Protein Structure Prediction Software and Tools

1. Bhageerath: An automated energy based protein tertiary structure prediction web server. Starting with sequence and secondary structure information, the web server predicts 5 native-like candidate structures for the protein.

Ref.: B. Jayaram, K. Bhushan, et al., "Bhageerath: An energy based web enabled computer software suite for limiting the search space of tertiary structures of small globular proteins", Nucl. Acids Res., 2006, 34, 6195-6204. http://nar.oxfordjournals.org/content/34/21/6195.long

2. BhageerathH+:BhageerathH+ software suite implements a hybrid approach by integrating some of the in-house developed methods and seems to deliver reliable structures for the query proteins from their sequence information. The BhageerathH+ software suite is an advanced version of BhageerathH which primarily comprises seven major modules namely secondary structure prediction, conformational sampling, structure scoring for selecting the best conformations, side chain optimization and energy minimization for quality improvement and top five structure selection

B Jayaram, Priyanka Dhingra, Avinash Mishra, Rahul Kaushik, Goutam Mukherjee, Ankita Singh and Shashank Shekhar, "Bhageerath-H: A homology ab initio hybrid server for predicting tertiary structures of monomeric soluble proteins", BMC Bioinformatics, 2014, 15(Suppl 16):S7 (8 December 2014). http://www.biomedcentral.com/1471-2105/15/S16/S7

3. StrGen (Structure Generation from given dihedrals):StrGen takes the sequence and/or secondary structure information as input and provides the file with Ramachandran values for helix, sheet and loop dihedrals. The dihedrals may be further modified as per the user requirement, to obtain the final structure in PDB format.

Ref.: Priyanka Dhingra and B. Jayaram, "A homology/ab initio hybrid algorithm for sampling near-native protein conformations", J Comput.Chem., 2013 34, 1925-36, http://onlinelibrary.wiley.com/doi/10.1002/jcc.23339/abstract

4. Persistence Length (Filters for Globular Protein Evaluation) Persistence length is the maximum length of the uninterrupted polymer chain persisting in a particular direction. It can be used for flexible polymer chains like proteins, DNA and synthetic polymers. A biophysical filter, which calculates the maximum length of the polypeptide chain in one direction. It is one of the filters employed in the Bhageerath web server for rejection of the non-native like structures from the initial ensemble of trial structures.

Ref.: P. Narang, K. Bhushan, S. Bose and B. Jayaram, "A computational pathway for bracketing native-like structures for small alpha helical globular proteins", Phys. Chem. Chem. Phys., 2005, 7, 2364-2375. http://pubs.rsc.org/en/content/articlelanding/2005/CP/b502226f

5. Radius of Gyration (Filters for Globular Protein Evaluation): Radius of gyration describes the overall spread of the molecule and is defined as the root mean square distance of the collection of atoms from their common centre of gravity. Radius of gyration analysis for a dataset of ~1000 globular proteins from PDB database is performed and the values are plotted against N3/5(N is the no. of Amino Acids). Rg = 0.395*N3/5 + 7.257 .

Ref.: P. Narang, K. Bhushan, S. Bose and B. Jayaram, "A computational pathway for bracketing native-like structures for small alpha helical globular proteins", Phys. Chem. Chem. Phys., 2005, 7, 2364-2375." http://pubs.rsc.org/en/content/articlelanding/2005/CP/b502226f

6. Hydrophobicity Ratio: It comes under the category of biophysical filters, whereby it can help in accepting or rejecting a candidate structure depending on the ratio of accessible surface areas of the hydrophobic and hydrophilic residues.

7. Packing Fraction: It comes under the category of biophysical filters, whereby it can help to evaluate the value of packing fraction for a given protein and to find out whether the value is in acceptable limits for globular protein or not.

8.Protein Regulatory Index (ProRegIn): ProRegIn is based on the regularity in the loop dihedral angles of the amino acids. ProRegIn classifies all 20 amino acids in a protein into regular and irregular category for both phi and psi. It can be used to separate improbable structures from native-like probable structures. ProRegIn is currently used as one of the filters in Bhageerath methodology.

Ref.: L. Thukral, S. R. Shenoy, K. Bhusan and B.Jayaram, "ProRegIn: A regularity index for the selection of native-like tertiary structures of proteins", J. Biosci., 2007, 32, 71-81. http://www.ncbi.nlm.nih.gov/pubmed/17426381

9. Protein structure optimizer: The protein structure optimizer minimizes the energy of the protein structure using a combination of steepest descent and conjugate gradient minimization algorithms. The software uses Cornell et al, 1995 Force Field equation.

10. 15) Protein Structure Energy Evaluation (ProSEE) Scoring Function for Protein Structure Evaluation calculates intramolecular energy of a protein in component-wise break up.

Ref.: P. Narang, K. Bhushan, S. Bose, and B. Jayaram, "Protein structure evaluation using an all-atom energy based empirical scoring function", J. Biomol. Str. Dyn., 2006, 23,385-406.

11. Superimpose: RMSD stands for Root Mean Square Deviation. It is the square root of the average of the squared distance between each mapped pair of point. It is commonly used to measure degree of similarity in protein structure. RMSD is used in 3D geometry of molecules to measure distance between a given set of points, typically atoms.

