A method to search for similar protein local structures at ligand-binding sites and its application to adenine recognition

We have developed a method of searching for similar spatial arrangements of atoms around a given chemical moiety in proteins that bind a common ligand. The first step in this method is to consider a set of atoms that closely surround a given chemical moiety. Then, to compare the spatial arrangements of such surrounding atoms in different proteins, they are translated and rotated so that the chemical moieties are superposed on each other. Spatial arrangements of surrounding atoms in a pair of proteins are judged to be similar, when there are many corresponding atoms occupying similar spatial positions. Because the method focuses on the arrangements of surrounding atoms, it can detect structural similarities of binding sites in proteins that are dissimilar in their amino acid sequences or in their chain folds. We have applied this method to identify modes of nucleotide base recognition by proteins. An all-against-all comparison of the arrangements of atoms surrounding adenine moieties revealed an unexpected structural similarity between protein kinases, cAMP-dependent protein kinase (cAPK), and casein kinase-1 (CK1), and D-Ala:D-Ala ligase (DD-ligase) at their adenine-binding sites, despite a lack of similarity in their chain folds. The similar local structure consists of a four-residue segment and three sequentially separated residues. In particular the four-residue segments of these enzymes were found to have nearly identical conformations in their backbone parts, which are involved in the recognition of adenine. This common local structure was also found in substrate-free three-dimensional structures of other proteins that are similar to DD-ligase in the chain fold and of other protein kinases. As the proteins with different folds were found to share a common local structure, these proteins seem to constitute a remarkable example of convergent evolution for the same recognition mechanism. Received: 9 December 1996 / Accepted: 7 February 1997     

Spind: a package for computing spatially corrected accuracy measures

Using an appropriate accuracy measure is essential for assessing prediction accuracy in species distribution modelling. Therefore, model evaluation as an analytical uncertainty is a challenging problem. Although a variety of accuracy measures for the assessment of prediction errors in presence/absence models is available, there is a lack of spatial accuracy measures, i.e. measures that are sensitive to the spatial arrangement of the predictions. We present ‘spind’, a new software package (based on the R software program) that provides spatial performance measures for grid‐based models. These accuracy measures are generalized, spatially corrected versions of the classical ones, thus enabling comparisons between them. Our method for evaluation consists of the following steps: 1) incorporate additional autocorrelation until spatial autocorrelation in predictions and actuals is balanced, 2) cross‐classify predictions and adjusted actuals in a 4 × 4 contingency table, 3) use a refined weighting pattern for errors, and 4) calculate weighted Kappa, sensitivity, specificity and subsequently ROC, AUC, TSS to get spatially corrected indices. To illustrate the impact of our spatial method we present an example of simulated data as well as an example of presence/absence data of the plant species Dianthus carthusianorum across Germany. Our analysis includes a statistic for the comparison of spatial and classical (non‐spatial) indices. We find that our spatial indices tend to result in higher values than classical ones. These differences are statistically significant at medium and high autocorrelation levels. We conclude that these spatial accuracy measures may contribute to evaluate prediction errors in presence/absence models, especially in case of medium or high degree of similarity of adjacent data, i.e. aggregated (clumped) or continuous species distributions.     

Ignoring spatial effects results in inadequate models for variation in littoral macroinvertebrate diversity

Studies focusing on the effects of spatial processes versus environmental filtering on aquatic metacommunities have so far been focused almost entirely on relatively isolated systems, such as sets of different lakes or streams. In contrast, metacommunity patterns and underlying processes within a single aquatic system have received less attention. In this study, we aimed to examine how strongly variations in different diversity indices are affected by spatial processes (dispersal) versus local environmental conditions (species sorting) within a large lake system. Modern biodiversity research focuses on multiple diversity facets because different indices may be uncorrelated within and between facets, and they may thus describe different phenomena. We investigated the relationship of littoral macroinvertebrate diversity with environmental and spatial factors using 10 indices of species, functional and taxonomic diversity. Using spatial factors as proxies of dispersal, we decomposed variation in diversity indices into fractions attributable to environmental and spatial factors. Our results highlighted generally equal or higher importance of spatial processes in controlling the variation in diversity indices when compared to local environmental variables. Local environmental conditions accounted for higher proportion of variation only in a single index (i.e. taxonomic diversity). These findings suggest that the effects of high dispersal rates (mass effects) may override the influences of local environmental conditions (species sorting) on the diversity in highly‐connected aquatic system, such as large lakes and marine coastal systems. Our results further suggest that biodiversity assessment and environmental monitoring in highly‐connected systems cannot rely solely on the idea of environmental control. We hence recommend that the roles of both environmental and spatial processes should be integrated in basic and applied ecological research of aquatic systems.     

