M4T: a Comparative Protein Structure Modeling Server

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2007 May 23

PMID 17517764

Citations 66

Authors

Narcis Fernandez-Fuentes

Carlos J Madrid-Aliste

Brajesh Kumar Rai

J Eduardo Fajardo

Andras Fiser

Affiliations

Soon will be listed here.

Abstract

Multiple Mapping Method with Multiple Templates (M4T) (http://www.fiserlab.org/servers/m4t) is a fully automated comparative protein structure modeling server. The novelty of M4T resides in two of its major modules, Multiple Templates (MT) and Multiple Mapping Method (MMM). The MT module of M4T selects and optimally combines the sequences of multiple template structures through an iterative clustering approach that takes into account the 'unique' contribution of each template, its sequence similarity to other template sequences and to the target sequences, and the quality of its experimental resolution. MMM module is a sequence-to-structure alignment method that is aimed at improving the alignment accuracy, especially at lower sequence identity levels. The current implementation of MMM takes inputs from three profile-to-profile-based alignment methods and iteratively compares and ranks alternatively aligned regions according to their fit in the structural environment of the template structure. The performance of M4T was benchmarked on CASP6 comparative modeling target sequences and on a larger independent test set and showed a favorable performance to current state-of-the-art methods.

Citing Articles

Prostruc: an open-source tool for 3D structure prediction using homology modeling.

Pawar S, Banini W, Shamsuddeen M, Jumah T, Dolling N, Tiamiyu A Front Chem. 2024; 12:1509407.

PMID: 39717221 PMC: 11664737. DOI: 10.3389/fchem.2024.1509407.

Biochemical characterisation of a PL24 ulvan lyase from seaweed-associated sp. FNV38.

Rodrigues V, Jouanneau D, Fernandez-Fuentes N, Onime L, Huws S, Odaneth A J Appl Phycol. 2024; 36(2):697-711.

PMID: 38765689 PMC: 11101340. DOI: 10.1007/s10811-023-03136-3.

Functional assessment of AtPAP17; encoding a purple acid phosphatase involved in phosphate metabolism in Arabidopsis thaliana.

Jamali Langeroudi A, Sabet M, Jalali-Javaran M, Zamani K, Lohrasebi T, Malboobi M Biotechnol Lett. 2023; 45(5-6):719-739.

PMID: 37074554 DOI: 10.1007/s10529-023-03375-x.

Contact-Assisted Threading in Low-Homology Protein Modeling.

Bhattacharya S, Roche R, Shuvo M, Moussad B, Bhattacharya D Methods Mol Biol. 2023; 2627:41-59.

PMID: 36959441 PMC: 10340115. DOI: 10.1007/978-1-0716-2974-1_3.

HS-Generating Cytosolic L-Cysteine Desulfhydrase and Mitochondrial D-Cysteine Desulfhydrase from Sweet Pepper ( L.) Are Regulated During Fruit Ripening and by Nitric Oxide.

Munoz-Vargas M, Lopez-Jaramillo J, Gonzalez-Gordo S, Paradela A, Palma J, Corpas F Antioxid Redox Signal. 2023; 39(1-3):2-18.

PMID: 36950799 PMC: 10585658. DOI: 10.1089/ars.2022.0222.

References

Fiser A, Sali A . Modeller: generation and refinement of homology-based protein structure models. Methods Enzymol. 2003; 374:461-91. DOI: 10.1016/S0076-6879(03)74020-8. View

Shen M, Sali A . Statistical potential for assessment and prediction of protein structures. Protein Sci. 2006; 15(11):2507-24. PMC: 2242414. DOI: 10.1110/ps.062416606. View

Berman H, Westbrook J, Feng Z, Gilliland G, Bhat T, Weissig H . The Protein Data Bank. Nucleic Acids Res. 1999; 28(1):235-42. PMC: 102472. DOI: 10.1093/nar/28.1.235. View

McGuffin L, Bryson K, Jones D . The PSIPRED protein structure prediction server. Bioinformatics. 2000; 16(4):404-5. DOI: 10.1093/bioinformatics/16.4.404. View

Stuart A, Fiser A, Sanchez R, Melo F, Sali A . Comparative protein structure modeling of genes and genomes. Annu Rev Biophys Biomol Struct. 2000; 29:291-325. DOI: 10.1146/annurev.biophys.29.1.291. View

Li W, Pio F, Pawlowski K, Godzik A . Saturated BLAST: an automated multiple intermediate sequence search used to detect distant homology. Bioinformatics. 2001; 16(12):1105-10. DOI: 10.1093/bioinformatics/16.12.1105. View

Shi J, Blundell T, Mizuguchi K . FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J Mol Biol. 2001; 310(1):243-57. DOI: 10.1006/jmbi.2001.4762. View

Baker D, Sali A . Protein structure prediction and structural genomics. Science. 2001; 294(5540):93-6. DOI: 10.1126/science.1065659. View

Li W, Jaroszewski L, Godzik A . Tolerating some redundancy significantly speeds up clustering of large protein databases. Bioinformatics. 2002; 18(1):77-82. DOI: 10.1093/bioinformatics/18.1.77. View

10.

Marti-Renom M, Madhusudhan M, Fiser A, Rost B, Sali A . Reliability of assessment of protein structure prediction methods. Structure. 2002; 10(3):435-40. DOI: 10.1016/s0969-2126(02)00731-1. View

11.

Boeckmann B, Bairoch A, Apweiler R, Blatter M, Estreicher A, Gasteiger E . The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res. 2003; 31(1):365-70. PMC: 165542. DOI: 10.1093/nar/gkg095. View

12.

Contreras-Moreira B, Fitzjohn P, Bates P . In silico protein recombination: enhancing template and sequence alignment selection for comparative protein modelling. J Mol Biol. 2003; 328(3):593-608. DOI: 10.1016/s0022-2836(03)00309-7. View

13.

Zemla A . LGA: A method for finding 3D similarities in protein structures. Nucleic Acids Res. 2003; 31(13):3370-4. PMC: 168977. DOI: 10.1093/nar/gkg571. View

14.

Prasad J, Comeau S, Vajda S, Camacho C . Consensus alignment for reliable framework prediction in homology modeling. Bioinformatics. 2003; 19(13):1682-91. DOI: 10.1093/bioinformatics/btg211. View

15.

Venclovas C, Zemla A, Fidelis K, Moult J . Assessment of progress over the CASP experiments. Proteins. 2003; 53 Suppl 6:585-95. DOI: 10.1002/prot.10530. View

16.

Sali A, Blundell T . Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol. 1993; 234(3):779-815. DOI: 10.1006/jmbi.1993.1626. View

17.

Sippl M . Recognition of errors in three-dimensional structures of proteins. Proteins. 1993; 17(4):355-62. DOI: 10.1002/prot.340170404. View

18.

Thompson J, Higgins D, Gibson T . CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994; 22(22):4673-80. PMC: 308517. DOI: 10.1093/nar/22.22.4673. View

19.

Altschul S, Madden T, Schaffer A, Zhang J, Zhang Z, Miller W . Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997; 25(17):3389-402. PMC: 146917. DOI: 10.1093/nar/25.17.3389. View

20.

Sanchez R, Sali A . Evaluation of comparative protein structure modeling by MODELLER-3. Proteins. 1997; Suppl 1:50-8. DOI: 10.1002/(sici)1097-0134(1997)1+<50::aid-prot8>3.3.co;2-w. View