TY - JOUR AU - Watson, J. D. AU - Laskowski, R. A. AU - Thornton, J. M. PY - 2005 DA - 2005// TI - Predicting protein function from sequence and structural data JO - Curr Opin Struct Biol VL - 15 UR - https://doi.org/10.1016/j.sbi.2005.04.003 DO - 10.1016/j.sbi.2005.04.003 ID - Watson2005 ER - TY - JOUR AU - Krishnadev, O. AU - Srinivasan, N. PY - 2011 DA - 2011// TI - AlignHUSH: alignment of HMMs using structure and hydrophobicity information JO - BMC Bioinformatics VL - 12 UR - https://doi.org/10.1186/1471-2105-12-275 DO - 10.1186/1471-2105-12-275 ID - Krishnadev2011 ER - TY - JOUR AU - Pandit, S. B. AU - Gosar, D. AU - Abhiman, S. AU - Sujatha, S. AU - Dixit, S. S. AU - Mhatre, N. S. PY - 2002 DA - 2002// TI - SUPFAM--a database of potential protein superfamily relationships derived by comparing sequence-based and structure-based families: implications for structural genomics and function annotation in genomes JO - Nucleic Acids Res VL - 30 UR - https://doi.org/10.1093/nar/30.1.289 DO - 10.1093/nar/30.1.289 ID - Pandit2002 ER - TY - JOUR AU - Pandit, S. B. AU - Bhadra, R. AU - Gowri, V. S. AU - Balaji, S. AU - Anand, B. AU - Srinivasan, N. PY - 2004 DA - 2004// TI - SUPFAM: a database of sequence superfamilies of protein domains JO - BMC Bioinformatics VL - 5 UR - https://doi.org/10.1186/1471-2105-5-28 DO - 10.1186/1471-2105-5-28 ID - Pandit2004 ER - TY - JOUR AU - Sinha, S. C. AU - Sprang, S. R. PY - 2006 DA - 2006// TI - Structures, mechanism, regulation and evolution of class III nucleotidyl cyclases JO - Rev Physiol Biochem Pharmacol VL - 157 ID - Sinha2006 ER - TY - JOUR AU - Tesmer, J. J. AU - Sprang, S. R. PY - 1998 DA - 1998// TI - The structure, catalytic mechanism and regulation of adenylyl cyclase JO - Curr Opin Struct Biol VL - 8 UR - https://doi.org/10.1016/S0959-440X(98)80090-0 DO - 10.1016/S0959-440X(98)80090-0 ID - Tesmer1998 ER - TY - JOUR AU - Tesmer, J. J. AU - Sunahara, R. K. AU - Gilman, A. G. AU - Sprang, S. R. PY - 1997 DA - 1997// TI - Crystal structure of the catalytic domains of adenylyl cyclase in a complex with Gsalpha.GTPgammaS JO - Science VL - 278 UR - https://doi.org/10.1126/science.278.5345.1907 DO - 10.1126/science.278.5345.1907 ID - Tesmer1997 ER - TY - JOUR AU - Shenoy, A. R. AU - Visweswariah, S. S. PY - 2006 DA - 2006// TI - Mycobacterial adenylyl cyclases: biochemical diversity and structural plasticity JO - FEBS Lett VL - 580 UR - https://doi.org/10.1016/j.febslet.2006.05.034 DO - 10.1016/j.febslet.2006.05.034 ID - Shenoy2006 ER - TY - JOUR AU - Shenoy, A. R. AU - Sivakumar, K. AU - Krupa, A. AU - Srinivasan, N. AU - Visweswariah, S. S. PY - 2004 DA - 2004// TI - A survey of nucleotide cyclases in actinobacteria: unique domain organization and expansion of the class III cyclase family in Mycobacterium tuberculosis JO - Comp Funct Genomics VL - 5 UR - https://doi.org/10.1002/cfg.349 DO - 10.1002/cfg.349 ID - Shenoy2004 ER - TY - JOUR AU - Ramakrishnan, G. AU - Ochoa-Montano, B. AU - Raghavender, U. S. AU - Mudgal, R. AU - Joshi, A. G. AU - Chandra, N. R. PY - 2015 DA - 2015// TI - Enriching the annotation of Mycobacterium tuberculosis H37Rv proteome using remote homology detection approaches: insights into structure and function JO - Tuberculosis (Edinb) VL - 95 UR - https://doi.org/10.1016/j.tube.2014.10.009 DO - 10.1016/j.tube.2014.10.009 ID - Ramakrishnan2015 ER - TY - JOUR AU - Kelley, L. A. AU - Mezulis, S. AU - Yates, C. M. AU - Wass, M. N. AU - Sternberg, M. J. PY - 2015 DA - 2015// TI - The Phyre2 web