or DNA-binding protein.10333Mon, 20 May 2013 18:30:26 -0400 http://crick.mbu.iisc.ernet.in/~PIC/Protein Interactions Calculator (PIC) is a server which recognizes various kinds of interactions; such as disulphide bonds, hydrophobic interactions, hydrogen bonds, aromatic interactions, and ionic interactions within a protein or between proteins in a complex.10372Tue, 21 May 2013 12:50:41 -0400 http://www.russell.embl.de/pints/Patterns in Non-homologous Tertiary Structures (PINTS) finds similarities between protein structures containing structural patterns and provides a statistical measure of local structural similiarities.10106Tue, 21 May 2013 07:20:16 -0400 http://enzyme.ucd.ie/cgi-bin/pKD/server_start.cgipKa Design (pKD) takes as input a protein structure and allows you to redesign the protein pKa value for that molecule. The server calculates a set of point mutations that will cause the desired pKa change.10223Sat, 18 May 2013 05:20:35 -0400 http://pknot.life.nctu.edu.tw/pKNOT (Protein Knot) is a tool that can detect knots in proteins as well as providing information on knotted proteins in PDB. pKNOT-v2 has been updated with a homology modeling tool such that the server can now accept protein sequences in addition to 3D structures or PDB IDs and return knot analysis.10379Tue, 21 May 2013 07:00:12 -0400 http://pocketquery.csb.pitt.eduPocketQuery is a web service for exploring the properties of protein-protein interaction interfaces. Users can interactively explore hot spot and anchor residues, as well as hot regions, defined by clusters of residues, at the interface of protein-protein interactions.13739Tue, 21 May 2013 14:20:13 -0400 http://polyview.cchmc.org/conform.htmlPOLYVIEW-MM is a web server that integrates high quality animation of molecular motion into structural and functional analysis of macromolecules. Structural annotations such as mapping of known interaction sites from structural homologs, mapping of cavities and ligand binding sites, transmembrane regions and protein domains are also integrated into the visualization.10660Mon, 20 May 2013 22:20:32 -0400 http://mathbio.nimr.mrc.ac.uk/wiki/POPSParameter OPtimised Surfaces (POPS) is an algorithm to calculate accessible surfaces areas at atomic and residue level.10121Mon, 20 May 2013 04:30:24 -0400 http://pre-s.protein.osaka-u.ac.jp/prebi/Prediction of Biological Interfaces (PreBI) is a server for predicting protein-protein interfaces in protein structures that maximizes both the degree of complementarity and the interface area.10268Sat, 18 May 2013 11:20:18 -0400 http://wishart.biology.ualberta.ca/shiftor/cgi-bin/preditor_current.pyPREDITOR predicts torsion angles in proteins from NMR chemical shift data and sequence homology. PREDITOR combines sequence alignment methods with advanced chemical shift analysis techniques to generate its torsion angle predictions.10306Mon, 20 May 2013 11:20:25 -0400 http://probis.cmm.ki.siProtein Binding Sites (ProBiS) is a web server which detects protein binding sites based on local structural alignments. Algorithms have been parallelized to allow for faster computing against the PDB. Pre-calculated protein similarity profiles for over 29,000 non-redundant proteins are also available.10710Mon, 20 May 2013 01:20:18 -0400 http://bidd.cz3.nus.edu.sg/cgi-bin/prof/protein/profnew.cgiProtein Features (PROFEAT) is a tool for computing commonly-used structural and physicochemical features of proteins and peptides from amino acid sequence. New functions include computation of protein-protein and protein-small molecule interactions, topological descriptors for peptide sequences and small molecule structures. New feature groups of descriptors have also been added.10281Sun, 19 May 2013 18:50:31 -0400 http://www.ebi.ac.uk/thornton-srv/databases/ProFunc/ProFunc takes a PDB-format structure as input and predicts the likely function of the protein based on various sequence and structural analysis methods.10008Sat, 18 May 2013 19:20:14 -0400 http://ProKware.mbc.nctu.edu.tw/ProKware is a tool for investigating protein structural properties such as domains, functional sites, and post-translational modifications. To use some features a stand-alone piece of software is necessary; currently available for windows only.10249Mon, 20 May 2013 11:30:06 -0400 http://bioportal.weizmann.ac.il/promate/ProMateus extends ProMate, a protein binding site predictor, and allows the user to suggest new features that might improve the prediction of the binding site locations.10342Sun, 19 May 2013 10:20:11 -0400 http://projects.villa-bosch.de/dbase/ps2/Protein Structure Annotation Tool (ProSAT2) is a tool for the visualization of sequence based, residue-specific annotations mapped onto three-dimensional (3D) protein structures10239Mon, 