A conceptual framework for the spatial analysis of functional trait diversity

Functional trait diversity is a popular tool in modern ecology, mainly used to infer assembly processes and ecosystem functioning. Patterns of functional trait diversity are shaped by ecological processes such as environmental filtering, species interactions and dispersal that are inherently spatial, and different processes may operate at different spatial scales. Adding a spatial dimension to the analysis of functional trait diversity may thus increase our ability to infer community assembly processes and to predict change in assembly processes following disturbance or land‐use change. Richness, evenness and divergence of functional traits are commonly used indices of functional trait diversity that are known to respond differently to large‐scale filters related to environmental heterogeneity and dispersal and fine‐scale filters related to species interactions (competition). Recent developments in spatial statistics make it possible to separately quantify large‐scale patterns (variation in local means) and fine‐scale patterns (variation around local means) by decomposing overall spatial autocorrelation quantified by Moran's coefficient into its positive and negative components using Moran eigenvector maps (MEM). We thus propose to identify the spatial signature of multiple ecological processes that are potentially acting at different spatial scales by contrasting positive and negative components of spatial autocorrelation for each of the three indices of functional trait diversity. We illustrate this approach with a case study from riparian plant communities, where we test the effects of disturbance on spatial patterns of functional trait diversity. The fine‐scale pattern of all three indices was increased in the disturbed versus control habitat, suggesting an increase in local scale competition and an overall increase in unexplained variance in the post‐disturbance versus control community. Further research using simulation modeling should focus on establishing the proposed link between community assembly rules and spatial patterns of functional trait diversity to maximize our ability to infer multiple processes from spatial community structure.     

Decay of similarity of gamasid mite assemblages parasitic on Palaearctic small mammals: geographic distance, host-species composition or environment

Aim The similarity between parasite assemblages should decrease with increasing geographic distance between them, increasing dissimilarity in environmental conditions, and/or increasing dissimilarity of the local host fauna, depending on the dispersal abilities of the parasites and the intimacy of their associations with the host. We tested for a decay in the similarity of gamasid mite assemblages parasitic on small mammals with increasing geographic, ‘environmental’ and ‘host faunal’ (= ‘host’) distances. Location We used data on assemblages of haematophagous gamasid mites (superfamily Dermanyssoidea) parasitic on small mammals (Insectivora, Lagomorpha and Rodentia) from 26 different regions of the northern Palaearctic. Methods Similarity in mite assemblages was investigated at the compound community level across all regions, and at the component community level, across populations of the same host species for each of 11 common host species. Similarity between pairs of mite communities was estimated using both the Jaccard and the Sorensen indices. Environmental distance was estimated as the dissimilarity between locations in a composite measure of climatic variables, and host faunal distance was simply taken as the reciprocal of indices of similarity between the composition of host faunas in different locations. Generalized Linear Models (GLM) and Akaike's Information Criterion were used to select the best model of decay in similarity as a function of geographic, ‘environmental’ and ‘host faunal’ distances. Results Overall, despite slight differences among host species, the similarity in mite assemblages decreased with both increasing ‘environmental’ distance and increasing ‘host faunal’ distance, but was generally unaffected by geographic distance between regions. The similarity of component communities of gamasid mites among host populations was determined mainly by similarity in the physical environment, whereas that of compound communities varied mainly with host‐species composition. Main conclusions Our results indicate that the general decay in community similarity with increasing geographic distances does not apply to assemblages of gamasid mites; it is possible that they can overcome great distances by means of passive dispersal (either by phoresy or wind‐borne), or more likely they occur wherever their hosts are found as a result of tight cospeciation in the past. Mite assemblages on small mammalian hosts seem to be affected mainly by local environmental conditions, and, to a much lesser extent, by the species composition of local host communities.     

