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Databases

  • Protein Model Portal  •  The Protein Model Portal has been developed to foster effective usage of molecular models in biomedical research by providing convenient and comprehensive access to structural information for a protein - both experimental structures and theoretical models. Protein Model Portal is a component of the Nature PSI Structural Biology Knowledgebase. [less]
  • SwissSidechain  •  SwissSidechain is a structural and molecular mechanics database of hundreds of non-natural amino-acid sidechains that can be used to study in silico their insertion into natural peptides or proteins.  [less]

Tools

  • SWISS-MODEL Workspace  •  SWISS-MODEL is a fully automated web based protein structure homology-modeling expert system. The SWISS-MODEL Workspace is a web-based integrated service which assist and guides the user in building protein homology models at different levels of complexity. A personal working environment (workspace), where several modelling projects can be carried out in parallel, is provided for each user. [less]
  • SwissDock  •  SwissDock is a protein ligand docking server, accessible via the ExPASy web server, and based on EADock DSS. The purpose of this server is to make protein-ligand docking accessible to a wide scientific community worldwide. [less]
  • Agadir  •  Agadir predicts the helical behaviour of monomeric peptides. It only considers short range interactions. Conditions such as pH, temperature and ionic strength are used in the calculation. Modifications of the termini are also allowed. Keep in mind that Agadir is not a program to predict secondary structure of proteins.  [less]
  • APSSP  •  Advanced Protein Secondary Structure Prediction Server  [less]
  • Ascalaph  •  Ascalaph is a general purpose molecular modeling software that performs quantum mechanics calculations for initial molecular model development, molecular mechanics and dynamics simulations in the gas or in condensed phase. It can interact with external molecular modeling packages (MDynaMix, NWChem, CP2K and PC GAMESS/Firefly). [less]
  • CFSSP  •  This server predicts secondary structure of protein from the amino acid sequence. In this server, Chou & Fasman algorithm has been implemented. [less]
  • Click2Drug  •  Directory of computational drug design tools, containing many links to databases, chemical structure representation, molecular modeling, homology modeling, binding site prediction, docking, screening, target prediction, ligand design, binding free energy estimation etc. [less]
  • COILS  •  COILS is a program that compares a sequence to a database of known parallel two-stranded coiled-coils and derives a similarity score. By comparing this score to the distribution of scores in globular and coiled-coil proteins, the program then calculates the probability that the sequence will adopt a coiled-coil conformation. [less]
  • CPHmodels  •  CPHmodels 3.2 is a protein homology modeling server. The template recognition is based on profile-profile alignment guided by secondary structure and exposure predictions [less]
  • DisEMBL  •  Disordered proteins or protein segments lack a folded tertiary structure. They are thought to be intrinsically disordered regions providing essential biological functions. DisEMBL is a tool for prediction of disordered/unstructured regions within a protein sequence. [less]
  • DLP-SVM  •  DLP-SVM is a domain linker predictor. It is composed of three loop-length dependent SVM predictors of domain linkers (SVM-All, SVM-Long and SVM-Short), and SVM-Joint, which combines the results of SVM-Short and SVM-Long into a single consolidated prediction. [less]
  • ESyPred3D  •  ESyPred3D is an automated homology modeling program. The method gets benefit of the increased alignment performances of a new alignment strategy using neural networks. Alignments are obtained by combining, weighting and screening the results of several multiple alignment programs. The final three dimensional structure is built using the modeling package MODELLER [less]
  • FUGUE  •  FUGUE is a program for recognizing distant homologues by sequence-structure comparison. It utilizes environment-specific substitution tables and structure-dependent gap penalties, where scores for amino acid matching and insertions/deletions are evaluated depending on the local environment of each amino acid residue in a known structure [less]
  • Geno3D  •  Geno3D is an automatic web server for protein molecular modelling [less]
  • GlobPlot  •  GlobPlot is a web service that allows the user to plot the tendency within the query protein for order/globularity and disorder [less]
  • GOR  •  Protein secondary structure prediction [less]
  • HHpred  •  Homology detection & structure prediction by HMM-HMM comparison [less]
