RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning.

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), founding member of the Worldwide Protein Data Bank (wwPDB), is the US data center for the open-access PDB archive. As wwPDB-designated Archive Keeper, RCSB PDB is also responsible for PDB data security. Annually, RCSB PDB serves >10 000 depositors of three-dimensional (3D) biostructures working on all permanently inhabited continents. RCSB PDB delivers data from its research-focused RCSB.org web portal to many millions of PDB data consumers based in virtually every United Nations-recognized country, territory, etc. This Database Issue contribution describes upgrades to the research-focused RCSB.org web portal that created a one-stop-shop for open access to ∼200 000 experimentally-determined PDB structures of biological macromolecules alongside >1 000 000 incorporated Computed Structure Models (CSMs) predicted using artificial intelligence/machine learning methods. RCSB.org is a 'living data resource.' Every PDB structure and CSM is integrated weekly with related functional annotations from external biodata resources, providing up-to-date information for the entire corpus of 3D biostructure data freely available from RCSB.org with no usage limitations. Within RCSB.org, PDB structures and the CSMs are clearly identified as to their provenance and reliability. Both are fully searchable, and can be analyzed and visualized using the full complement of RCSB.org web portal capabilities.

Multiple spatial reference frames underpin perceptual recalibration to audio-visual discrepancies.

In dynamic multisensory environments, the perceptual system corrects for discrepancies arising between modalities. For instance, in the ventriloquism aftereffect (VAE), spatial disparities introduced between visual and auditory stimuli lead to a perceptual recalibration of auditory space. Previous research has shown that the VAE is underpinned by multiple recalibration mechanisms tuned to different timescales, however it remains unclear whether these mechanisms use common or distinct spatial reference frames. Here we asked whether the VAE operates in eye- or head-centred reference frames across a range of adaptation timescales, from a few seconds to a few minutes. We developed a novel paradigm for selectively manipulating the contribution of eye- versus head-centred visual signals to the VAE by manipulating auditory locations relative to either the head orientation or the point of fixation. Consistent with previous research, we found both eye- and head-centred frames contributed to the VAE across all timescales. However, we found no evidence for an interaction between spatial reference frames and adaptation duration. Our results indicate that the VAE is underpinned by multiple spatial reference frames that are similarly leveraged by the underlying time-sensitive mechanisms.

Linking Multi-Modal MRI to Clinical Measures of Visual Field Loss After Stroke.

Loss of vision across large parts of the visual field is a common and devastating complication of cerebral strokes. In the clinic, this loss is quantified by measuring the sensitivity threshold across the field of vision using static perimetry. These methods rely on the ability of the patient to report the presence of lights in particular locations. While perimetry provides important information about the intactness of the visual field, the approach has some shortcomings. For example, it cannot distinguish where in the visual pathway the key processing deficit is located. In contrast, brain imaging can provide important information about anatomy, connectivity, and function of the visual pathway following stroke. In particular, functional magnetic resonance imaging (fMRI) and analysis of population receptive fields (pRF) can reveal mismatches between clinical perimetry and maps of cortical areas that still respond to visual stimuli after stroke. Here, we demonstrate how information from different brain imaging modalities-visual field maps derived from fMRI, lesion definitions from anatomical scans, and white matter tracts from diffusion weighted MRI data-provides a more complete picture of vision loss. For any given location in the visual field, the combination of anatomical and functional information can help identify whether vision loss is due to absence of gray matter tissue or likely due to white matter disconnection from other cortical areas. We present a combined imaging acquisition and visual stimulus protocol, together with a description of the analysis methodology, and apply it to datasets from four stroke survivors with homonymous field loss (two with hemianopia, two with quadrantanopia). For researchers trying to understand recovery of vision after stroke and clinicians seeking to stratify patients into different treatment pathways, this approach combines multiple, convergent sources of data to characterize the extent of the stroke damage. We show that such an approach gives a more comprehensive measure of residual visual capacity-in two particular respects: which locations in the visual field should be targeted and what kind of visual attributes are most suited for rehabilitation.