A truce with neutral theory: local deterministic factors, species traits and dispersal limitation together determine patterns of diversity in stream invertebrates

1. Studies seeking to explain local patterns of diversity have typically relied on niche explanations, reflected in correlations with local environmental conditions, or neutral theory, invoking dispersal processes and speciation. 2. We used macroinvertebrate community data from 10 streams that varied independently in local ecological conditions and spatial proximity. Neutral theory predicts that similarity in communities will be negatively associated with distance between sites, while niche theory suggests that community similarity will be positively associated with similarity in local ecological conditions. 3. Similarity in total invertebrate, grazer and predator assemblages showed negative relationships with distance and, for grazers and predators, positive relationships with local ecological conditions. However, the best model predicting community similarity in all three cases included aspects of both local ecological conditions and distance between sites. 4. When assemblages were analysed according to dispersal ability, high-dispersal species were shown to be freely accessing all sites and community similarity was not well predicted by either local ecology or spatial separation. Assemblages of species with low and moderate dispersal ability were best predicted by combined models, including distance between sites and local ecological factors. 5. The results suggest that the perceived dichotomy between neutral and local environmental processes in determining local patterns of diversity may not be useful. Neutral and niche processes structured these communities differentially depending on trophic level and species traits. 6. We emphasize the potential for both dispersal processes and local environmental conditions to explain local patterns of diversity.     

Bioassessment in a metacommunity context: Are diatom communities structured solely by species sorting?

Aquatic ecosystems face a variety of anthropogenic pressures, urging the development of efficient biological indicators. In addition to local environmental conditions, the community structure of indicator organisms is affected by spatial processes, such as high and limited dispersal rates. Understanding the relative roles of environmental factors and spatial processes for ecological communities should thus be associated with bioassessment practices. We examined the main drivers, both environmental and spatial, influencing community structure and several indices derived from diatom communities. We sampled 81 stony littoral sites in a large boreal lake system (305 km²), where relatively large gradients in water chemistry (35 variables measured) exist, but no dispersal limitation can be expected. Instead, high dispersal rates should interfere with species sorting. Our response variables, including commonly-used diatom indices, diversity indices and taxonomic distinctness indices, were better explained by pure effects of spatial variables and shared effects of spatial and environmental variables than by pure effects of environmental variables. Thus, high dispersal rates between sites are likely to interfere with environmental filtering and can result in clear spatial structures in index values used in bioassessment. Bioassessment should thus acknowledge the importance of spatial processes and not take it for granted that only local environmental conditions determine index values. Failure to consider high dispersal rates may lead to biased information about the state of freshwater ecosystems. The same idea should also be considered in systems with similarly highly-connected sets of bioassessment sites, such as marine coastal systems and stream networks.     

Similarities and differences of gene expression in yeast stress conditions

MOTIVATION AND METHODS: All living organisms and the survival of all cells critically depend on their ability to sense and quickly adapt to changes in the environment and to other stress conditions. We study stress response mechanisms in Saccharomyces cerevisiae by identifying genes that, according to very stringent criteria, have persistent co-expression under a variety of stress conditions. This is enabled through a fast clique search method applied to the intersection of several co-expression graphs calculated over the data of Gasch et al. This method exploits the topological characteristics of these graphs. RESULTS: We observe cliques in the intersection graphs that are much larger than expected under a null model of changing gene identities for different stress conditions but maintaining the co-expression topology within each one. Persistent cliques are analyzed to identify enriched function as well as enriched regulation by a small number of TFs. These TFs, therefore, characterize a universal and persistent reaction to stress response. We further demonstrate that the vertices (genes) of many cliques in the intersection graphs are co-localized in the yeast genome, to a degree far beyond the random expectation. Co-localization can hypothetically contribute to a quick co-ordinated response. We propose the use of persistent cliques in further study of properties of co-regulation.     

Contrasting patterns and mechanisms of spatial turnover for native and exotic freshwater fish in Europe

Aim We compare the distribution patterns of native and exotic freshwater fish in Europe, and test whether the same mechanisms (environmental filtering and/or dispersal limitation) govern patterns of decrease in similarity of native and exotic species composition over geographical distance (spatial species turnover). Locations Major river basins of Europe. Methods Data related to geography, habitat diversity, regional climate and species composition of native and exotic freshwater fish were collated for 26 major European river basins. We explored the degree of nestedness in native and exotic species composition, and quantified compositional similarity between river basins according to the beta‐sim (independent of richness gradient) and Jaccard (dependent of richness gradient) indices of similarity. Multiple regression on distance matrices and variation‐partitioning approaches were used to quantify the relative roles of environmental filtering and dispersal limitation in shaping patterns of decreasing compositional similarity over geographical distance. Results Native and exotic species exhibited significant nested patterns of species composition, indicating that differences in fish species composition between river basins are primarily the result of species loss, rather than species replacement. Both native and exotic compositional similarity decreased significantly with increasing geographical distance between river basins. However, gradual changes in species composition with geographical distance were found only for exotic species. In addition, exotic species displayed a higher rate of similarity decay (higher species turnover rate) with geographical distance, compared with native species. Lastly, the majority of explained variation in exotic compositional similarity was uniquely related to geography, whereas native compositional similarity was either uniquely explained by geography or jointly explained by environment and geography. Main conclusions Our study suggests that large‐scale patterns of spatial turnover for exotic freshwater fish in Europe are generated by human‐mediated dispersal limitation, whereas patterns of spatial turnover for native fish result from both dispersal limitation relative to historical events (isolation by mountain ranges, glacial history) and environmental filtering.     