  • HTMSRAP  •  Helical TransMembrane Segment Rotational Angle Prediction [less]
  • Jmol  •  Jmol is an open-source Java viewer for chemical structures in 3D. [less]
  • Jpred  •  Secondary Structure Prediction Server [less]
  • LiveBench  •  LiveBench provides simple evaluation of the structure prediction servers from the point of view of a potential user. The evaluation of sensitivity and specificity of the available servers can help the user develop sequence analysis strategies and assess the confidence of the obtained predictions. [less]
  • MakeMultimer.py  •  Macromolecular structure pdb files that represent multimeric molecules often do not contain the coordinates of all multimer subunits. For such files, MakeMultimer.py calculates the coordinates of the missing subunits from the BIOMT transformation matrices contained in the pdb file.  [less]
  • MARCOIL  •  predicting coiled-coils in protein sequences [less]
  • MarvinSpace  •  MarvinSpace is a Java-based software for visualization, modeling and interactive rendering [less]
  • MeDor  •  Disordered proteins or protein segments lack a folded tertiary structure. They are thought to be intrinsically disordered regions providing essential biological functions. MeDor is a metaserver for predicting protein disorder [less]
  • MolTalk  •  MolTalk is a computational environment (programming library with an integrated scripting language) for doing structural bioinformatics. It interprets PDB formatted files and creates an object representation of the structure-chain-residue-atom hierarchy. [less]
  • MovieMaker  •  MovieMaker is a web server that allows short (~10 sec), downloadable movies to be generated of protein dynamics. It accepts PDB files or PDB accession numbers as input and automatically outputs colorful animations covering a wide range of protein motions and other dynamic processes. [less]
  • NetSurfP  •  NetSurfP server predicts the surface accessibility and secondary structure of amino acids in an amino acid sequence. The method also simultaneously predicts the reliability for each prediction, in the form of a Z-score. The Z-score is related to the surface prediction, and not the secondary structure.  [less]
  • NetTurnP  •  NetTurnP predicts if an amino acid is located in a Beta-turn or not. Optional, NetTurnP is also able to predict the nine Beta-turn subtypes.  [less]
  • NQ-Flipper  •  NQ-Flipper recognizes unfavorable rotamers of Asn and Gln residues in protein structures and corrects them. [less]
  • OpenStructure  •  The OpenStructure library project aims to provide an open-source, modular, flexible, molecular modelling and visualization environment. It is targeted at interested users and method developers in the field of structural bioinformatics. Its cleanly designed API available in both Python an C++ provides a command line interface for batch processing as well as a graphical user interface fully scriptable in Python. [less]
  • PDBePISA  •  PDBePISA is an interactive tool for the exploration of macromolecular (protein, DNA/RNA and ligand) interfaces, prediction of probable quaternary structures (assemblies), database searches of structurally similar interfaces and assemblies, as well as searches on various assembly and PDB entry parameters. [less]
  • Phyre2  •  As with Phyre, the new system is designed around the idea that you have a protein sequence/gene and want to predict its three-dimensional (3D) structure. Whereas Phyre used a profile-profile alignment algorithm, Phyre2 uses the alignment of hidden Markov models via HHsearch to significantly improve accuracy of alignment and detection rate. [less]
  • Poodle  •  Disordered proteins or protein segments lack a folded tertiary structure. They are thought to be intrinsically disordered regions providing essential biological functions, so predicting such disorder should help understand protein functions. [less]
  • PoPMuSiC  •  The PoPMuSiC program is a tool for the computer-aided design of mutant proteins with controlled stability properties. It evaluates the changes in stability of a given protein or peptide under single-site mutations, on the basis of the protein's structure. [less]
  • PROCHECK  •  PROCHECK checks the stereochemical quality of a protein structure, producing a number of PostScript plots analysing its overall and residue-by-residue geometry. It includes PROCHECK-NMR for checking the quality of structures solved by NMR.  [less]
  • PROF  •  Secondary Structure Prediction System [less]
  • ProSA-web  •  Program of error recognition in 3D structures [less]
  • ProtBud  •  Comparison of asymmetric units and biological units from PDB and PQS [less]
  • Protein Disorder Predictors  •  List is a list or Protein Disorder Predictors [less]
