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Antibodies play an important role in the immune system by binding to molecules called antigens at their respective epitopes. These interfaces or epitopes are structural entities determined by the interactions between an antibody and an antigen, making them ideal systems to analyze by using docking programs. Since the advent of high-throughput antibody sequencing, the ability to perform epitope mapping using only the sequence of the antibody has become a high priority. ClusPro, a leading protein-protein docking server, together with its template-based modeling version, ClusPro-TBM, have been re-purposed to map epitopes for specific antibody-antigen interactions by using the Antibody Epitope Mapping server (AbEMap). ClusPro-AbEMap offers three different modes for users depending on the information available on the antibody as follows: (i) X-ray structure, (ii) computational/predicted model of the structure or (iii) only the amino acid sequence. The AbEMap server presents a likelihood score for each antigen residue of being part of the epitope. We provide detailed information on the server's capabilities for the three options and discuss how to obtain the best results. In light of the recent introduction of AlphaFold2 (AF2), we also show how one of the modes allows users to use their AF2-generated antibody models as input. The protocol describes the relative advantages of the server compared to other epitope-mapping tools, its limitations and potential areas of improvement. The server may take 45-90 min depending on the size of the proteins., (© 2023. Springer Nature Limited.)

Antibodies are key proteins produced by the immune system to target pathogen proteins termed antigens via specific binding to surface regions called epitopes. Given an antigen and the sequence of an antibody the knowledge of the epitope is critical for the discovery and development of antibody based therapeutics. In this work, we present a computational protocol that uses template-based modeling and docking to predict epitope residues. This protocol is implemented in three major steps. First, a template-based modeling approach is used to build the antibody structures. We tested several options, including generation of models using AlphaFold2. Second, each antibody model is docked to the antigen using the fast Fourier transform (FFT) based docking program PIPER. Attention is given to optimally selecting the docking energy parameters depending on the input data. In particular, the van der Waals energy terms are reduced for modeled antibodies relative to x-ray structures. Finally, ranking of antigen surface residues is produced. The ranking relies on the docking results, that is, how often the residue appears in the docking poses' interface, and also on the energy favorability of the docking pose in question. The method, called PIPER-Map, has been tested on a widely used antibody-antigen docking benchmark. The results show that PIPER-Map improves upon the existing epitope prediction methods. An interesting observation is that epitope prediction accuracy starting from antibody sequence alone does not significantly differ from that of starting from unbound (i.e., separately crystallized) antibody structure., (© 2022 Wiley Periodicals LLC.)

We develop a Regression-based Ranking by Pairwise Cluster Comparisons (RRPCC) method to rank clusters of similar protein complex conformations generated by an underlying docking program. The method leverages robust regression to predict the relative quality difference between any pair or clusters and combines these pairwise assessments to form a ranked list of clusters, from higher to lower quality. We apply RRPCC to clusters produced by the automated docking server ClusPro and, depending on the training/validation strategy, we show improvement by 24-100% in ranking acceptable or better quality clusters first, and by 15-100% in ranking medium or better quality clusters first. We compare the RRPCC-ClusPro combination to a number of alternatives, and show that very different machine learning approaches to scoring docked structures yield similar success rates. Finally, we discuss the current limitations on sampling and scoring, looking ahead to further improvements. Interestingly, some features important for improved scoring are internal energy terms that occur only due to the local energy minimization applied in the refinement stage following rigid body docking., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2021 The Authors.)

The development of fast Fourier transform (FFT) algorithms enabled the sampling of billions of complex conformations and thus revolutionized protein-protein docking. FFT-based methods are now widely available and have been used in hundreds of thousands of docking calculations. Although the methods perform "soft" docking, which allows for some overlap of component proteins, the rigid body assumption clearly introduces limitations on accuracy and reliability. In addition, the method can work only with energy expressions represented by sums of correlation functions. In this paper we use a well-established protein-protein docking benchmark set to evaluate the results of these limitations by focusing on the performance of the docking server ClusPro, which implements one of the best rigid body methods. Furthermore, we explore the theoretical limits of accuracy when using established energy terms for scoring, provide comparison with flexible docking algorithms, and review the historical performance of servers in the CAPRI docking experiment., Competing Interests: Declaration of Interests Acpharis Inc. offers commercial licenses to PIPER. D.K. and S.V. occasionally consult for Acpharis, and own stock in the company. However, the PIPER program and the use of the ClusPro server are free for academic and governmental use., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