Using Integrative Modeling Platform to compute, validate, and archive a model of a protein complex structure.

Biology is advanced by producing structural models of biological systems, such as protein complexes. Some systems are recalcitrant to traditional structure determination methods. In such cases, it may still be possible to produce useful models by integrative structure determination that depends on simultaneous use of multiple types of data. An ensemble of models that are sufficiently consistent with the data is produced by a structural sampling method guided by a data-dependent scoring function. The variation in the ensemble of models quantified the uncertainty of the structure, generally resulting from the uncertainty in the input information and actual structural heterogeneity in the samples used to produce the data. Here, we describe how to generate, assess, and interpret ensembles of integrative structural models using our open source Integrative Modeling Platform program (https://integrativemodeling.org).

The Effect of Perceptual Learning on Face Recognition in Individuals with Central Vision Loss.

Purpose: To examine whether perceptual learning can improve face discrimination and recognition in older adults with central vision loss. Methods: Ten participants with age-related macular degeneration (ARMD) received 5 days of training on a face discrimination task (mean age, 78 ± 10 years). We measured the magnitude of improvements (i.e., a reduction in threshold size at which faces were able to be discriminated) and whether they generalized to an untrained face recognition task. Measurements of visual acuity, fixation stability, and preferred retinal locus were taken before and after training to contextualize learning-related effects. The performance of the ARMD training group was compared to nine untrained age-matched controls (8 = ARMD, 1 = juvenile macular degeneration; mean age, 77 ± 10 years). Results: Perceptual learning on the face discrimination task reduced the threshold size for face discrimination performance in the trained group, with a mean change (SD) of -32.7% (+15.9%). The threshold for performance on the face recognition task was also reduced, with a mean change (SD) of -22.4% (+2.31%). These changes were independent of changes in visual acuity, fixation stability, or preferred retinal locus. Untrained participants showed no statistically significant reduction in threshold size for face discrimination, with a mean change (SD) of -8.3% (+10.1%), or face recognition, with a mean change (SD) of +2.36% (-5.12%). Conclusions: This study shows that face discrimination and recognition can be reliably improved in ARMD using perceptual learning. The benefits point to considerable perceptual plasticity in higher-level cortical areas involved in face-processing. This novel finding highlights that a key visual difficulty in those suffering from ARMD is readily amenable to rehabilitation.

Modeling Biological Complexes Using Integrative Modeling Platform.

Integrative structure modeling provides 3D models of macromolecular systems that are based on information from multiple types of experiments, physical principles, statistical inferences, and prior structural models. Here, we provide a hands-on realistic example of integrative structure modeling of the quaternary structure of the actin, tropomyosin, and gelsolin protein assembly based on electron microscopy, solution X-ray scattering, and chemical crosslinking data for the complex as well as excluded volume, sequence connectivity, and rigid atomic X-ray structures of the individual subunits. We follow the general four-stage process for integrative modeling, including gathering the input information, converting the input information into a representation of the system and a scoring function, sampling alternative model configurations guided by the scoring function, and analyzing the results. The computational aspects of this approach are implemented in our open-source Integrative Modeling Platform (IMP), a comprehensive and extensible software package for integrative modeling ( https://integrativemodeling.org ). In particular, we rely on the Python Modeling Interface (PMI) module of IMP that provides facile mixing and matching of macromolecular representations, restraints based on different types of information, sampling algorithms, and analysis including validations of the input data and output models. Finally, we also outline how to deposit an integrative structure and corresponding experimental data into PDB-Dev, the nascent worldwide Protein Data Bank (wwPDB) resource for archiving and disseminating integrative structures ( https://pdb-dev.wwpdb.org ). The example application provides a starting point for a user interested in using IMP for integrative modeling of other biomolecular systems.

Distinct mechanisms govern recalibration to audio-visual discrepancies in remote and recent history.

