Biomedical subjects

Ben Webb

Publications and source records attributed to Ben Webb.

3 recordsLinked to original sources

PubMed2004

MODBASE, a database of annotated comparative protein structure models, and associated resources.

MODBASE (http://salilab.org/modbase) is a relational database of annotated comparative protein structure models for all available protein sequences matched to at least one known protein structure. The models are calculated by MODPIPE, an automated modeling pipeline that relies on the MODELLER package for fold assignment, sequence-structure alignment, model building and model assessment (http:/salilab.org/modeller). MODBASE uses the MySQL relational database management system for flexible querying and CHIMERA for viewing the sequences and structures (http://www.cgl.ucsf.edu/chimera/). MODBASE is updated regularly to reflect the growth in protein sequence and structure databases, as well as improvements in the software for calculating the models. For ease of access, MODBASE is organized into different data sets. The largest data set contains 1,26,629 models for domains in 659,495 out of 1,182,126 unique protein sequences in the complete Swiss-Prot/TrEMBL database (August 25, 2003); only models based on alignments with significant similarity scores and models assessed to have the correct fold despite insignificant alignments are included. Another model data set supports target selection and structure-based annotation by the New York Structural Genomics Research Consortium; e.g. the 53 new structures produced by the consortium allowed us to characterize structurally 24,113 sequences. MODBASE also contains binding site predictions for small ligands and a set of predicted interactions between pairs of modeled sequences from the same genome. Our other resources associated with MODBASE include a comprehensive database of multiple protein structure alignments (DBALI, http://salilab.org/dbali) as well as web servers for automated comparative modeling with MODPIPE (MODWEB, http://salilab. org/modweb), modeling of loops in protein structures (MODLOOP, http://salilab.org/modloop) and predicting functional consequences of single nucleotide polymorphisms (SNPWEB, http://salilab. org/snpweb).

Amino Acid Sequence↗

PubMed2002

Anxiety-related bias in the classification of emotionally ambiguous facial expressions.

High- and low-trait socially anxious individuals classified the emotional expressions of photographic quality continua of interpolated ("morphed") facial images that were derived from combining 6 basic prototype emotional expressions to various degrees, with the 2 adjacent emotions arranged in an emotion hexagon. When fear was 1 of the 2 component emotions, the high-trait group displayed enhanced sensitivity for fear. In a 2nd experiment where a mood manipulation was incorporated, again, the high-trait group exhibited enhanced sensitivity for fear. The low-trait group was sensitive for happiness in the control condition. The mood-manipulated group had increased sensitivity for anger expressions, and trait anxiety did not moderate these effects. Interpretations of the results related to the classification of fearful expressions are discussed.

Adolescent↗

PubMedDate not supplied

Processing of first-order motion in marmoset visual cortex is influenced by second-order motion.

We measured the responses of single neurons in marmoset visual cortex (V1, V2, and the third visual complex) to moving first-order stimuli and to combined first- and second-order stimuli in order to determine whether first-order motion processing was influenced by second-order motion. Beat stimuli were made by summing two gratings of similar spatial frequency, one of which was static and the other was moving. The beat is the product of a moving sinusoidal carrier (first-order motion) and a moving low-frequency contrast envelope (second-order motion). We compared responses to moving first-order gratings alone with responses to beat patterns with first-order and second-order motion in the same direction as each other, or in opposite directions to each other in order to distinguish first-order and second-order direction-selective responses. In the majority (72%, 67/93) of cells (V1 73%, 45/62; V2 70%, 16/23; third visual complex 75%, 6/8), responses to first-order motion were significantly influenced by the addition of a second-order signal. The second-order envelope was more influential when moving in the opposite direction to the first-order stimulus, reducing first-order direction sensitivity in V1, V2, and the third visual complex. We interpret these results as showing that first-order motion processing through early visual cortex is not separate from second-order motion processing; suggesting that both motion signals are processed by the same system.

Action Potentials↗