portal for protein modeling, prediction and analysis JO - Nat Protoc VL - 10 UR - https://doi.org/10.1038/nprot.2015.053 DO - 10.1038/nprot.2015.053 ID - Kelley2015 ER - TY - JOUR AU - Mitchell, A. AU - Chang, H. Y. AU - Daugherty, L. AU - Fraser, M. AU - Hunter, S. AU - Lopez, R. PY - 2015 DA - 2015// TI - The InterPro protein families database: the classification resource after 15 years JO - Nucleic Acids Res VL - 43 UR - https://doi.org/10.1093/nar/gku1243 DO - 10.1093/nar/gku1243 ID - Mitchell2015 ER - TY - JOUR AU - Rauch, A. AU - Leipelt, M. AU - Russwurm, M. AU - Steegborn, C. PY - 2008 DA - 2008// TI - Crystal structure of the guanylyl cyclase Cya2 JO - Proc Natl Acad Sci U S A VL - 105 UR - https://doi.org/10.1073/pnas.0808473105 DO - 10.1073/pnas.0808473105 ID - Rauch2008 ER - TY - JOUR AU - Shenoy, A. R. AU - Srinivasan, N. AU - Subramaniam, M. AU - Visweswariah, S. S. PY - 2003 DA - 2003// TI - Mutational analysis of the Mycobacterium tuberculosis Rv1625c adenylyl cyclase: residues that confer nucleotide specificity contribute to dimerization JO - FEBS Lett VL - 545 UR - https://doi.org/10.1016/S0014-5793(03)00580-5 DO - 10.1016/S0014-5793(03)00580-5 ID - Shenoy2003 ER - TY - JOUR AU - Ketkar, A. D. AU - Shenoy, A. R. AU - Ramagopal, U. A. AU - Visweswariah, S. S. AU - Suguna, K. PY - 2006 DA - 2006// TI - A structural basis for the role of nucleotide specifying residues in regulating the oligomerization of the Rv1625c adenylyl cyclase from M. tuberculosis JO - J Mol Biol VL - 356 UR - https://doi.org/10.1016/j.jmb.2005.12.017 DO - 10.1016/j.jmb.2005.12.017 ID - Ketkar2006 ER - TY - JOUR AU - Overbeek, R. AU - Fonstein, M. AU - D'Souza, M. AU - Pusch, G. D. AU - Maltsev, N. PY - 1999 DA - 1999// TI - The use of gene clusters to infer functional coupling JO - Proc Natl Acad Sci U S A VL - 96 UR - https://doi.org/10.1073/pnas.96.6.2896 DO - 10.1073/pnas.96.6.2896 ID - Overbeek1999 ER - TY - JOUR AU - Date, S. V. PY - 2008 DA - 2008// TI - The Rosetta stone method JO - Methods Mol Biol VL - 453 UR - https://doi.org/10.1007/978-1-60327-429-6_7 DO - 10.1007/978-1-60327-429-6_7 ID - Date2008 ER - TY - JOUR AU - Finn, R. D. AU - Bateman, A. AU - Clements, J. AU - Coggill, P. AU - Eberhardt, R. Y. AU - Eddy, S. R. PY - 2014 DA - 2014// TI - Pfam: the protein families database JO - Nucleic Acids Res VL - 42 UR - https://doi.org/10.1093/nar/gkt1223 DO - 10.1093/nar/gkt1223 ID - Finn2014 ER - TY - JOUR AU - Tatusova, T. AU - Ciufo, S. AU - Federhen, S. AU - Fedorov, B. AU - McVeigh, R. AU - O'Neill, K. PY - 2015 DA - 2015// TI - Update on RefSeq microbial genomes resources JO - Nucleic Acids Res VL - 43 UR - https://doi.org/10.1093/nar/gku1062 DO - 10.1093/nar/gku1062 ID - Tatusova2015 ER - TY - JOUR AU - Kersey, P. J. AU - Allen, J. E. AU - Christensen, M. AU - Davis, P. AU - Falin, L. J. AU - Grabmueller, C. PY - 2014 DA - 2014// TI - Ensembl Genomes 2013: scaling up access to genome-wide data JO - Nucleic Acids Res VL - 42 UR - https://doi.org/10.1093/nar/gkt979 DO - 10.1093/nar/gkt979 ID - Kersey2014 ER - TY - JOUR AU - Lew, J. M. AU - Kapopoulou, A. AU - Jones, L. M. AU - Cole, T. PY - 2011 DA - 2011// TI - TubercuList--10 years after JO - Tuberculosis (Edinb) VL - 91 UR - https://doi.org/10.1016/j.tube.2010.09.008 DO - 10.1016/j.tube.2010.09.008 ID - Lew2011 ER - TY - JOUR AU - UniProt, C. PY - 2015 DA - 2015// TI - UniProt: a hub for protein information JO - Nucleic Acids Res VL - 43 ID - UniProt2015 ER - TY - JOUR AU - Eddy, S. R. PY - 2011 DA - 