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1. DeepComplex: A Web Server of Predicting Protein Complex Structures by Deep Learning Inter-chain Contact Prediction and Distance-Based Modelling

   https://doi.org/10.3389/fmolb.2021.716973  

   Quadir, Farhan; Roy, Raj S.; Soltanikazemi, Elham; Cheng, Jianlin (August 2021, Frontiers in Molecular Biosciences)

   Proteins interact to form complexes. Predicting the quaternary structure of protein complexes is useful for protein function analysis, protein engineering, and drug design. However, few user-friendly tools leveraging the latest deep learning technology for inter-chain contact prediction and the distance-based modelling to predict protein quaternary structures are available. To address this gap, we develop DeepComplex, a web server for predicting structures of dimeric protein complexes. It uses deep learning to predict inter-chain contacts in a homodimer or heterodimer. The predicted contacts are then used to construct a quaternary structure of the dimer by the distance-based modelling, which can be interactively viewed and analysed. The web server is freely accessible and requires no registration. It can be easily used by providing a job name and an email address along with the tertiary structure for one chain of a homodimer or two chains of a heterodimer. The output webpage provides the multiple sequence alignment, predicted inter-chain residue-residue contact map, and predicted quaternary structure of the dimer. DeepComplex web server is freely available at http://tulip.rnet.missouri.edu/deepcomplex/web_index.html 

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2. Job Dispatching Policies for Queueing Systems with Unknown Service Rates

   https://doi.org/10.1145/3466772.3467047  

   Choudhury, Tuhinangshu; Joshi, Gauri; Wang, Weina; Shakkottai, Sanjay (July 2021, ACM MobiHoc: International Symposium on Theory, Algorithmic Foundations, and Protocol Design for Mobile Networks)

   null (Ed.)

   In multi-server queueing systems where there is no central queue holding all incoming jobs, job dispatching policies are used to assign incoming jobs to the queue at one of the servers. Classic job dispatching policies such as join-the-shortest-queue and shortest expected delay assume that the service rates and queue lengths of the servers are known to the dispatcher. In this work, we tackle the problem of job dispatching without the knowledge of service rates and queue lengths, where the dispatcher can only obtain noisy estimates of the service rates by observing job departures. This problem presents a novel exploration-exploitation trade-off between sending jobs to all the servers to estimate their service rates, and exploiting the currently known fastest servers to minimize the expected queueing delay. We propose a bandit-based exploration policy that learns the service rates from observed job departures. Unlike the standard multi-armed bandit problem where only one out of a finite set of actions is optimal, here the optimal policy requires identifying the optimal fraction of incoming jobs to be sent to each server. We present a regret analysis and simulations to demonstrate the effectiveness of the proposed bandit-based exploration policy. 

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3. CGRAP: A Web Server for Coarse-Grained Rigidity Analysis of Proteins

   https://doi.org/10.3390/sym13122401  

   Turcan, Alistair; Zivkovic, Anna; Thompson, Dylan; Wong, Lorraine; Johnson, Lauren; Jagodzinski, Filip (December 2021, Symmetry)

   Elucidating protein rigidity offers insights about protein conformational changes. An understanding of protein motion can help speed drug development, and provide general insights into the dynamic behaviors of biomolecules. Existing rigidity analysis techniques employ fine-grained, all-atom modeling, which has a costly run-time, particularly for proteins made up of more than 500 residues. In this work, we introduce coarse-grained rigidity analysis, and showcase that it provides flexibility information about a protein that is similar in accuracy to an all-atom modeling approach. We assess the accuracy of the coarse-grained method relative to an all-atom approach via a comparison metric that reasons about the largest rigid clusters of the two methods. The apparent symmetry between the all-atom and coarse-grained methods yields very similar results, but the coarse-grained method routinely exhibits 40% reduced run-times. The CGRAP web server outputs rigid cluster information, and provides data visualization capabilities, including a interactive protein visualizer. 

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4. Availability of web servers significantly boosts citations rates of bioinformatics methods for protein function and disorder prediction

   https://doi.org/10.1093/bioadv/vbad184  

   Song, Jiangning; Kurgan, Lukasz; Arighi, ed., Cecilia (December 2023, Bioinformatics Advances)

   Abstract MotivationDevelopment of bioinformatics methods is a long, complex and resource-hungry process. Hundreds of these tools were released. While some methods are highly cited and used, many suffer relatively low citation rates. We empirically analyze a large collection of recently released methods in three diverse protein function and disorder prediction areas to identify key factors that contribute to increased citations. ResultsWe show that provision of a working web server significantly boosts citation rates. On average, methods with working web servers generate three times as many citations compared to tools that are available as only source code, have no code and no server, or are no longer available. This observation holds consistently across different research areas and publication years. We also find that differences in predictive performance are unlikely to impact citation rates. Overall, our empirical results suggest that a relatively low-cost investment into the provision and long-term support of web servers would substantially increase the impact of bioinformatics tools. 

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5. Zero Queueing for Multi-Server Jobs

   https://doi.org/10.1145/3410220.3453924  

   Wang, Weina; Xie, Qiaomin; Harchol-Balter, Mor (May 2021, ACM SIGMETRICS / International Conference on Measurement and Modeling of Computer Systems)

   null (Ed.)

   Cloud computing today is dominated by multi-server jobs. These are jobs that request multiple servers simultaneously and hold onto all of these servers for the duration of the job. Multi-server jobs add a lot of complexity to the traditional one-server-per-job model: an arrival might not "fit" into the available servers and might have to queue, blocking later arrivals and leaving servers idle. From a queueing perspective, almost nothing is understood about multi-server job queueing systems; even understanding the exact stability region is a very hard problem. In this paper, we investigate a multi-server job queueing model under scaling regimes where the number of servers in the system grows. Specifically, we consider a system with multiple classes of jobs, where jobs from different classes can request different numbers of servers and have different service time distributions, and jobs are served in first-come-first-served order. The multi-server job model opens up new scaling regimes where both the number of servers that a job needs and the system load scale with the total number of servers. Within these scaling regimes, we derive the first results on stability, queueing probability, and the transient analysis of the number of jobs in the system for each class. In particular we derive sufficient conditions for zero queueing. Our analysis introduces a novel way of extracting information from the Lyapunov drift, which can be applicable to a broader scope of problems in queueing systems. 

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