Mechanical response of single crystals to light, temperature, and/or force-an emerging platform for the development of new organic actuating materials for soft robotics-has recently been quantitatively described by a general and robust mathematical model ( Chem. Rev . 2015 , 115 , 12440 - 12490 ). The model can be used to extract accurate activation energies and kinetics of solid-state chemical reactions simply by tracking the time-dependent bending of the crystal. Here we illustrate that deviations of the macroscopic strain in the crystal from that predicted by the model reveal the existence of additional, "hidden" chemical or physical processes, such as sustained structural relaxation between the chemical transformation and the resulting macroscopic deformation of the crystal. This is illustrated with photobendable single crystals of 4-hydroxy-2-(2-pyridinylmethylene)hydrazide, a photochemical switch that undergoes E- to -Z isomerization. The irreversible isomerization in these crystals results in amorphization and plastic deformation that are observed as poor correlation between the transformation extent and the induced strains. The occurrence of these processes was independently confirmed by X-ray diffraction and differential scanning calorimetry. An extended mathematical model is proposed to account for this complex mechanical response.

Microfluidic devices offer new technical possibilities for a precise manipulation of Caenorhabditis elegans due to the comparable length scale. C. elegans is a small, free-living nematode worm that is a popular model system for genetic, genomic, and high-throughput experimental studies of animal development and neurobiology. In this paper, we demonstrate a microfluidic system in polydimethylsiloxane (PDMS) for dispensing of a single C. elegans worm into a 96-well plate. It consists of two PDMS layers, a flow and a control layer. Using five microfluidic pneumatic valves in the control layer, a single worm is trapped upon optical detection with a pair of optical fibers integrated perpendicular to the constriction channel and then dispensed into a microplate well with a dispensing tip attached to a robotic handling system. Due to its simple design and facile fabrication, we expect that our microfluidic chip can be expanded to a multiplexed dispensation system of C. elegans worms for high-throughput drug screening.

When exposed to external stimuli such as heat or light, certain single crystals can acquire momentum and undergo motion. On a molecular scale, the motility of such dynamic single crystals is triggered by a phase transition or chemical reaction without gaseous products, and macroscopically manifests as either slow (reversible or irreversible) deformation, or as rapid, almost instantaneous propulsion of the crystals that is oftentimes accompanied by disintegration. While the elastic energy of the slow reconfiguration processes such as bending, twisting and coiling can be utilized for actuation of other objects, the fast disintegrative processes could be exploited to initiate pressure-sensitive applications. This short review intends to summarize recent developments in the growing research on dynamic crystals, especially aspects of the mechanism of rapid motion of thermosalient and photosalient (leaping) crystals. The collective evidence indicates that these solids are organic-based analogues of the inorganic martensitic materials. While qualitative explanation of the molecular processes that lead to the related dynamic phenomena can be provided, quantification of their kinematics, estimation of the useful work that can be extracted, and prediction of their occurrence are yet to be established. Harnessing the potential of these materials to rapidly and efficiently perform the fundamentally important process of transduction of heat or light into kinetic energy appears as a prospective basis for their application in motion gears and devices.

The thermosalient crystals of terephthalic acid are extraordinarily mechanically compliant and reversibly shape-shift between two forms with different crystal habits. While the transition of form II to form I is spontaneous, the transition of form I to form II is latent and can be triggered by applying local mechanical stress, whereby crystals leap several centimeters in air. This mechanosalient effect (mechanically stimulated motility) is due to sudden release of strain that has accrued in the crystal of form I, which is a metastable structure at ambient conditions. High-speed optical analysis and serial scanning electron microscopy reveal that the mechanical effect is due to rapid reshaping of crystal domains on a millisecond time scale triggered by mechanical stimulation. Mechanically pre-deformed crystals taken over the thermal phase transition exhibit memory effects and partially regain their shape, while cracked, sliced, or otherwise damaged crystals tend to recover their macroscopic integrity by restorative action of intermolecular π-π interactions in a manner which resembles the behavior of shape-memory and self-healing polymers. These observations provide additional evidence that the thermo-/photo-/mechanosalient effects are macroscopic manifestations of martensitic-type transitions in molecular solids.