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Competing Interests: Conflicts of interest The authors declare no conflicts of interest.

Summary: MoMA-LoopSampler is a sampling method that globally explores the conformational space of flexible protein loops. It combines a large structural library of three-residue fragments and a novel reinforcement-learning-based approach to accelerate the sampling process while maintaining diversity. The method generates a set of statistically likely loop states satisfying geometric constraints, and its ability to sample experimentally observed conformations has been demonstrated. This paper presents a web user interface to MoMA-LoopSampler through the illustration of a typical use-case., Availability and Implementation: MoMA-LoopSampler is freely available at: https://moma.laas.fr/applications/LoopSampler/. We recommend users to create an account, but anonymous access is possible. In most cases, jobs are completed within a few minutes. The waiting time may increase depending on the server load, but it very rarely exceeds an hour. For users requiring more intensive use, binaries can be provided upon request., Supplementary Information: Supplementary data are available at Bioinformatics online., (© The Author(s) 2021. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Background: Mycosis fungoides (MF) and Sézary Syndrome (SS) are the most common cutaneous T-cell lymphomas. MF/SS is accompanied by considerable morbidity from pain, itching and disfigurement., Aim: To identify factors associated with poorer health-related quality of life (HRQoL) in patients newly diagnosed with MF/SS., Methods: Patients enrolled into Prospective Cutaneous Lymphoma International Prognostic Index (PROCLIPI; an international observational study in MF/SS) had their HRQoL assessed using the Skindex-29 questionnaire. Skindex-29 scores were analysed in relation to patient- and disease-specific characteristics., Results: The study population consisted of 237 patients [60·3% male; median age 60 years, (interquartile range 49-70)], of whom 179 had early MF and 58 had advanced MF/SS. In univariate analysis, HRQoL, as measured by Skindex-29, was worse in women, SS, late-stage MF, those with elevated lactate dehydrogenase, alopecia, high modified Severity Weighted Assessment Tool and confluent erythema. Linear regression models only identified female gender (β = 8·61; P = 0·003) and alopecia (β = 9·71, P = 0·02) as independent predictors of worse global HRQoL. Item-level analysis showed that the severe impairment in symptoms [odds ratio (OR) 2·14, 95% confidence interval (CI) 1·19-3·89] and emotions (OR 1·88, 95% CI 1·09-3·27) subscale scores seen in women was caused by more burning/stinging, pruritus, irritation and greater feelings of depression, shame, embarrassment and annoyance with their diagnosis of MF/SS., Conclusions: HRQoL is significantly more impaired in newly diagnosed women with MF/SS and in those with alopecia. As Skindex-29 does not include existential questions on cancer, which may cause additional worry and distress, a comprehensive validated cutaneous T-cell lymphoma-specific questionnaire is urgently needed to more accurately assess disease-specific HRQoL in these patients. What's already known about this topic? Cross-sectional studies of mixed populations of known and newly diagnosed patients with mycosis fungoides (MF)/Sézary syndrome (SS) have shown significant impairment in health-related quality of life (HRQoL). Previous studies on assessing gender-specific differences in HRQoL in MF/SS are conflicting. More advanced-stage disease and pruritus is associated with poorer HRQoL in patients with MF/SS. What does this study add? This is the first prospective study to investigate HRQoL in a homogenous group of newly diagnosed patients with MF/SS. In patients newly diagnosed with MF/SS, HRQoL is worse in women and in those with alopecia and confluent erythema. MF/SS diagnosis has a multidimensional impact on patient HRQoL, including a large burden of cutaneous symptoms, as well as a negative impact on emotional well-being., (© 2019 British Association of Dermatologists.)

Motivation: Loop portions in proteins are involved in many molecular interaction processes. They often exhibit a high degree of flexibility, which can be essential for their function. However, molecular modeling approaches usually represent loops using a single conformation. Although this conformation may correspond to a (meta-)stable state, it does not always provide a realistic representation., Results: In this paper, we propose a method to exhaustively sample the conformational space of protein loops. It exploits structural information encoded in a large library of three-residue fragments, and enforces loop-closure using a closed-form inverse kinematics solver. A novel reinforcement-learning-based approach is applied to accelerate sampling while preserving diversity. The performance of our method is showcased on benchmark datasets involving 9-, 12- and 15-residue loops. In addition, more detailed results presented for streptavidin illustrate the ability of the method to exhaustively sample the conformational space of loops presenting several meta-stable conformations., Availability and Implementation: We are developing a software package called MoMA (for Molecular Motion Algorithms), which includes modeling tools and algorithms to sample conformations and transition paths of biomolecules, including the application described in this work. The binaries can be provided upon request and a web application will also be implemented in the short future., Supplementary Information: Supplementary data are available at Bioinformatics online., (© The Author(s) 2019. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)