Modelling plant species distribution in alpine grasslands using airborne imaging spectroscopy

Remote sensing using airborne imaging spectroscopy (AIS) is known to retrieve fundamental optical properties of ecosystems. However, the value of these properties for predicting plant species distribution remains unclear. Here, we assess whether such data can add value to topographic variables for predicting plant distributions in French and Swiss alpine grasslands. We fitted statistical models with high spectral and spatial resolution reflectance data and tested four optical indices sensitive to leaf chlorophyll content, leaf water content and leaf area index. We found moderate added-value of AIS data for predicting alpine plant species distribution. Contrary to expectations, differences between species distribution models (SDMs) were not linked to their local abundance or phylogenetic/functional similarity. Moreover, spectral signatures of species were found to be partly site-specific. We discuss current limits of AIS-based SDMs, highlighting issues of scale and informational content of AIS data.     

Forest community analysis and the point-centered quarter method

The point-centered-quarter (PCQ) method has been applied in community analysis since the publication of the method nearly 50 years ago. This and other distance methods offer increased sampling efficiency over fixed-area plots (FAP), but have long been known to produce biased density estimates when plant distribution deviates from random spatial patterns. Spatial indices have been developed to quantify the direction of this bias when plant distributions are aggregated or evenly distributed. Its continued use, especially in community analysis, requires additional scrutiny in measurements of community structure. We measured 14 forest stands of varying age, elevation and disturbance regime using FAP and PCQ methods. Density estimates were biased, with the point-centered quarter method lower than fixed-area plot estimates when stems were aggregated and higher when stems were evenly spaced. In general the PCQ method underestimated species richness. The efficiency of the PCQ method makes it popular for ordination studies, although comparison of community structure varied from 18% to 90% similarity between the measurements of species basal area in the same stands using the two different methods. The bias observed in calculations of stem density, species abundance and community similarity indicate that use of the PCQ method should be approached with caution when used in community level analysis.     

上海市绿化植物中四种常见刺蛾的生态位及其种间竞争

为明确上海城市绿化植物中常见刺蛾的种间关系,定量研究了黄刺蛾、桑褐刺蛾、丽绿刺蛾及褐边绿刺蛾在营养、时间、空间资源序列上的生态位指数。结果表明:褐边绿刺蛾比其它刺蛾能较广泛地利用寄主资源,生态位宽度指数为0.5447;黄刺蛾、桑褐刺蛾在时间序列上占有较大优势,生态位宽度指数分别为0.4304和0.4415;而黄刺蛾的茧则在空间资源利用中优于其它刺蛾,生态位宽度指数为0.5441。在种间,桑褐刺蛾与丽绿刺蛾利用营养资源较为接近,其生态位重叠指数(2.6647)、生态位相似比例(0.5199)和种间竞争系数(0.7015)均高于其它共存种类;黄刺蛾和桑褐刺蛾利用时间资源较相似,生态位相似比例和种间竞争系数分别为0.4846、0.5222;而桑褐刺蛾和褐边绿刺蛾则在空间资源利用中较为接近,其生态位重叠指数(2.7495)、生态位相似比例(0.9165)和种间竞争系数(0.9959)在共存种间均为最高。     

'Gatherings' of social grooming among wild chimpanzees: implications for evolution of sociality

Chimpanzees (Pan troglodytes) often groom in gatherings that cannot simply be divided into unilateral dyadic grooming interactions. This feature of grooming is studied at two different levels: grooming cliques and grooming clusters. Grooming cliques are defined as directly connected configurations of grooming interactions at any given moment, and when any member of a clique successively grooms any member of another clique within 5min and within a distance of 3m, all the members of both cliques are defined as being in the same grooming cluster. Twenty-seven types of cliques are observed, with the largest one consisting of seven individuals. Mutual and/or polyadic cliques account for more than 25% of all cliques. The size of grooming clusters varies from two to 23 individuals, and almost 70% of the grooming time is spent in polyadic clusters. Although adult males groom the longest in relatively smaller clusters (size=2-4), adult females groomed the longest in clusters of five or more individuals. A review of the literature implies that mutual and polyadic cliques occur less often in other primate species than in chimpanzees. The importance of overlapping interactions for these kinds of gatherings and its possible significance in the evolution of sociality is discussed in this article.     