2011// TI - Accelerated Profile HMM Searches JO - PLoS Comput Biol VL - 7 UR - https://doi.org/10.1371/journal.pcbi.1002195 DO - 10.1371/journal.pcbi.1002195 ID - Eddy2011 ER - TY - JOUR AU - Pei, J. AU - Kim, B. H. AU - Grishin, N. V. PY - 2008 DA - 2008// TI - PROMALS3D: a tool for multiple protein sequence and structure alignments JO - Nucleic Acids Res VL - 36 UR - https://doi.org/10.1093/nar/gkn072 DO - 10.1093/nar/gkn072 ID - Pei2008 ER - TY - JOUR AU - Edgar, R. C. PY - 2004 DA - 2004// TI - MUSCLE: multiple sequence alignment with high accuracy and high throughput JO - Nucleic Acids Res VL - 32 UR - https://doi.org/10.1093/nar/gkh340 DO - 10.1093/nar/gkh340 ID - Edgar2004 ER - TY - JOUR AU - Tamura, K. AU - Stecher, G. AU - Peterson, D. AU - Filipski, A. AU - Kumar, S. PY - 2013 DA - 2013// TI - MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. JO - Mol Biol Evol VL - 30 UR - https://doi.org/10.1093/molbev/mst197 DO - 10.1093/molbev/mst197 ID - Tamura2013 ER - TY - JOUR AU - Krogh, A. AU - Larsson, B. AU - Heijne, G. AU - Sonnhammer, E. L. PY - 2001 DA - 2001// TI - Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes JO - J Mol Biol VL - 305 UR - https://doi.org/10.1006/jmbi.2000.4315 DO - 10.1006/jmbi.2000.4315 ID - Krogh2001 ER - TY - JOUR AU - Petersen, T. N. AU - Brunak, S. AU - Heijne, G. AU - Nielsen, H. PY - 2011 DA - 2011// TI - SignalP 4.0: discriminating signal peptides from transmembrane regions JO - Nat Methods VL - 8 UR - https://doi.org/10.1038/nmeth.1701 DO - 10.1038/nmeth.1701 ID - Petersen2011 ER - TY - JOUR AU - Bennett-Lovsey, R. M. AU - Herbert, A. D. AU - Sternberg, M. J. AU - Kelley, L. A. PY - 2008 DA - 2008// TI - Exploring the extremes of sequence/structure space with ensemble fold recognition in the program Phyre JO - Proteins VL - 70 UR - https://doi.org/10.1002/prot.21688 DO - 10.1002/prot.21688 ID - Bennett-Lovsey2008 ER - TY - JOUR AU - Sali, A. AU - Blundell, T. L. PY - 1993 DA - 1993// TI - Comparative protein modelling by satisfaction of spatial restraints JO - J Mol Biol VL - 234 UR - https://doi.org/10.1006/jmbi.1993.1626 DO - 10.1006/jmbi.1993.1626 ID - Sali1993 ER - TY - JOUR AU - Pronk, S. AU - Pall, S. AU - Schulz, R. AU - Larsson, P. AU - Bjelkmar, P. AU - Apostolov, R. PY - 2013 DA - 2013// TI - GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit JO - Bioinformatics VL - 29 UR - https://doi.org/10.1093/bioinformatics/btt055 DO - 10.1093/bioinformatics/btt055 ID - Pronk2013 ER - TY - JOUR AU - Kanehisa, M. AU - Goto, S. AU - Sato, Y. AU - Kawashima, M. AU - Furumichi, M. AU - Tanabe, M. PY - 2014 DA - 2014// TI - Data, information, knowledge and principle: back to metabolism in KEGG JO - Nucleic Acids Res VL - 42 UR - https://doi.org/10.1093/nar/gkt1076 DO - 10.1093/nar/gkt1076 ID - Kanehisa2014 ER - TY - JOUR AU - Punta, M. AU - Coggill, P. C. AU - Eberhardt, R. Y. AU - Mistry, J. AU - Tate, J. AU - Boursnell, C. PY - 2012 DA - 2012// TI - The Pfam protein families database JO - Nucleic Acids Res VL - 40 UR - https://doi.org/10.1093/nar/gkr1065 DO - 10.1093/nar/gkr1065 ID - Punta2012 ER - TY - JOUR AU - Robert, X. AU - Gouet, P. PY - 2014 DA - 2014// TI - Deciphering key features in protein structures with the new ENDscript server JO - Nucleic Acids Res VL - 42 UR - https://doi.org/10.1093/nar/gku316 DO - 10.1093/nar/gku316 ID - Robert2014 ER - TY - STD TI - The PyMOL Molecular Graphics System, Version 1.4.1. Schrodinger, LLC. https://www.pymol.org. UR - https://www.pymol.org ID - ref35 ER -