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. CHpredicts: Prediction of CH-O, CH-PI interactions in backbone residues of a protein 
  13. GammaPred: Identification of gamma-turn containing residues in a given protein sequence.
  14. LPIcom: Analysis and prediction of ligand protein interaction.
  15. PEPstr: Prediction of structure of peptides.
  16. PEPstrMODStructural prediction of peptides containing natural, non-natural and modified residues.  
  17. PLDbench: Benchmarking of docking software on peptide-ligand complexes. 
  18. RRCpred: A Webserver for predicting residue-residue contact.
  19. SARpred: A neural network based method predicts the real value of surface acessibility.
  20. SRTpred: A method for the classification of protein sequence as secretory or non-secretory protein.
  21. STARPDB: A webserver for annotating structure of a protein using simililarity based approach.
  22. TBBpred: A webserver for the prediction of transmembrane Beta barrel regions in a given protein sequence.
  23. TSP-PRED: A webservice for predicting Tertiary Structure of proteins.

 

External Links to web servers developed/mainatined by Indian groups

This section provides URL/links to important websites developed and maintained by Indian 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. 3dswappred: prediction of 3D domain swapping from protein sequence using Random Forest approach.
  3. 3PFDB+: improved search protocol and update for the identification of representatives of protein sequence domain families.
  4. 3PFDB: 3PFDB a database of best representative PSSM profiles (BRPs) of protein families generated using a novel data mining approach.
  5. AADS: an automated active site identification docking and scoring protocol for protein targets based on physicochemical descriptors.
  6. Bhageerath-H Strgen: A homology/ab initio hybrid algorithm for sampling near:native protein conformations.
  7. Bhageerath: an energy based web enabled computer software suite for limiting the search space of tertiary structures of small globular proteins.
  8. CADB3.0: Conformational Angles DataBase
  9. D2N: Distance to the native.
  10. DB Dehydrogenase: an online integrated structural database on enzyme dehydrogenase.
  11. DOR: a Database of Olfactory Receptors Integrated Repository for Sequence and Secondary Structural Information of Olfactory Receptors in Selected Eukaryotic Genomes.
  12. GraProStr: Ranking the quality of protein structure models using sidechain based network properties.
  13. HARMONY: a server for the assessment of protein structures.
  14. iRDP: Engineering Proteins for Thermostability with iRDP Web Server.
  15. IWS: integrated web server for protein sequence and structure analysis.
  16. Layers: A molecular surface peeling algorithm and its applications to analyze protein structures.
  17. Lectindb: a plant lectin database.
  18. LenVarDB: database of length:variant protein domains.
  19. LySDB : Lysozyme Structural DataBase.
  20. MaxMod: a hidden Markov model based novel interface to MODELLER for improved prediction of protein 3D models.
  21. Mycobacterium tuberculosis Structural proteome.: Structural annotation of Mycobacterium tuberculosis proteome.
  22. Myosinome: a database of myosins from select eukaryotic genomes to facilitate analysis of sequence:structure:function relationships.
  23. NNvPDB: Neural Network based Protein Secondary Structure Prediction with PDB Validation.
  24. OneG: a computational tool for predicting cryptic intermediates in the unfolding kinetics of proteins under native conditions.
  25. PASS2 version 4: an update to the database of structure:based sequence alignments of structural domain superfamilies.
  26. PASS2.5: Database for the structure-based sequence alignment of distantly related SCOP domain superfamilies: update to version 5 and added features.
  27. PASS2: an automated database of protein alignments organised as structural superfamilies.
  28. PcSM: Capturing native/native like structures with a physicochemical metric (pcSM) in protein folding.
  29. PDBparam: Online Resource for Computing Structural Parameters of Proteins.
  30. PPS: A computing engine to find Palindromes in all Protein sequences.
  31. ProRegIn: a regularity index for the selection of native like tertiary structures of proteins.
  32. ProSTRIP: A method to find similar structural repeats in three:dimensional protein structures.
  33. ProTSAV: A protein tertiary structure analysis and validation server.
  34. PSST2.0: Protein Data Bank Sequence Search Tool.
  35. Ramachandran plot: Ramachandran plot on the web
  36. RM2TS: From Ramachandran Maps to Tertiary Structures of Proteins.
  37. RV-Typer: A Web Server for Typing of Rhinoviruses Using Alignment-Free Approach.
  38. Sanjeevini: a freely accessible web:server for target directed lead molecule discovery.
  39. SEM (Symmetry Equivalent Molecules): A web based GUI to generate and visualize the macromolecules.
  40. SMS 2.0: an updated database to study the structural plasticity of short peptide fragments in non:redundant proteins.
  41. SSEP2.0: Secondary Structural Elements of Proteins.
  42. SUPFAM: implications for structural genomics and function annotation in genomes.
  43. SVMPBPred: SVM based protein block prediction method using sequence profiles and secondary structures.
  44. THGS: a web:based database of Transmembrane Helices in Genome Sequences.
  45. VPDB: Viral Protein Structural Database.