Table 3:
Web servers/tools for characterization of protein interfaces
| Physical and chemical properties | |||
|---|---|---|---|
| Web server/tool and link | Reported characteristics | Results | Visual interface |
| CASTp [60] http://cast.engr.uic.edu | Pockets & cavities | Residue ASA, Residue Volume | 3D (JMol, Chime) |
| ConSurf [65] http://consurf.tau.ac.il/ | Conservation info based of multiple sequence alignment or protein structure. | Conservation score | Yes (JMol) |
| GALINTER [130] (source code is available upon request) | Protein–protein interfaces | Spatial alignment according to the vector representations of van der Waals interactions and hydrogen bonds based on their geometry | No |
| LIGPLOT [131] http://www.biochem.ucl.ac.uk/bsm/ligplot/ligplot.html | Non-covalent interactions of protein complexes | H-bonds, hydrophobic forces and their strengths, atomic ASA. | 2D |
| MAPPIS [132] http://bioinfo3d.cs.tau.ac.il/MAPPIS/ | Protein–protein binding sites | Common spatial arrangements of physico-chemical properties like H-bond donor, acceptor, aliphatic, aromatic, hydrophobic. | 3D (JMol) |
| MolSurfer [133] http://projects.villa-bosch.de/mcm/software/molsurfer | protein–protein and protein–DNA/RNA interfaces. | Complementarity, hydrophobicity and electrostatic potential. | 3D (WebMol) |
| MultiBind [132] http://bioinfo3d.cs.tau.ac.il/MultiBind/ | Small ligand binding sites | Common spatial arrangements of physico-chemical properties like H-bond donor, acceptor, aliphatic, aromatic, hydrophobic. | 2D |
| PIC [134] http://crick.mbu.iisc.ernet.in/~PIC/ | Non-covalent interactions of protein complexes | hydrogen &disulphide bonds, hydrophobic, ionic & aromatic- aromatic interactions, ASA. | 3D (RasMol, JMol) |
| ProFace [135] http://202.141.148.29/resources/bioinfo/ interface/ | Protein–protein interfaces | Interface area, surface area, fraction of non-polar atoms, non-polar interface area, residue propensity, fraction of buried atoms. | 3D (Rasmol, Chime) |
| ProTherm [136] http://gibk26.bse.kyutech.ac.jp/jouhou/ Protherm/protherm.html | Thermodynamic parameters of wild type and mutant protein. | Gibbs free energy change, enthalpy change, heat capacity change, transition temperature Mutated residue numbers | No |
| PROTORP http://www.bioinformatics.sussex.ac.uk/protorp/ | Non-covalent interactions of protein complexes. | Interface ASA, percentage polar atom in interface and on surface, planarity, eccentricity, secondary structure info, hydrogen and disulfide bonds, salt bridges, gap volume, gap volume index. | No |
| Q-SiteFinder [137] http://bmbpcu36.leeds.ac.uk/qsitefinder/ | Ligand binding site | Site volume, protein volume | 3D (Chime, Mage) |
| ScoreCons [68] http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/valdar/scorecons_server.pl | Conservation info based on multiple sequence alignment. | Conservation score | No |
| SurfNet [138] http://www.biochem.ucl.ac.uk/~roman/surfnet/surfnet.html | Surfaces and void regions. | Computation of gaps, clefts, cavities and binding sites, van der Waals surfaces | 3D (Rasmol, Raster3D, Sybyl) |
| Hot spot databases and prediction servers | Strategy | Availability | Technique |
| ASEdb [27] http://nic.ucsf.edu/asedb/ | Experimental | Database | Alanine scanning |
| BID [70] http://tsailab.tamu.edu/BID/ | Experimental | Database | Collection of several experimental techniques. |
| FoldX [76] http://foldx.crg.es/ | Energy-based | Tool and server | Computational alanine scanning |
| HotSprint [84] http://prism.ccbb.ku.edu.tr/hotsprint/ | Conservation, accessibility, residue propensity | Database | Empirical formula |
| ISIS [95] http://cubic.bioc.columbia.edu/services/isis/ | Sequence-based | Tool | Machine learning |
| KFC [85] http://kfc.mitchell-lab.org/ | Atomic contacts, residue size, H-bond | Server | Machine learning |
| Robetta [74] http://robetta.org/submit.jsp | Energy-based | Server | Computational alanine scanning |
In the first part, the web servers and tools for physical and chemical properties of protein interfaces are listed. The hot spot related databases/web servers are listed in the second part where the hot spot detection strategy, the availability and the used technique are given, respectively.