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PubMed2004

PLASS: protein-ligand affinity statistical score--a knowledge-based force-field model of interaction derived from the PDB.

We have developed PLASS (Protein-Ligand Affinity Statistical Score), a pair-wise potential of mean-force for rapid estimation of the binding affinity of a ligand molecule to a protein active site. This scoring function is derived from the frequency of occurrence of atom-type pairs in crystallographic complexes taken from the Protein Data Bank (PDB). Statistical distributions are converted into distance-dependent contributions to the Gibbs free interaction energy for 10 atomic types using the Boltzmann hypothesis, with only one adjustable parameter. For a representative set of 72 protein-ligand structures, PLASS scores correlate well with the experimentally measured dissociation constants: a correlation coefficient R of 0.82 and RMS error of 2.0 kcal/mol. Such high accuracy results from our novel treatment of the volume correction term, which takes into account the inhomogeneous properties of the protein-ligand complexes. PLASS is able to rank reliably the affinity of complexes which have as much diversity as in the PDB.

Computational Biology↗
PubMed1998

On developing a knowledge base in infancy.

The development of conceptual categories from 7 to 11 months of age was explored in 5 experiments using an object-examination task. Infants in this age range categorized the global domains of animals, vehicles, and furniture. Plants and kitchen utensils were tested at 11 months, and these domains were also categorized. When 9-month-olds were tested on kitchen utensils, they did not categorize them. Subdivisions within the animal and furniture domains were also examined. Infants did not show any subcategorization of furniture. In the animal domain both 9- and 11-month-olds responded to the life-form distinction between dogs and birds, but they did not differentiate the mammal categories of dogs and cats until 11 months. This early organization of the conceptual system into global domains that become increasingly differentiated is discussed in relation to the adult conceptual system and its breakdown in semantic dementia.

Age Factors↗
PubMed1990

The role of knowledge-based expectations in music perception: evidence from musical restoration.

The perceptual restoration of musical sounds was investigated in 5 experiments with Samuel's (1981a) discrimination methodology. Restoration in familiar melodies was compared to phonemic restoration in Experiment 1. In the remaining experiments, we examined the effect of expectations (generated by familiarity, predictability, and musical schemata) on musical restoration. We investigated restoration in melodies by comparing familiar and unfamiliar melodies (Experiment 2), as well as unfamiliar melodies varying in tonal and rhythmic predictability (Experiment 3). Expectations based on both familiarity and predictability were found to reduce restoration at the melodic level. Restoration at the submelodic level was investigated with scales and chords in Experiments 4 and 5. At this level, key-based expectations were found to increase restoration. Implications for music perception, as well as similarities between restoration in music and speech, are discussed.

Adult↗
PubMed1990

Adult age differences in memory in relation to availability and accessibility of knowledge-based schemas.

Three experiments investigated whether, over adulthood, the use of schemas to process and remember new information increases (developmental shift hypothesis), decreases (production deficiency hypothesis) or remains constant (age-invariance hypothesis). Effects of schema access were studied by having young, middle-aged, and old music experts and nonexperts recall information that was relevant or irrelevant to music (Experiment 1) and by comparing young and old participants' memory for prose passages when they knew or did not know the subject of the passage (Experiments 2 and 3). In each case, schema access facilitated memory equally across age levels, supporting the age-invariance hypothesis and implying that the basic structures and operations of memory do not necessarily change with age. Possible limits on the independence of age and schema utilization were considered in relation to the conditions under which each of the two alternative hypotheses might hold.

Adult↗
PubMed1991

Implicit and explicit knowledge bases in artificial grammar learning.

Two experiments examined the claim for distinct implicit and explicit learning modes in the artificial grammar-learning task (Reber, 1967, 1989). Subjects initially attempted to memorize strings of letters generated by a finite-state grammar and then classified new grammatical and nongrammatical strings. Experiment 1 showed that subjects' assessment of isolated parts of strings was sufficient to account for their classification performance but that the rules elicited in free report were not sufficient. Experiment 2 showed that performing a concurrent random number generation task under different priorities interfered with free report and classification performance equally. Furthermore, giving different groups of subjects incidental or intentional learning instructions did not affect classification or free report.