Scale‐dependent processes of community assemblyin an African rift lake

1. Ecologists continue to debate whether the assembly of communities of species is more strongly influenced by dispersal limitations or niche‐based factors. Analytical approaches that account for both mechanisms can help to resolve controls of community assembly. 2. We compared littoral snail assemblages in Lake Tanganyika at three different spatial scales (5–25 m, 0.5–10 km and 0.5–27 km) to test whether spatial distance or environmental differences are better predictors of community similarity. 3. At the finest scale (5–25 m), snail assemblages shifted strongly with depth but not across similar lateral distances, indicating a stronger response to environmental gradients than dispersal opportunities. 4. At the two larger scales (0.5–27 km), both environmental similarity and shoreline distance between sites predicted assemblage similarity across sites. Additionally, canonical correspondence analysis revealed that snail abundances were significantly correlated with algal carbon‐to‐nitrogen ratio and wave energy. 5. Our results indicate that the factors governing assemblage structure are scale dependent; niche‐based mechanisms act across all spatial scales, whereas community similarity declines with distance only at larger spatial separations.     

Evaluation of Forest Recovery over Time and Space Using Permanent Plots Monitored over 30 Years in a Jamaican Montane Rain Forest

Conservation of tropical forest biodiversity increasingly depends on its recovery following severe human disturbance. Our ability to measure recovery using current similarity indices suffers from two limitations: different sized individuals are treated as equal, and the indices are proportionate (a community with twice the individuals of every species as compared with the reference community would be assessed as identical). We define an alternative recovery index for trees – the Tanner index, as the mean of the quantitative Bray-Curtis similarity indices of species composition for stem density and for basal area. We used the new index to compare the original (pre-gap) and post-gap composition of five experimental gap plots (each 90–100 m²) and four control plots over 24–35 years in the Blue Mountains of Jamaica. After 24–35 years, these small gaps surrounded by undisturbed forest had recovered 68% of the sum of per species stem density and 29% of the sum of per species basal area, a recovery index of 47%. Four endemic species were especially reduced in density and basal area. With the incorporation of basal area and stem density, our index reduces over-estimations of forest recovery obtained using existing similarity indices (by 24%–41%), and thus yields more accurate estimates of forest conservation status. Finally, our study indicates that the two kinds of comparisons: 1) over time between pre-gap and post-gap composition and 2) over space between gap plots and spatial controls (space-for-time substitution) yield broadly similar results, which supports the value of using space-for-time substitutions in studying forest recovery, at least in this tropical montane forest.     

Measuring biodiversity to explain community assembly: a unified approach

One of the oldest challenges in ecology is to understand the processes that underpin the composition of communities. Historically, an obvious way in which to describe community compositions has been diversity in terms of the number and abundances of species. However, the failure to reject contradictory models has led to communities now being characterized by trait and phylogenetic diversities. Our objective here is to demonstrate how species, trait and phylogenetic diversity can be combined together from large to local spatial scales to reveal the historical, deterministic and stochastic processes that impact the compositions of local communities. Research in this area has recently been advanced by the development of mathematical measures that incorporate trait dissimilarities and phylogenetic relatedness between species. However, measures of trait diversity have been developed independently of phylogenetic measures and conversely most of the phylogenetic diversity measures have been developed independently of trait diversity measures. This has led to semantic confusions particularly when classical ecological and evolutionary approaches are integrated so closely together. Consequently, we propose a unified semantic framework and demonstrate the importance of the links among species, phylogenetic and trait diversity indices. Furthermore, species, trait and phylogenetic diversity indices differ in the ways they can be used across different spatial scales. The connections between large‐scale, regional and local processes allow the consideration of historical factors in addition to local ecological deterministic or stochastic processes. Phylogenetic and trait diversity have been used in large‐scale analyses to determine how historical and/or environmental factors affect both the formation of species assemblages and patterns in species richness across latitude or elevation gradients. Both phylogenetic and trait diversity have been used at different spatial scales to identify the relative impacts of ecological deterministic processes such as environmental filtering and limiting similarity from alternative processes such as random speciation and extinction, random dispersal and ecological drift. Measures of phylogenetic diversity combine phenotypic and genetic diversity and have the potential to reveal both the ecological and historical factors that impact local communities. Consequently, we demonstrate that, when used in a comparative way, species, trait and phylogenetic structures have the potential to reveal essential details that might act simultaneously in the assembly of species communities. We highlight potential directions for future research. These might include how variation in trait and phylogenetic diversity alters with spatial distances, the role of trait and phylogenetic diversity in global‐scale gradients, the connections between traits and phylogeny, the importance of trait rarity and independent evolutionary history in community assembly, the loss of trait and phylogenetic diversity due to human impacts, and the mathematical developments of biodiversity indices including within‐species variations.     

