Surprising similarities in structure comparison

Gibrat, Jean‐François; Madej, Thomas; Bryant, Stephen H.

doi:10.1016/s0959-440x(96)80058-3

Cited by 993 publications

(734 citation statements)

References 61 publications

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“…Thus, in Figure 1a-c, the three trypsin-like serine proteases appear to be very similar to each other; this similarity is supported by statistical estimates (E(2775)) from DALI [8] and weakly supported by VAST [9] (Table 1). Structurally, all three trypsin-like serine proteases share the same symmetric β-barrel structure; they have two α helices in similar positions and the structures of the active sites are the same.…”

Section: Homology and Statistical Significance -The Argument From Parmentioning

confidence: 62%

“…Homologs found by different search methods. Box plot of the CATH homolog coverage achieved by 86 query domains from different CATH homologous superfamilies under different error criteria for SSEARCH [54], PSI-BLAST [4], COMPASS [19•], DALI [8] and VAST [9]. The upper and lower edges of the boxes are at the 75th and 25th percentile, respectively, with the upper and lower whiskers at the 90th and 10th percentile.…”

Section: Discussionmentioning

confidence: 99%

“…Nonetheless, profile-profile methods still fail to correctly identify similarities that can be identified through three-dimensional structure alignment ( Figure 3) with programs such as CE [46], DALI [8], Structal [47] and VAST [9]. The magnitude of the difference in performance, however, depends greatly on both the level of selectivity specified and how overall performance is summarized.…”

Section: Progress In Sequence Similarity Searchingmentioning

confidence: 99%

“…DALI [8] performs about as well as PSI-BLAST and provides estimates that are considerably more accurate than other structure alignment methods (Figure 2) [51••]. By contrast, the estimates produced by COMPASS [19•] and VAST [9] cannot be reliably used to identify homologs, because proteins with different topologies (which are very unlikely to share a common ancestor) can have similarities with expectation values many orders of magnitude lower than expected by chance.…”

Section: Evaluating Search Algorithmsmentioning

confidence: 99%

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The limits of protein sequence comparison?

Pearson

Sierk

2005

Current Opinion in Structural Biology

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Modern sequence alignment algorithms are used routinely to identify homologous proteins, proteins that share a common ancestor. Homologous proteins always share similar structures and often have similar functions. Over the past 20 years, sequence comparison has become both more sensitive, largely because of profile-based methods, and more reliable, because of more accurate statistical estimates. As sequence and structure databases become larger, and comparison methods become more powerful, reliable statistical estimates will become even more important for distinguishing similarities that are due to homology from those that are due to analogy (convergence). The newest sequence alignment methods are more sensitive than older methods, but more accurate statistical estimates are needed for their full power to be realized.

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Section: Homology and Statistical Significance -The Argument From Parmentioning

confidence: 62%

Section: Discussionmentioning

confidence: 99%

Section: Progress In Sequence Similarity Searchingmentioning

confidence: 99%

Section: Evaluating Search Algorithmsmentioning

confidence: 99%

See 2 more Smart Citations

The limits of protein sequence comparison?

Pearson

Sierk

2005

Current Opinion in Structural Biology

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“…55 Again, this was based primarily on structural comparison using DALI 56 and VAST, 57 along with the presence of S-adenosyl-L-homocysteine. Methlytransferase have extremely low sequence homology (3-18%), but most methyltransferase bind the cofactor in a similar manner.…”

Section: Functional Annotation Of Hypothetical Proteinsmentioning

confidence: 99%

Comparison of protein active site structures for functional annotation of proteins and drug design

et al. 2006

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Rapid and accurate functional assignment of novel proteins is increasing in importance, given the completion of numerous genome sequencing projects and the vastly expanding list of unannotated proteins. Traditionally, global primary‐sequence and structure comparisons have been used to determine putative function. These approaches, however, do not emphasize similarities in active site configurations that are fundamental to a protein's activity and highly conserved relative to the global and more variable structural features. The Comparison of Protein Active Site Structures (CPASS) database and software enable the comparison of experimentally identified ligand‐binding sites to infer biological function and aid in drug discovery. The CPASS database comprises the ligand‐defined active sites identified in the protein data bank, where the CPASS program compares these ligand‐defined active sites to determine sequence and structural similarity without maintaining sequence connectivity. CPASS will compare any set of ligand‐defined protein active sites, irrespective of the identity of the bound ligand. Proteins 2006. © 2006 Wiley‐Liss, Inc.

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Fold assignments for amino acid sequences of the CASP2 experiment

Rice¹,

Fischer²,

Weiß³

et al. 1997

Proteins

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New and newly extended methods for fold assignment were tested for their abilities to assign folds to amino acid target sequences of unknown three-dimensional structure. These target sequences, released through the CASP2 experiment, are not obviously related to any sequence of known three-dimensional (3D) structure. We assigned 3D folds to target sequences and filed these predictions with CASP2 before their 3D structures were released. The methods tested were . When the 3D structures of the sequences were released, 17 of our predictions were evaluated. Of these 17, we assigned high probabilities to 11, of which 9 were correct. Five of these correct predictions were of known 3D structures similar to the targets and four of these were of new folds. The evaluation demonstrated that our methods were effective in assigning the proper fold to more than half of the CASP2 targets with known folds (5/9) and also were able to detect half of the sequences that corresponded to no known folds (4/8). Even when the correct fold is assigned to a sequence, proper alignment of the sequence to the structure remains a challenge. Our methods were able to produce accurate alignments (F1.2 mean residue shift error from the structural alignment) for four of the targets, including the particularly difficult alignment (only 7% residue identity in the structurally aligned regions) of the ferrochelatase sequence to the fold of a periplasmic binding protein. Proteins, Suppl.

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Surprising similarities in structure comparison

Cited by 993 publications

References 61 publications

The limits of protein sequence comparison?

The limits of protein sequence comparison?

Comparison of protein active site structures for functional annotation of proteins and drug design

Fold assignments for amino acid sequences of the CASP2 experiment

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