12. Protein Angle Descriptor: This tool calculates the valence angles & dihedral in the main chain of the protein

Ref.: P. Narang, K. Bhushan, S. Bose and B. Jayaram, "A computational pathway for bracketing native-like structures for small alpha helical globular proteins", Phys. Chem. Chem. Phys., 2005, 7, 2364-2375. url: http://pubs.rsc.org/en/content/articlelanding/2005/CP/b502226f

13. Beta Gamma Turn Prediction (BG Pred) : BG Pred web server has the potential to predict beta turn, gamma turn and their types in user input protein sequence using simple statistical approach based on propensities of occurrence of amino acid at a specific position. It also generates motif structure (secondary structure-turn-secondary structure) with predicted turn type within the range of 3.6 Ã… RMSD of the native structure..

14. PROTEIN SECONDARY STRUCTURE CHARACTERIZATION (PROSECSC): A tool to predict secondary structure of protein sequence.

15. pcSM Software: pcSM: Capturing Native Protein Structures with a Physico-Chemical Metric.

15. Bhageerath-H Strgen: Bhageerath-H Strgen: A Web tool for protein decoy generation.

16. D2N : D2N: Distance to Native.

17. Ramchandran Maps to Tertiary Structures of Proteins (RM2TS): We have divided the allowed (Φ, Ψ) space in Ramachandran maps into 27 distinct conformations sufficient to regenerate a structure to within 5 Å from the native, at least for small proteins, thus reducing the structure prediction problem to a specification of an alphanumeric string i.e. amino acid sequence together with one of the 27 conformations preferred by each amino acid residue.

Ref.: Debarati DasGupta, Rahul Kaushik, and B. Jayaram "From Ramachandran Maps to Tertiary Structures of Proteins", J. Phys. Chem. B , 2015 . 119 (34), pp 11136 - 11145. DOI: 10.1021/acs.jpcb.5b02999

18. Protein Structure Analysis and Validation (ProTSAV): ProTSAV is a meta-server, which has a collection of model quality assessment programs that evaluate the quality of a protein and correctness of the structural model. It predicts a global quality score for submitted input structure.

Ref.: Ankita Singh, Rahul Kaushik, Avinash Mishra, Asheesh Shanker and B. Jayaram "ProTSAV: A Protein Tertiary Structure Analysis and Validation Server", BBA - Proteins and Proteomics, 2015. Volume 1864, Issue 1, January 2016, Pages 11 - 19. DOI: 10.1016/j.bbapap.2015.10.004

19. Structural Difficulty (SD) Index: Structural Difficulty (SD) index, which is derived from secondary structures, homology and physico-chemical features of protein sequences, reflects the capability of predicting good quality structures with some of the best methodologies available currently. The SD index also helps to assess the plausiblity for developing proteome level structural databases for various organisms.

Ref.: Rahul Kaushik, B. Jayaram "Structural difficulty index: A reliable measure for modelability of protein tertiary structures", Protein Engineering Design and Selection, 2016, 29(9), 391-97. doi: 10.1093/protein/gzw025.

20. Plasmodium Vivax Structural Databank (PvaxDB): PvaxDB databank is a dynamic depository of structural information of Plasmodium vivax which includes sequence and structure based annotations.

Ref.: Singh,A., Kaushik,R., Kuntal,H. et al. "PvaxDB: a comprehensive structural repository of Plasmodium vivax proteome". Database, 2018. Vol.2018: doi:10.1093/database/bay021.

21. Plasmodium Vivax P01 Structural Databank: PvP01DB databank is a dynamic repository of structural information of Plasmodium vivax P01 which includes sequence and structure-based annotations.

Ref.: Ankita Singh, Rahul Kaushik, Dheeraj Kumar Chaurasia, Manpreet Singh, B Jayaram "PvP01-DB: computational structural and functional characterization of soluble proteome of PvP01 strain of Plasmodium vivax", Database , Volume 2020, 2020. https://doi.org/10.1093/database/baaa036

22. Sequence 2 Function: Seq2Func is an efficient and novel approach to predict protein function from its sequence, which uses the structural-chemical properties of amino acids in place of conventional classifications of the building blocks of proteins. Seq2Func uses NCL+mask BLAST methodology (New Chemical Logic for amino acid properties implemented with maskBLAST) to annotate proteins in terms of Gene Ontology.

Ref.: P. Amita; R. Toran; E. Avinash; B. Jayaram; "MASK BLAST WITH A NEW CHEMICAL LOGIC OF AMINO ACIDS FOR IMPROVED PROTEIN FUNCTION PREDICTION: Protein Function Prediction using New Chemical Logic", Proteins: Structure, Function, and Bioinformatics , 2021. https://doi.org/10.1002/prot.26069

Rahul Kaushik, Ankita Singh and B. Jayaram. "Where informatics lags chemistry leads".Biochemistry, 2018, 55(5): 503-505. DOI: 10.1021/acs.biochem.7b01073

23. Sequence 2 Enzymes: Seq2Enz method is a new way of assigning enzyme class to a protein sequence using the structural-chemical properties of amino acids in place of conventional classifications of the building blocks of proteins. Seq2Enz uses NCL+mask BLAST methodology (New Chemical Logic for amino acid properties implemented with maskBLAST) for finding a similar enzyme class by scoring the most frequent ones in the hits.

Ref.: Amita Pathak, B.Jayaram, "Seq2Enz: An application of mask BLAST methodology with a new chemical logic of amino acids for improved enzyme function prediction", Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 2021. https://doi.org/10.1016/j.bbapap.2021.140721

24. Protein Function Prediction Tool (S2F): S2F is a refined and improved amalgamation of several softwares for protein function prediction which are based on different sequence-based approaches. The metaserver provides a single platform to the users to get functional insights of a query protein through different sources like DeepGo, PFP, STRING, Eggnog, InterProScan, Pannzer2 and Seq2Func. This way a user will not miss the opportunity of finding possible functions for a protein sequence. S2F provides the maximum GO terms with high confidence to the users.