Phyre2 is a web-based tool for predicting and analyzing protein structure and function. Phyre2 uses advanced remote homology detection methods to build 3D models, predict ligand binding sites, and analyze amino acid variants in a protein sequence. Phyre2 is a suite of tools available on the web to predict and analyze protein structure, function and mutations. The focus of Phyre2 is to provide biologists with a simple and intuitive interface to state-of-the-art protein bioinformatics tools. Phyre2 replaces Phyre, the original version of the server for which we previously published a paper in Nature Protocols. In this updated protocol, we describe Phyre2, which uses advanced remote homology detection methods to build 3D models, predict ligand binding sites and analyze the effect of amino acid variants (e.g., nonsynonymous SNPs (nsSNPs)) for a user's protein sequence. Users are guided through results by a simple interface at a level of detail they determine. This protocol will guide users from submitting a protein sequence to interpreting the secondary and tertiary structure of their models, their domain composition and model quality. A range of additional available tools is described to find a protein structure in a genome, to submit large number of sequences at once and to automatically run weekly searches for proteins that are difficult to model. The server is available at http://www.sbg.bio.ic.ac.uk/phyre2
 . A typical structure prediction will be returned between 30 min and 2 h after submission.

/pdf/the-phyre2-web-portal-for-protein-modeling-prediction-and-xppnx59tej.pdf

The Phyre2 web portal for protein modeling, prediction and analysis

Here, we present FireDock, an efficient method for the refinement and rescoring of rigid-body docking solutions. The refinement process consists of two main steps: (1) rearrangement of the interface side-chains and (2) adjustment of the relative orientation of the molecules. Our method accounts for the observation that most interface residues that are important in recognition and binding do not change their conformation significantly upon complexation. Allowing full side-chain flexibility, a common procedure in refinement methods, often causes excessive conformational changes. These changes may distort preformed structural signatures, which have been shown to be important for binding recognition. Here, we restrict side-chain movements, and thus manage to reduce the false-positive rate noticeably. In the later stages of our procedure (orientation adjustments and scoring), we smooth the atomic radii. This allows for the minor backbone and side-chain movements and increases the sensitivity of our algorithm. FireDock succeeds in ranking a near-native structure within the top 15 predictions for 83% of the 30 enzyme-inhibitor test cases, and for 78% of the 18 semiunbound antibody-antigen complexes. Our refinement procedure significantly improves the ranking of the rigid-body PatchDock algorithm for these cases. The FireDock program is fully automated. In particular, to our knowledge, FireDock's prediction results are comparable to current state-of-the-art refinement methods while its running time is significantly lower. The method is available at http://bioinfo3d.cs.tau.ac.il/FireDock/.

FireDock: fast interaction refinement in molecular docking.

Augmented Reality (AR) is a fast rising technology and it has been applied in many fields such as gaming, learning, entertainment, medical, military, sports, etc. This paper reviews some of the academic studies of AR applications in manufacturing operations. Comparatively, it is lesser addressed due to stringent requirements of high accuracy, fast response and the desirable alignment with industrial standards and practices such that the users will not find drastic transition when adopting this new technology. This paper looks into common manufacturing activities such as product design, robotics, facilities layout planning, maintenance, CNC machining simulation and assembly planning. Some of the issues and future trends of AR technology are also addressed. 

Virtual and Augmented Reality Applications in Manufacturing

Facility layout problem (FLP) is defined as the placement of facilities in a plant area, with the aim of determining the most effective arrangement in accordance with some criteria or objectives under certain constraints, such as shape, size, orientation, and pick-up/drop-off point of the facilities. It has been over six decades since Koopmans and Beckmann published their seminal paper on modeling the FLP. Since then, there have been improvements to these researchers’ original quadratic assignment problem. However, research on many aspects of the FLP is still in its initial stage; hence, the issue is an interesting field to work on. Here, a review of literature is made by referring to numerous papers about FLPs. The study is mainly motivated by the current and prospective trends of research on such points as layout evolution, workshop characteristics, problem formulation, and solution methodologies. It points to gaps in the literature and suggests promising directions for future research on FLP.