Adult↗
PubMed1996

ABGEN: a knowledge-based automated approach for antibody structure modeling.

Immunoglobulin (Ig) amino acid sequences are highly conserved and often have sequence homology ranging from 70 to 95%. Antigen binding fragments (Fab), variable region fragments (Fv), and single chain Fv (scFv) of more than 50 myeloma proteins and monoclonal antibodies (mAb) have been crystallized and display a high degree of structural similarity. Based on this observation, several homology modeling approaches have been developed for the prediction of Fab and Fv structures prior to their experimental determination. We have extracted features from existing Ig sequences, 44 known Fab and Fv structures to create an automated AntiBody structure GENeration (ABGEN) algorithm for obtaining structural models of antibody fragments. ABGEN utilizes a homology based scaffolding technique, and includes the use of invariant and strictly conserved residues, structural motifs of known Fab, canonical features of hypervariable loops, torsional constraints for residue replacements and key inter-residue interactions. The validity of the ABGEN algorithm has been tested using a five-fold cross validation with the existing Fab structures. Molecular mechanics and dynamics methods have been implemented with ABGEN models to accurately predict two Fab structures of anti-sweetener antibodies prior to crystallographic determinations.

Algorithms↗
PubMed1999

An evaluation of EMBASE within the NHS: findings of the Database Access Project working partnership to extend the knowledge base of healthcare.

An earlier article in the Innovations on the Internet Series introduced the Database Access Project (DAPs) at Southmead Health Services NHS Trust, which piloted the introduction and use of EMBASE via the Internet and NHSnet. This follow-up article assesses the results of the Project, and reports on its findings. In particular, it considers the usefulness of EMBASE in terms of coverage and content for different groups of NHS users and aspects of take-up in terms of access arrangements and patterns of usage. It also considers the likely impact on the library and information service in terms of providing training and user support and meeting related demands, for example the acquisition of full-text articles as a result of increased levels of searching. The value of retaining access to EMBASE was recognized by the majority of those who participated in the Project, despite its acknowledged overlap with other databases. The coverage of the database was identified as being relevant by a majority of users; both its expanded European coverage and its coverage of drug-related and mental health literature were identified as important aspects. The project identified a clear preference for remote access to the database, although there was still a need to visit the library for retrieval of full text. Lack of time both for training and for actual database use, and lack of confidence in applying search skills and in appraising research were identified as key challenges to database searching. The authors highlight the special role of information professionals in providing training and support for NHS professionals in the acquisition of search skills and critical appraisal skills in order to encourage effective database use.

Computer User Training↗
PubMed1998

Different derivations of knowledge-based potentials and analysis of their robustness and context-dependent predictive power.

The possibility of defining effective potentials from known protein structures, which are sufficiently accurate to be used for protein-structure-prediction purposes, is investigated. Three types of distance potentials and three types of backbone torsion potentials are defined, based on propensities of amino acid pairs to be separated by a given spatial distance or to be associated to a backbone torsion angle domain. Their differences reside in the way the physical correlations between the amino acids and the conformational states are extracted from the bulk interactions due to the presence of many residues in a protein. For the distance potentials, a physical meaning can be associated to the different definitions, given that some of the potentials favor hydrophobic interactions and others favor interactions between oppositely charged residues. The performance of the different torsion and distance potentials in structure prediction procedures, in particular native-fold recognition and evaluation of protein stability changes upon point mutations, is analyzed. It appears to differ according to the specific proteins and protein environments. In particular, one of the distance potentials performs better than the others for membrane proteins and in protein regions involving charged residues, but less well in other protein regions. Furthermore, the dependence of the potentials on the characteristics of the proteins from which they are derived is analyzed. It is shown that the dependence of the potentials on the length, amino acid composition and secondary-structure content of the proteins from the dataset is either very limited or rather strong, according to the type of potential. The results obtained suggest that the main problem limiting the performance of database-derived potentials is their lack of universality: each potential describes with satisfactory accuracy only the interactions present in certain protein environments.

Algorithms↗