  • Protein Model Portal  •  The Protein Model Portal has been developed to foster effective usage of molecular models in biomedical research by providing convenient and comprehensive access to structural information for a protein - both experimental structures and theoretical models. Protein Model Portal is a component of the Nature PSI Structural Biology Knowledgebase. [less]
  • PSIPRED  •  The PSIPRED Protein Structure Prediction Server aggregates several of our structure prediction methods into one location. Users can submit a protein sequence, perform the prediction of their choice and receive the results of the prediction via e-mail. [less]
  • PyMOL  •  PyMOL is a user-sponsored molecular visualization system on an open-source foundation.  [less]
  • QMEAN  •  Estimating the quality of predicted structural models is a crucial step in homology modeling. Scoring functions analyze different structural features of the protein models in order to generate a quality estimate. QMEAN consists of four statistical potential terms (two non-bonded interaction terms, a torsion angle term and a solvation term) and two components describing the agreement between predicted and observed secondary structure and solvent accessibility. [less]
  • RasMol  •  RasMol is a program for molecular graphics visualization. [less]
  • SAM-T08  •  This server finds similar protein sequences in NR and aligns them, providing sequence logos that show relative conservation of different positions. Local structure predictions are done with neural nets for several different local structure alphabets, and hidden Markov models are created. Fold recognition and alignment to proteins in the Protein Data Bank are done, and a full three-dimensional model is constructed. [less]
  • Scratch Protein Predictor  •  SCRATCH is a server for predicting protein tertiary structure and structural features. The SCRATCH software suite includes predictors for secondary structure, relative solvent accessibility, disordered regions, domains, disulfide bridges, single mutation stability, residue contacts versus average, individual residue contacts and tertiary structure. [less]
  • SOPMA  •  Secondary structure prediction. [less]
  • Strap  •  Java-based software for structural alignments of proteins [less]
  • Swiss-PdbViewer  •  Swiss-PdbViewer (aka DeepView) is an application that provides a user friendly interface allowing to analyze several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface. [less]
  • SwissParam  •  SwissParam is a fully automatic server that provides topology and parameters for small organic molecules, compatible with the CHARMM all atoms force field, for use with CHARMM and GROMACS. [less]
  • TLS Motion Determination  •  TLS Motion Determination analyzes a macromolecular crystal structure for evidence of flexibility, e.g. local or inter-domain motions. It does this by partitioning individual chains into multiple segments that are modeled as rigid bodies undergoing TLS (Translation/Libration/Screw) vibrational motion. It generates all possible partitions up to a maximum number of segments.  [less]
  • TMPred  •  The TMpred program makes a prediction of membrane-spanning regions and their orientation. The algorithm is based on the statistical analysis of TMbase, a database of naturally occurring transmembrane proteins [less]
  • TopMatch  •  Computational tools for the alignment and superposition of protein structures are essential instruments in structural biology. TopMatch-web provides an easy-to-use interface to a suite of techniques for protein structure alignments. Given a pair of protein structures, TopMatch calculates a list of alignments ordered by structural similarity. The corresponding superpositions can be explored in a 3D molecule viewer which highlights the structurally equivalent parts of the proteins. [less]
  • TopPred  •  Topology prediction of membrane proteins [less]
  • TopSearch  •  TopSearch is a new powerful gateway to protein structures and their structural relationships. Given a query structure the search engine instantly returns a list of known protein structures sorted by structural similarity. TopSearch operates on three structural levels: chains, biological assemblies and quaternary structures, and asymmetric units. [less]
  • VMD - Visual Molecular Dynamics  •  VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS X, Unix, or Windows, is distributed free of charge, and includes source code. [less]
  • WHAT IF  •  WHAT IF is a versatile molecular modelling package that is specialized on working with proteins and the molecules in their environment like water, ligands, nucleic acids, etc.  [less]
  • YASARA  •  YASARA is a molecular-graphics, -modeling and -simulation program for Windows, Linux and Mac OS X [less]