Classification of facility layout problems: a review study

Treating flexibility in molecular docking is a major challenge in cell biology research. Here we describe the background and the principles of existing flexible protein-protein docking methods, focusing on the algorithms and their rational. We describe how protein flexibility is treated in different stages of the docking process: in the preprocessing stage, rigid and flexible parts are identified and their possible conformations are modeled. This preprocessing provides information for the subsequent docking and refinement stages. In the docking stage, an ensemble of pre-generated conformations or the identified rigid domains may be docked separately. In the refinement stage, small-scale movements of the backbone and side-chains are modeled and the binding orientation is improved by rigid-body adjustments. For clarity of presentation, we divide the different methods into categories. This should allow the reader to focus on the most suitable method for a particular docking problem.

https://www.onlinelibrary.wiley.com/doi/pdf/10.1002/prot.22170

Principles of Flexible Protein-Protein Docking

A branch-and-bound algorithm for the continuous facility layout problem

Aligning proteins based on their structural similarity is a fundamental problem in molecular biology with applications in many settings, including structure classification, database search, function prediction, and assessment of folding prediction methods. Structural alignment can be done via several methods, including contact map overlap (CMO) maximization that aligns proteins in a way that maximizes the number of common residue contacts. In this paper, we develop a reduction-based exact algorithm for the CMO problem. Our approach solves CMO directly rather than after transformation to other combinatorial optimization problems. We exploit the mathematical structure of the problem in order to develop a number of efficient lower bounding, upper bounding, and reduction schemes. Computational experiments demonstrate that our algorithm runs significantly faster than existing exact algorithms and solves some hard CMO instances that were not solved in the past. In addition, the algorithm produces protein cluste...

A reduction-based exact algorithm for the contact map overlap problem.

A fundamental problem in molecular biology is the comparison of 3-dimensional protein folds in order to develop similarity measures and exploit them for protein clustering, database searches, and drug design. Contact map overlap (CMO) is one of the most reliable and robust measures of protein structure similarity. Fold comparison can be done by aligning the amino acid residues of two proteins in a way that maximizes the number of common residue contacts. CMO maximization is gaining increasing attention because it results in protein clusterings in good agreement with classification by experts. However, CMO maximization is an ${\mathcal{NP}}$-hard problem and few exact algorithms exist for solving this problem to global optimality.

In this paper, we propose a branch-and-reduce exact algorithm for the CMO problem. Contrary to previous approaches, we do not transform CMO to other combinatorial optimization problems for solution. Instead, we address the problem directly in its natural form. By exploiting the problem's mathematical structure, we develop bounding and reduction procedures that lead to a very efficient algorithm. We present extensive computational results for over 36000 test problems from the literature. These results demonstrate that our algorithm is significantly faster and solves many more challenging test sets than the best previous algorithms for CMO. Furthermore, the algorithm results in protein clusters that are in excellent agreement with the SCOP database.

A branch-and-reduce algorithm for the contact map overlap problem

Motivation: The protein side-chain conformation problem is a central problem in proteomics with wide applications in protein structure prediction and design. Computational complexity results show that the problem is hard to solve. Yet, instances from realistic applications are large and demand fast and reliable algorithms.

Results: We propose a new global optimization algorithm, which for the first time integrates residue reduction and rotamer reduction techniques previously developed for the protein side-chain conformation problem. We show that the proposed approach simplifies dramatically the topology of the underlining residue graph. Computations show that our algorithm solves problems using only 1--10% of the time required by the mixed-integer linear programming approach available in the literature. In addition, on a set of hard side-chain conformation problems, our algorithm runs 2--78 times faster than SCWRL 3.0, which is widely used for solving these problems.

Availability: The implementation is available as an online server at http://eudoxus.scs.uiuc.edu/r3.html

Contact: [email protected]

Residue-rotamer-reduction algorithm for the protein side-chain conformation problem

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A branch-and-bound algorithm for the continuous facility layout problem

A reduction-based exact algorithm for the contact map overlap problem.

A branch-and-reduce algorithm for the contact map overlap problem

Residue-rotamer-reduction algorithm for the protein side-chain conformation problem