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Structural Proteomics

Broadly structure of protein is responsible for its function, thus structural annotation is one of major challenges in the field of computational biology. This page list of wide range of web server that includes servers for predicting i) tertiary structure, ii) secondary structure, iii) super secondary structure, iii) surface accessibility and iv) residue-residue contact in a protein.

Prediction of Protein Structure (Raghava's Group)

  1.  ALPHApred: A neural network based method for predicting alpha-turn in a protein.
  2. APSSP:  Advanced Protein Secondary Structure Prediction Server.
  3. APSSP2: Prediction of secondary structure of proteins from their amino acid sequence.
  4. Ar_NHpred: Identification of aromatic-backbone NH interaction in protein residues.
  5. BetaTPred: Statistical-based method for predicting Beta Turns in a protein.
  6. BetaTPred2: Statistical-based method for predicting Beta Turns in a protein.
  7. BetaTPred3: Prediction of beta turns and their types.
  8. BetaTurns: Prediction of beta turn types.
  9. BhairPred: Prediction of beta hairpins in proteins using ANN and SVM techniques.
  10. BTEVAL: Evaluation of beta-turns prediction methods.
  11. ccPDB: Compilation and Creation of datasets from PDB.
  12. ccPDB 2.0: An updated version of datasets created and compiled from Protein Data Bank.
  13. CHpredicts: Prediction of CH-O, CH-PI interactions in backbone residues of a protein 
  14. GammaPred: Identification of gamma-turn containing residues in a given protein sequence.
  15. LPIcom: Analysis and prediction of ligand protein interaction.
  16. PEPstr: Prediction of structure of peptides.
  17. PEPstrMOD: Structural prediction of peptides containing natural, non-natural and modified residues.  
  18. PLDbench: Benchmarking of docking software on peptide-ligand complexes. 
  19. RRCpred: A Webserver for predicting residue-residue contact.
  20. SARpred: A neural network based method predicts the real value of surface acessibility.
  21. SRTpred: A method for the classification of protein sequence as secretory or non-secretory protein.
  22. STARPDB: A webserver for annotating structure of a protein using simililarity based approach.
  23. TBBpred: A webserver for the prediction of transmembrane Beta barrel regions in a given protein sequence.
  24. TSP-PRED: A webservice for predicting Tertiary Structure of proteins.

External Links to web servers developed/maintained by other groups

This section provides URL/links to important websites developed and maintained by other researchers. It exclude servers by Raghava's group, which is given in above section. 