20 May 2013 18:40:12 -0400 http://prodata.swmed.edu/ProSMoS/ProSMoS facilitates protein structure patterns searches. The web program converts 3D structures into an interaction matrix model including such details as the secondary structural element (SSE) type, handedness of connections between SSEs, coordinates of SSE start and ends, etc and then retrieves all structures from a database that contain this pattern.10598Tue, 21 May 2013 07:30:12 -0400 http://pcidb.russelllab.org/A network of protein-chemical structure interactions. Progress in structure determination methods means that the set of experimentally determined 3D structures of proteins in complex with small molecules is growing exponentially. ProtChemSI exploits and extends this useful set of structures by both collecting and annotating the existing data as well as providing models of potential complexes inferred by protein or chemical structure similarity.13496Sat, 18 May 2013 16:20:27 -0400 http://bioportal.weizmann.ac.il/dipol/The Protein Dipole server calculates and displays the net charge, dipole moment and mean radius of any 3-dimensional protein structure.10381Thu, 16 May 2013 06:20:17 -0400 http://lfp.qb.fcen.uba.ar/embnet/charge.php?app=Frustratometer&chains=NOThe Protein Frustratometer is an energy landscape theory inspired algorithm that aims at quantifying the degree of local frustration manifested in protein molecules. By analyzing protein frustration one can gain insight into protein biological function and how mutations alter this function.13767Mon, 20 May 2013 11:20:22 -0400 http://www.dsimb.inserm.fr/dsimb_tools/peeling3/Protein Peeling is an approach for splitting a protein three dimensional (3D) structure into protein units, an intermediate level of protein structure description between protein domains and secondary structures.10276Tue, 21 May 2013 19:00:17 -0400 http://protemot.csbb.ntu.edu.tw/The Protein motif (Protemot) server predicts protein binding sites based on structural templates automatically extracted from crystal structures of protein-ligand complexes in the PDB.10307Tue, 21 May 2013 13:50:13 -0400 http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/A database for protein structural change upon ligand binding.13497Tue, 21 May 2013 17:30:12 -0400 http://biodev.extra.cea.fr/rasmot3d/The RASMOT-3D PRO web server performs systematic searches in 3D protein structures for a set of residues exhibiting a particular topology. Input is a PDB file for the motif of interest; output is an interactive list of protein structures exhibiting resides of similar topology.10544Tue, 21 May 2013 18:10:27 -0400 http://wishart.biology.ualberta.ca/rci/cgi-bin/rci_cgi_1_d.pyRCI (Random Coil Index) is a method for predicting protein flexibility using secondary chemical shifts.10410Tue, 21 May 2013 16:30:31 -0400 http://gibk26.bio.kyutech.ac.jp/jouhou/readout/Readout is a server for the calculation of direct and indirect readout energy Z-scores which estimate the degree of sequence specificity of the protein-DNA complex. Readout can be useful for checking the quality of protein-DNA interactions in three dimensional (3D) structures.10292Tue, 21 May 2013 10:40:24 -0400 http://proteinformatics.charite.de/rhythm/RHYTHM predicts buried vs. exposed residues of helical membrane proteins. Users input either primary, secondary or tertiary structure information. Output includes secondary structure and topology information, and the contact type and conservation of each residue.10605Sun, 19 May 2013 16:10:13 -0400 http://www.cs.toronto.edu/~hilal/rnacontext/RNAcontext: a new motif-finding method designed to elucidate RNA-binding protein (RBP) specific sequence and structural preferences with greater accuracy than existing approahces. 13404Mon, 13 May 2013 23:20:13 -0400 http://www.cs.utoronto.ca/~juris/data/rnsc/Restricted Neighborhood Search Clustering Algorithm (RNSC): efficiently partitions networks into clusters using a cost function. Used to detect known and predict still undiscovered protein complexes within the cell's protein-protein interaction (PPI) network. The increasing amount of available PPI data necessitates an accurate and scalable approach to protein complex identification.13405Tue, 14 May 2013 21:00:17 -0400 http://www.nii.ac.in/sbspks.htmlSBSPKS contains web tools for structure based sequence analysis of polyketide synthases. Model_3D_PKS for modeling, visualization and analysis of 3D PKS catalytic domains; Dock_Dom_Anal for identification of key interacting residues in docking, and NRPS-PKS for identification of catalytic domains.10628Tue, 21 May 2013 04:40:24 -0400 http://bioserv.rpbs.jussieu.fr/cgi-bin/SCitSCit is a set of tools facilitating the analysis and editing of protein side chain conformations. Using