To maintain perceptual coherence, the brain corrects for discrepancies between the senses. If, for example, lights are consistently offset from sounds, representations of auditory space are remapped to reduce this error (spatial recalibration). While recalibration effects have been observed following both brief and prolonged periods of adaptation, the relative contribution of discrepancies occurring over these timescales is unknown. Here we show that distinct multisensory recalibration mechanisms operate in remote and recent history. To characterise the dynamics of this spatial recalibration, we adapted human participants to audio-visual discrepancies for different durations, from 32 to 256 seconds, and measured the aftereffects on perceived auditory location. Recalibration effects saturated rapidly but decayed slowly, suggesting a combination of transient and sustained adaptation mechanisms. When long-term adaptation to an audio-visual discrepancy was immediately followed by a brief period of de-adaptation to an opposing discrepancy, recalibration was initially cancelled but subsequently reappeared with further testing. These dynamics were best fit by a multiple-exponential model that monitored audio-visual discrepancies over distinct timescales. Recent and remote recalibration mechanisms enable the brain to balance rapid adaptive changes to transient discrepancies that should be quickly forgotten against slower adaptive changes to persistent discrepancies likely to be more permanent.

Criterion-free measurement of motion transparency perception at different speeds.

Transparency perception often occurs when objects within the visual scene partially occlude each other or move at the same time, at different velocities across the same spatial region. Although transparent motion perception has been extensively studied, we still do not understand how the distribution of velocities within a visual scene contribute to transparent perception. Here we use a novel psychophysical procedure to characterize the distribution of velocities in a scene that give rise to transparent motion perception. To prevent participants from adopting a subjective decision criterion when discriminating transparent motion, we used an "odd-one-out," three-alternative forced-choice procedure. Two intervals contained the standard-a random-dot-kinematogram with dot speeds or directions sampled from a uniform distribution. The other interval contained the comparison-speeds or directions sampled from a distribution with the same range as the standard, but with a notch of different widths removed. Our results suggest that transparent motion perception is driven primarily by relatively slow speeds, and does not emerge when only very fast speeds are present within a visual scene. Transparent perception of moving surfaces is modulated by stimulus-based characteristics, such as the separation between the means of the overlapping distributions or the range of speeds presented within an image. Our work illustrates the utility of using objective, forced-choice methods to reveal the mechanisms underlying motion transparency perception.

Position matching between the visual fields in strabismus.

The misalignment of visual input in strabismus disrupts positional judgments. We measured positional accuracy in the extrafoveal visual field (1°-7° eccentricity) of a large group of strabismic subjects and a normal control group to identify positional distortions associated with the direction of strabismus. Subjects performed a free localization task in which targets were matched in opposite hemifields whilst fixating on a central cross. The constant horizontal error of each response was taken as a measure of accuracy, in addition to radial and angular error. In monocular conditions, all stimuli were viewed by one eye; thus, the error reflected spatial bias. In dichoptic conditions, the targets were seen by separate eyes; thus, the error reflected the perceived stimulus shift produced by ocular misalignment in addition to spatial bias. In both viewing conditions, both groups showed reliable over- and underestimations of visual field position, here termed a compression of response coordinates. The normal group showed compression in the left periphery, regardless of eye of stimulation. The strabismic group showed a visual field-specific compression that was clearly associated with direction of strabismus. The variation in perceived shift of strabismic subjects was largely accounted for by the biases present in monocular viewing, suggesting that binocular correspondence was uniform in the tested region. The asymmetric strabismic compression could not be reproduced in normal subjects through prism viewing, and its presence across viewing conditions suggests a hemifield-specific change in spatial coding induced by long-standing ocular misalignment.

The effect of normal aging and age-related macular degeneration on perceptual learning.