On the discriminability of hROIs, human visually selected regions-of-interest

Many studies have tried to answer an important question: is it possible to predict human visually selected regions-of-interest (hROIs)? hROIs are defined as the loci of eye fixations and they can be analyzed by their spatial distribution over the visual stimulus and their temporal ordering. We used a simplified set of geometrical spatial kernels and linear filter models as bottom-up conspicuity operators that produce algorithmically selected regions-of-interest, aROIs. As a direct approach we measured the ability of these aROIs to predict human scanpaths. The level of prediction is measured by two similarity indices: S _p for spatial similarity and S _s for temporal ordering similarity. At the same time we assessed the discriminability of the hROI loci, in terms of conspicuity, with respect to non-selected (not of interest) regions of an image. We prove that this discrimination is possible and further correlates with the positional similarity index S _p . Other human scanpath experimental conditions are presented in parsing diagrams and discussed. A general top–down/bottom–up scanpath model is finally formulated.     

Properties of similarity indices under niche-based and dispersal-based processes in communities

Little is known about the combined impact of habitat filtering and dispersal limitation on species turnover patterns. To gain new insights, we constructed a spatially explicit community model wherein we controlled dispersal distances, the strength of habitat filtering, and the grain of habitat heterogeneity to study the distance decay of several (dis)similarity indices. The impact of habitat filtering is dependent on the ratio between the grain of habitats and the mean dispersal distance. The behavior of (dis)similarity indices varies. First, incidence-based measures of species overlap are less affected by habitat filtering than are abundance-based indices. Second, species identity-based indices, derived from population genetics' F(ST), show interesting capacities to infer dispersal processes under neutrality but are also highly sensitive to habitat filtering. All indices except F(ST)-related indices under neutrality are very sensitive to overall species richness. Hence, community patterns showing contrasted diversity levels should be compared with caution. Partitioning similarity indices within and between habitats appears to be an efficient approach to assess the strength of habitat filtering, and we show that a torus-translation test is powerful for this purpose. We finally highlight the need for further analytical studies to achieve theoretical expectations of similarity decay under dispersal and niche processes.     

Protein Functional Surfaces: Global Shape Matching and Local Spatial Alignments of Ligand Binding Sites

Background

Protein surfaces comprise only a fraction of the total residues but are the most conserved functional features of proteins. Surfaces performing identical functions are found in proteins absent of any sequence or fold similarity. While biochemical activity can be attributed to a few key residues, the broader surrounding environment plays an equally important role.

Results

We describe a methodology that attempts to optimize two components, global shape and local physicochemical texture, for evaluating the similarity between a pair of surfaces. Surface shape similarity is assessed using a three-dimensional object recognition algorithm and physicochemical texture similarity is assessed through a spatial alignment of conserved residues between the surfaces. The comparisons are used in tandem to efficiently search the Global Protein Surface Survey (GPSS), a library of annotated surfaces derived from structures in the PDB, for studying evolutionary relationships and uncovering novel similarities between proteins.

Conclusion

We provide an assessment of our method using library retrieval experiments for identifying functionally homologous surfaces binding different ligands, functionally diverse surfaces binding the same ligand, and binding surfaces of ubiquitous and conformationally flexible ligands. Results using surface similarity to predict function for proteins of unknown function are reported. Additionally, an automated analysis of the ATP binding surface landscape is presented to provide insight into the correlation between surface similarity and function for structures in the PDB and for the subset of protein kinases.