a PDB file as input, the tools allow the user to perform such tasks as listing and/or modifying the values of the dihedral angles, listing structurally compatible rotamers for each residue and substituting side chains resulting in a new structure.9858Sat, 18 May 2013 03:40:35 -0400 http://www.igb.uci.edu/servers/psss.htmlSCRATCH is a suite of protein structure software and servers for the prediction of secondary structure, solvent accessibility, disulphide bridges, stability effects of single amino acid mutations, disordered regions, domains, beta-residue and beta-strand pairings, amino acid contact maps, and tertiary structure.9993Tue, 21 May 2013 15:30:30 -0400 http://www-cryst.bioc.cam.ac.uk/~sdm/sdm.phpSite Directed Mutator (SDM) is a web server for predicting effects of mutations on protein stability and function. Users input a wild type structure and the position and amino acid type of the mutation. An environment specific amino acid substitution frequency for homologous protein families is used to calculate a stability score.12191Tue, 21 May 2013 19:30:26 -0400 http://seemotif.csie.ntu.edu.twThe web server seeMotif allows users to interactively visualize sequence motifs on protein structures from Protein Data Bank (PDB).10586Mon, 20 May 2013 08:30:21 -0400 http://bioinfo3d.cs.tau.ac.il/SiteEngine/SiteEngine is a server that searches protein structures for regions that can potentially function as binding sites by scanning for regions on the surface of one protein structure that resemble a specific binding site on the other.10034Mon, 20 May 2013 23:30:08 -0400 http://sitehound.sanchezlab.orgSITEHOUND-web is a server that identifies ligand binding sites in protein structures. Users input a protein structure in PDB format. The program identifies putative ligand binding sites for various favorable probe molecules (i.e. carbon probe, phosphate probe) and displays the putative sites in interactive 3D representation.10595Fri, 17 May 2013 01:30:25 -0400 http://bioinfo.mc.ntu.edu.tw/slither/SLITHER is a web server for protein channel studies. It generates contiguous conformations of a molecule along a curved tunnel inside a protein and calculates the ensuing binding free energy profile.10609Tue, 21 May 2013 03:00:33 -0400 http://kryptonite.ucsd.edu/opal2/GetServicesList.doThe SMAP web service provides a user friendly interface and programming API to study protein-ligand interactions. Useful for understanding the structure, function and evolution of proteins and for designing safe therapeutics.10670Tue, 21 May 2013 18:30:19 -0400 http://pocket.uchicago.edu/SplitPocket is a web server for identification of functional surfaces of proteins from their structure coordinates. Identification is based on the geometric concept of a split pocket, which is a pocket split by a binding ligand. >26,000 structures in PDB have been found to have split pockets.10602Thu, 16 May 2013 18:10:31 -0400 http://mfrlab.org/grafss/spriteSPRITE is a protein structural motif database searching program. Users can upload a PDB file of a query protein structure, and SPRITE compares the input coordinates to a database of 3D side chain arrangements of sites and motifs using a graph theoretical approach. 13745Mon, 20 May 2013 23:00:13 -0400 http://sride.enzim.hu/Sride is a tool for identificating stabilizing residues in protein structure.9975Mon, 20 May 2013 14:40:24 -0400 http://luna.bioc.columbia.edu/SMS/STINGm/STING is a suite of tools for the analysis of protein sequence, structure, stability and function - and the relationships between them.10042Mon, 20 May 2013 02:10:24 -0400 http://ilyinlab.org/StSNP/StSNP (Structure SNP) is a server which provides the ability to analyze and compare human nonsynonymous SNPs (nsSNP) in protein structures, protein complexes, protein-protein interfaces and metabolic networks.10343Tue, 21 May 2013 00:40:31 -0400 http://bioinf-applied.charite.de/superlooper/SuperLooper is a web tool for the modeling of loops in globular and membrane proteins.10601Tue, 21 May 2013 03:00:29 -0400 http://oxytricha.princeton.edu/SWAKK/Sliding Window Analysis of Ka and Ks (SWAKK) is tool for detecting positive selection in proteins using a sliding window substitution rate analysis. The program can display the results on a 3D protein structure.10269Sun, 19 May 2013 13:20:09 -0400 http://topmatch.services.came.sbg.ac.at/TopMatch is a computational tool for protein structure alignment, for the visualization of structural similarities, and for highlighting relationships found in protein classifications.10507Sat, 18 May 2013 07:40:21 -0400 http://feature.stanford.edu/webfeature/WebFEATURE is a structural analysis tool for identifying 3D physiochemical motifs in molecular structures.10103Mon, 20 May 2013 23:50:24 -0400