We investigated whether perceptual learning could be used to improve peripheral word identification speed. The relationship between the magnitude of learning and age was established in normal participants to determine whether perceptual learning effects are age invariant. We then investigated whether training could lead to improvements in patients with age-related macular degeneration (AMD). Twenty-eight participants with normal vision and five participants with AMD trained on a word identification task. They were required to identify three-letter words, presented 10° from fixation. To standardize crowding across each of the letters that made up the word, words were flanked laterally by randomly chosen letters. Word identification performance was measured psychophysically using a staircase procedure. Significant improvements in peripheral word identification speed were demonstrated following training (71% ± 18%). Initial task performance was correlated with age, with older participants having poorer performance. However, older adults learned more rapidly such that, following training, they reached the same level of performance as their younger counterparts. As a function of number of trials completed, patients with AMD learned at an equivalent rate as age-matched participants with normal vision. Improvements in word identification speed were maintained at least 6 months after training. We have demonstrated that temporal aspects of word recognition can be improved in peripheral vision with training across a range of ages and these learned improvements are relatively enduring. However, training targeted at other bottlenecks to peripheral reading ability, such as visual crowding, may need to be incorporated to optimize this approach.

Estimation of cortical magnification from positional error in normally sighted and amblyopic subjects.

We describe a method for deriving the linear cortical magnification factor from positional error across the visual field. We compared magnification obtained from this method between normally sighted individuals and amblyopic individuals, who receive atypical visual input during development. The cortical magnification factor was derived for each subject from positional error at 32 locations in the visual field, using an established model of conformal mapping between retinal and cortical coordinates. Magnification of the normally sighted group matched estimates from previous physiological and neuroimaging studies in humans, confirming the validity of the approach. The estimate of magnification for the amblyopic group was significantly lower than the normal group: by 4.4 mm deg(-1) at 1° eccentricity, assuming a constant scaling factor for both groups. These estimates, if correct, suggest a role for early visual experience in establishing retinotopic mapping in cortex. We discuss the implications of altered cortical magnification for cortical size, and consider other neural changes that may account for the amblyopic results.

The challenges of developing a contrast-based video game for treatment of amblyopia.

Perceptual learning of visual tasks is emerging as a promising treatment for amblyopia, a developmental disorder of vision characterized by poor monocular visual acuity. The tasks tested thus far span the gamut from basic psychophysical discriminations to visually complex video games. One end of the spectrum offers precise control over stimulus parameters, whilst the other delivers the benefits of motivation and reward that sustain practice over long periods. Here, we combined the advantages of both approaches by developing a video game that trains contrast sensitivity, which in psychophysical experiments, is associated with significant improvements in visual acuity in amblyopia. Target contrast was varied adaptively in the game to derive a contrast threshold for each session. We tested the game on 20 amblyopic subjects (10 children and 10 adults), who played at home using their amblyopic eye for an average of 37 sessions (approximately 11 h). Contrast thresholds from the game improved reliably for adults but not for children. However, logMAR acuity improved for both groups (mean = 1.3 lines; range = 0-3.6 lines). We present the rationale leading to the development of the game and describe the challenges of incorporating psychophysical methods into game-like settings.

Characterizing the effects of multidirectional motion adaptation.

Recent sensory experience can alter our perception and change the response characteristics of sensory neurons. These effects of sensory adaptation are a ubiquitous property of perceptual systems and are believed to be of fundamental importance to sensory coding. Yet we know little about how adaptation to stimulus ensembles affects our perception of the environment as most psychophysical experiments employ adaptation protocols that focus on prolonged exposure to a single visual attribute. Here, we investigate how concurrent adaptation to multiple directions of motion affects perception of subsequently presented motion using the direction aftereffect. In different conditions, observers adapted to a stimulus ensemble comprised of dot directions sampled from different distributions or to bidirectional motion. Increasing the variance of normally distributed directions reduced the magnitude of the peak direction aftereffect and broadened its tuning profile. Sampling of asymmetric Gaussian and uniform distributions resulted in shifts of direction aftereffect tuning profiles consistent with changes in the perceived global direction of the adapting stimulus. Adding dots in a direction opposite or orthogonal to a unidirectional adapting stimulus led to a pronounced reduction in the direction aftereffect. A simple population-coding model, in which adaptation selectively alters the responsivity of direction-selective neurons, can accommodate the effects of multidirectional adaptation on the perceived direction of motion.

The effect of aging on crowded letter recognition in the peripheral visual field.

