Search Results - "Swindells, MB"

CATH – a hierarchic classification of protein domain structures by Orengo, CA, Michie, AD, Jones, S, Jones, DT, Swindells, MB, Thornton, JM

“…Background: Protein evolution gives rise to families of structurally related proteins, within which sequence identities can be extremely low. As a result,…”
Get full text

Getting the most from PSI–BLAST by Jones, David T, Swindells, Mark B

“…Most biologists now conduct sequence searches as a matter of course. But how do we know that a relationship predicted by a homology search is a true, rather…”
Get full text

Combining sensitive database searches with multiple intermediates to detect distant homologues by Salamov, Asaf A., Suwa, Makiko, Orengo, Christine A., Swindells, Mark B.

“…Using data from the CATH structure classification, we have assessed the blastp, fasta, smith–waterman and gapped-blast algorithms, developed a portable…”
Get full text

Diversity of conformational states and changes within the EF-hand protein superfamily by Yap, Kyoko L., Ames, James B., Swindells, Mark B., Ikura, Mitsuhiko

“…The EF‐hand motif, which assumes a helix‐loop‐helix structure normally responsible for Ca2+ binding, is found in a large number of functionally diverse Ca2+…”
Get full text

Protein clefts in molecular recognition and function by Laskowski, R A, Luscombe, N M, Swindells, M B, Thornton, J M

“…One of the primary factors determining how proteins interact with other molecules is the size of clefts in the protein's surface. In enzymes, for example, the…”
Get full text

NMR structure of the histidine kinase domain of the E. coli osmosensor EnvZ by Ikura, Mitsuhiko, Tanaka, Toshiyuki, Saha, Soumitra K, Tomomori, Chieri, Ishima, Rieko, Liu, Dingjiang, Tong, Kit I, Park, Heiyoung, Dutta, Rinku, Qin, Ling, Swindells, Mark B, Yamazaki, Toshimasa, Ono#, Akira M, Kainosho#, Masatsune, Inouye, Masayori

“…Bacteria live in capricious environments, in which they must continuously sense external conditions in order to adjust their shape, motility and physiology…”
Get full text

Effective Function Annotation through Catalytic Residue Conservation by George, Richard A., Spriggs, Ruth V., Bartlett, Gail J., Gutteridge, Alex, MacArthur, Malcolm W., Porter, Craig T., Al-Lazikani, Bissan, Thornton, Janet M., Swindells, Mark B.

“…Because of the extreme impact of genome sequencing projects, protein sequences without accompanying experimental data now dominate public databases. Homology…”
Get full text

Assessing protein coding region integrity in cDNA sequencing projects by Salamov, A.A, Nishikawa, T, Swindells, M.B

“…In cDNA sequencing projects, it is vital to know whether the protein coding region of a sequence is complete, or whether errors have occurred during library…”
Get full text

Solution structure of Calmodulin-W-7 complex: the basis of diversity in molecular recognition by Osawa, Masanori, Swindells, Mark B, Tanikawa, Jun, Tanaka, Toshiyuki, Mase, Toshiyasu, Furuya, Toshio, Ikura, Mitsuhiko

“…The solution structure of calcium-bound calmodulin (CaM) complexed with an antagonist, N-(6-aminohexyl)-5-chloro-1-naphthalenesulfonamide (W-7), has been…”
Get full text

A novel target recognition revealed by calmodulin in complex with Ca2+-calmodulin-dependent kinase kinase by Osawa, M, Tokumitsu, H, Swindells, M B, Kurihara, H, Orita, M, Shibanuma, T, Furuya, T, Ikura, M

“…The structure of calcium-bound calmodulin (Ca2+/CaM) complexed with a 26-residue peptide, corresponding to the CaM-binding domain of rat Ca2+/CaM-dependent…”
Get full text

Domain assignment for protein structures using a consensus approach: Characterization and analysis by Jones, Susan, Stewart, Michael, Michie, Alex, Swindells, Mark B., Orengo, Chirstine, Thornton, Janet M.

“…A consensus approach for the assignment of structural domains in proteins is presented. The approach combines a number of previously published algorithms, and…”
Get full text

A procedure for detecting structural domains in proteins by Swindells, Mark B.

“…A procedure is described for detecting domains in proteins of known structure. The method is based on the intuitively simple idea that each domain should…”
Get full text

Prioritizing the proteome: identifying pharmaceutically relevant targets by Swindells, Mark B, Overington, John P

“…Considerable attention is now being placed on prioritizing the proteome as the point of delivery for genomic information. Some of the challenges faced in…”
Get full text

NMR structure of the Streptomyces metalloproteinase inhibitor, SMPI, isolated from Streptomyces nigrescens TK-23: another example of an ancestral beta gamma-crystallin precursor structure by Ohno, A, Tate, S, Seeram, S S, Hiraga, K, Swindells, M B, Oda, K, Kainosho, M

“…The Streptomyces metalloproteinase inhibitor, SMPI, isolated from Streptomyces nigrescens TK-23, is a proteinaceous metalloproteinase inhibitor, and consists…”
Get full text

A procedure for the automatic determination of hydrophobic cores in protein structures by Swindells, Mark B.

“…An algorithm is described for automatically detecting hydrophobic cores in proteins of known structure. Three pieces of information are considered in order to…”
Get full text

Pre-formation of the semi-open conformation by the apo-calmodulin C-terminal domain and implications for binding IQ-motifs by Swindells, Mark B, Ikura, Mitsuhiko

“…Unanticipated similarities between apo-calmodulin and the myosin essential light chain suggest structural characteristics responsible for IQ-motif binding as…”
Get full text

GENIUS II: a high-throughput database system for linking ORFs in complete genomes to known protein three-dimensional structures by Yabuki, Yukimitsu, Mukai, Yuri, Swindells, Mark B., Suwa, Makiko

“…GENIUS II is an automated database system in which open reading frames (ORFs) in complete genomes are assigned to known protein three-dimensional (3D)…”
Get full text

Intrinsic φ,ψ propensities of amino acids, derived from the coil regions of known structures by Swindells, Mark B, MacArthur, Malcolm W, Thornton, Janet M

“…Many different factors contribute to secondary structure propensities, including phi, psi preferences, side-chain interactions, steric effects and hydrophobic…”
Get full text

Identification of a common fold in the replication terminator protein suggests a possible mode for DNA binding by Swindells, Mark B.

“…Recently, knowledge of how proteins regulate DNA-dependent activities has grown substantially. In particular, the number of DNA-binding-protein structures that…”
Get full text

Contemporary approaches to protein structure classification by Swindells, Mark B., Orengo, Christine A., Jones, David T., Hutchinson, E. Gail, Thornton, Janet M.

“…In a similar manner to sequence database searching, it is also possible to compare three‐dimensional protein structures. Such methods can be extremely useful…”
Get full text