  1. 3DSDSCAR:  Molecular dynamics simulation and quantum mechanical calculations on α-D-N-acetylneuraminic acid
  2. 2dSS : It is a web-server for visualising and comparing secondary structure predictions. It provides two main functionalities: 2D-alignment and compare predictions.
  3. 3dswappred:  prediction of 3D domain swapping from protein sequence using Random Forest approach.
  4. 3PFDB:  3PFDB a database of best representative PSSM profiles (BRPs) of protein families generated using a novel data mining approach.
  5. 3PFDB+:  improved search protocol and update for the identification of representatives of protein sequence domain families.
  6. AADS:  an automated active site identification docking and scoring protocol for protein targets based on physicochemical descriptors.
  7. Bhageerath:  an energy based web enabled computer software suite for limiting the search space of tertiary structures of small globular proteins.
  8. Bhageerath-H Strgen:  A homology/ab initio hybrid algorithm for sampling near native protein conformations.
  9. CADB3.0:  Conformational Angles DataBase
  10. Coils: It helps in prediction of Coiled Coil Regions in Proteins.
  11. CPHModels: Remote homology modeling using structure guided sequence profiles
  12. DAS: Transmembrane Prediction Server
  13. DeepLoc-1.0: It predicts the subcellular localization of eukaryotic proteins.
  14. DomPred: It is used for domain boundary prediction.
  15. DOR:  a Database of Olfactory Receptors Integrated Repository for Sequence and Secondary Structural Information of Olfactory Receptors in Selected Eukaryotic Genomes.
  16. GeNMR (Generate NMR structure): It generates 3D protein structures using NOE-derived distance restraints and NMR chemical shifts.
  17. GenThreader: Used for rapid protein fold recognition. Detect distant homology to proteins of known structure
  18. HARMONY:  a server for the assessment of protein structures.
  19. HMMSTR: A hidden Markov model for the prediction of sequence-structure correlations in proteins.
  20. InterProSurf: It predicts interacting amino acid residues in proteins that are most likely to interact with other proteins, given the 3D structures of subunits of a protein complex
  21. IWS:  integrated web server for protein sequence and structure analysis.
  22. JPRED: Protein secondary structure prediction server which provides predictions by the JNet algorithm. JPred also makes predictions of solvent accessibility and coiled-coil regions.
  23. Layers:  A molecular surface peeling algorithm and its applications to analyze protein structures.
  24. Lectindb:  a plant lectin database.
  25. LenVarDB:  database of length variant protein domains.
  26. LipoP 1.0: It allows prediction of where signal peptidases I & II cleavage sites from Gram negative bacteria will cleave a protein.
  27. LySDB :  Lysozyme Structural DataBase.
  28. MEMEMBED: It is used for the prediction of membrane protein orientation. It is able to quickly and accurately orientate both alpha-helical and beta-barrel membrane proteins within the lipid bilayer.
  29. MEMSAT2: It is used for transmembrane helix topology prediction and it is the second option available on the PSIPRED server
  30. MEMSATSVM: It is an improved transmembrane protein topology prediction using SVMs. It is capable of differentiating signal peptides from transmembrane helices.
  31. MODELLER: It predicts 3D structure of protein based on comparative modelling.
  32. Mycobacterium tuberculosis Structural proteome.:  Structural annotation of Mycobacterium tuberculosis proteome.
  33. Myosinome:  a database of myosins from select eukaryotic genomes to facilitate analysis of sequence, structure, function
  34. NNvPDB:  Neural Network based Protein Secondary Structure Prediction with PDB Validation.
  35. OneG:  a computational tool for predicting cryptic intermediates in the unfolding kinetics of proteins under native conditions.
  36. PASS2:  an automated database of protein alignments organised as structural superfamilies.
  37. PASS2.6:  Database for the structure-based sequence alignment of distantly related SCOP domain superfamilies
  38. PCONS: Protein structure prediction metaserver. It provides improved automated tools for protein structure prediction and analysis using consensus.
  39. PcSM:  Capturing native/native like structures with a physicochemical metric (pcSM) in protein folding.
  40. PDBparam: Online Resource for Computing Structural Parameters of Proteins.
  41. PHD : An automatic mail server for protein secondary structure prediction
  42. Phobius: Used for prediction of transmembrane topology and signal peptides.
  43. PHYRE: Protein Homology/analogY Recognition Engine. It helps in the prediction of the 3D structure of proteins.
  44. PPS:  A computing engine to find Palindromes in all Protein sequences.
  45. PRED-TMR2: The system gives a perfect prediction rating of 100% by classifying all the sequences in the transmembrane class.
  46. PRED-TMBB: It is based on Hidden Markov Model and is capable of predicting and discriminating beta-barrel outer membrane proteins.
  47. PredictProtein(PP): An internet service for sequence analysis and the prediction of aspects of protein structure and function. Users send a protein sequence and receive a single file with results from database comparisons and prediction methods
  48. ProRegIn:  a regularity index for the selection of native like tertiary structures of proteins.
  49. ProSTRIP:  A method to find similar structural repeats in three dimensional protein structures.
  50. ProtComp: It can be used to predict the subcellular localization for animal/fungal and plant proteins.
  51. Protein Prowler: It accepts amino acid sequences presented in the FASTA format and predicts the localization of the protein.
  52. PROTEUS2: It is a web server designed to support comprehensive protein structure prediction and structure-based annotation.
  53. ProTSAV:  A protein tertiary structure analysis and validation server.
  54. PSIPRED: This server allows users to perform secondary structure prediction, transmembrane topology prediction and protein fold recognition.
  55. PSST2.0:  Protein Data Bank Sequence Search Tool.
  56. Ramachandran plot:  Ramachandran plot on the web
  57. RaptorX: It facilitates the user to predict protein structure based on either a single- or multi-template threading.
  58. RM2TS:  From Ramachandran Maps to Tertiary Structures of Proteins.
  59. RV-Typer:  A Web Server for Typing of Rhinoviruses Using Alignment-Free Approach.
  60. Sanjeevini:  a freely accessible web server for target directed lead molecule discovery.
  61. SEM (Symmetry Equivalent Molecules):  A web based GUI to generate and visualize the macromolecules.
  62. SignalP: It predicts the presence and location of signal peptide cleavage sites in Gram-positive, Gram-negative and eukaryotic proteins.
  63. SMART:  Simple Modular Architecture Retrieval Tool; describes multiple information about the protein query.It is used for the identification and annotation of protein domains and the analysis of protein domain architectures.
  64. SMS 2.0:  an updated database to study the structural plasticity of short peptide fragments in non redundant proteins.
  65. SPLIT: Transmembrane Protein Topology Prediction Server provides modified hydrophobic moment index and clear, colorful output
  66. SSEP2.0:  Secondary Structural Elements of Proteins.
  67. SSPRED: Identification & classification of proteins involved in bacterial secretion systems.
  68. SUPFAM:  implications for structural genomics and function annotation in genomes.
  69. THGS:  a web based database of Transmembrane Helices in Genome Sequences
  70. TMHMM : Used for prediction of transmembrane helices in proteins.
  71. TMMOD: Hidden Markov Model for Transmembrane Protein Topology Prediction.
  72. TMpred: Prediction of Trans-membrane Regions and Orientation
  73. TMRPres2D: TransMembrane protein representation in 2 Dimensions tool
  74. TOPCONS: Computes consensus predictions of membrane protein topology using a Hidden Markov Model (HMM)
  75. VPDB:  Viral Protein Structural Database.