PURPOSE: Crowding describes the increased difficulty in identifying a target object when it is surrounded by nearby objects (flankers). A recent study investigated the effect of age on visual crowding and found equivocal results: Although crowded visual acuity was worse in older participants, crowding expressed as a ratio did not change with age. However, the spatial extent of crowding is a better index of crowding effects and remains unknown. In the present study, we used established psychophysical methods to characterize the effect of age on visual crowding (magnitude and extent) in a letter recognition task. METHODS: Letter recognition thresholds were determined for three different flanker separations in 54 adults (aged 18-76 years) with normal vision. Additionally, the spatial extent of crowding was established by measuring spacing thresholds: the flanker-to-target separation required to produce a given reduction in performance. Uncrowded visual acuity, crowded visual acuity, and spacing thresholds were expressed as a function of age, avoiding arbitrary categorization of young and old participants. RESULTS: Our results showed that uncrowded and crowded visual acuities do not change significantly as a function of age. Furthermore, spacing thresholds did not change with age and approximated Bouma's law (half eccentricity). CONCLUSIONS: These data show that crowding in adults is unaffected by senescence and provide additional evidence for distinct neural mechanisms mediating surround suppression and visual crowding, since the former shows a significant age effect. Finally, our data suggest that the well-documented age-related decline in peripheral reading ability is not due to age-related changes in visual crowding.

SAXS Merge: an automated statistical method to merge SAXS profiles using Gaussian processes.

Small-angle X-ray scattering (SAXS) is an experimental technique that allows structural information on biomolecules in solution to be gathered. High-quality SAXS profiles have typically been obtained by manual merging of scattering profiles from different concentrations and exposure times. This procedure is very subjective and results vary from user to user. Up to now, no robust automatic procedure has been published to perform this step, preventing the application of SAXS to high-throughput projects. Here, SAXS Merge, a fully automated statistical method for merging SAXS profiles using Gaussian processes, is presented. This method requires only the buffer-subtracted SAXS profiles in a specific order. At the heart of its formulation is non-linear interpolation using Gaussian processes, which provides a statement of the problem that accounts for correlation in the data.

Visual motion integration is mediated by directional ambiguities in local motion signals.

The output of primary visual cortex (V1) is a piecemeal representation of the visual scene and the response of any one cell cannot unambiguously guide sensorimotor behavior. It remains unsolved how subsequent stages of cortical processing combine ("pool") these early visual signals into a coherent representation. We (Webb et al., 2007, 2011) have shown that responses of human observers on a pooling task employing broadband, random dot motion can be accurately predicted by decoding the maximum likelihood direction from a population of motion-sensitive neurons. Whereas Amano et al. (2009) found that the vector average velocity of arrays of narrowband, two-dimensional (2-d) plaids predicts perceived global motion. To reconcile these different results, we designed two experiments in which we used 2-d noise textures moving behind spatially distributed apertures and measured the point of subjective equality between pairs of global noise textures. Textures in the standard stimulus moved rigidly in the same direction, whereas their directions in the comparison stimulus were sampled from a set of probability distributions. Human observers judged which noise texture had a more clockwise (CW) global direction. In agreement with Amano and colleagues, observers' perceived global motion coincided with the vector average stimulus direction. To test if directional ambiguities in local motion signals governed perceived global direction, we manipulated the fidelity of the texture motion within each aperture. A proportion of the apertures contained texture that underwent rigid translation and the remainder contained dynamic (temporally uncorrelated) noise to create locally ambiguous motion. Perceived global motion matched the vector average when the majority of apertures contained rigid motion, but with increasing levels of dynamic noise shifted toward the maximum likelihood direction. A class of population decoders utilizing power-law non-linearities can accommodate this flexible pooling.

Optimized atomic statistical potentials: assessment of protein interfaces and loops.

MOTIVATION: Statistical potentials have been widely used for modeling whole proteins and their parts (e.g. sidechains and loops) as well as interactions between proteins, nucleic acids and small molecules. Here, we formulate the statistical potentials entirely within a statistical framework, avoiding questionable statistical mechanical assumptions and approximations, including a definition of the reference state. RESULTS: We derive a general Bayesian framework for inferring statistically optimized atomic potentials (SOAP) in which the reference state is replaced with data-driven 'recovery' functions. Moreover, we restrain the relative orientation between two covalent bonds instead of a simple distance between two atoms, in an effort to capture orientation-dependent interactions such as hydrogen bonds. To demonstrate this general approach, we computed statistical potentials for protein-protein docking (SOAP-PP) and loop modeling (SOAP-Loop). For docking, a near-native model is within the top 10 scoring models in 40% of the PatchDock benchmark cases, compared with 23 and 27% for the state-of-the-art ZDOCK and FireDock scoring functions, respectively. Similarly, for modeling 12-residue loops in the PLOP benchmark, the average main-chain root mean square deviation of the best scored conformations by SOAP-Loop is 1.5 Å, close to the average root mean square deviation of the best sampled conformations (1.2 Å) and significantly better than that selected by Rosetta (2.1 Å), DFIRE (2.3 Å), DOPE (2.5 Å) and PLOP scoring functions (3.0 Å). Our Bayesian framework may also result in more accurate statistical potentials for additional modeling applications, thus affording better leverage of the experimentally determined protein structures. AVAILABILITY AND IMPLEMENTATION: SOAP-PP and SOAP-Loop are available as part of MODELLER (http://salilab.org/modeller).

Adaptation to implied tilt: extensive spatial extrapolation of orientation gradients.

To extract the global structure of an image, the visual system must integrate local orientation estimates across space. Progress is being made toward understanding this integration process, but very little is known about whether the presence of structure exerts a reciprocal influence on local orientation coding. We have previously shown that adaptation to patterns containing circular or radial structure induces tilt-aftereffects (TAEs), even in locations where the adapting pattern was occluded. These spatially "remote" TAEs have novel tuning properties and behave in a manner consistent with adaptation to the local orientation implied by the circular structure (but not physically present) at a given test location. Here, by manipulating the spatial distribution of local elements in noisy circular textures, we demonstrate that remote TAEs are driven by the extrapolation of orientation structure over remarkably large regions of visual space (more than 20°). We further show that these effects are not specific to adapting stimuli with polar orientation structure, but require a gradient of orientation change across space. Our results suggest that mechanisms of visual adaptation exploit orientation gradients to predict the local pattern content of unfilled regions of space.

Design of a single-chain polypeptide tetrahedron assembled from coiled-coil segments.

Protein structures evolved through a complex interplay of cooperative interactions, and it is still very challenging to design new protein folds de novo. Here we present a strategy to design self-assembling polypeptide nanostructured polyhedra based on modularization using orthogonal dimerizing segments. We designed and experimentally demonstrated the formation of the tetrahedron that self-assembles from a single polypeptide chain comprising 12 concatenated coiled coil-forming segments separated by flexible peptide hinges. The path of the polypeptide chain is guided by a defined order of segments that traverse each of the six edges of the tetrahedron exactly twice, forming coiled-coil dimers with their corresponding partners. The coincidence of the polypeptide termini in the same vertex is demonstrated by reconstituting a split fluorescent protein in the polypeptide with the correct tetrahedral topology. Polypeptides with a deleted or scrambled segment order fail to self-assemble correctly. This design platform provides a foundation for constructing new topological polypeptide folds based on the set of orthogonal interacting polypeptide segments.

A Weber-like law for perceptual learning.

What determines how much an organism can learn? One possibility is that the neural factors that limit sensory performance prior to learning, place an upper limit on the amount of learning that can take place. We tested this idea by comparing learning on a sensory task where performance is limited by cortical mechanisms, at two retinal eccentricities. Prior to learning, visual performance at the two eccentricities was either unmatched or equated in two different ways (through spatial scaling or visual crowding). The magnitude of learning was equivalent when initial levels of performance were matched regardless of how performance was equated. The magnitude of learning was a constant proportion of initial performance. This Weber-like law for perceptual learning demonstrates that it should be possible to predict the degree of perceptual improvement and the final level of performance that can be achieved via sensory training, regardless of what cortical constraint limits performance.