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Sampling protein-ligand binding pathways to recover crystallographic binding poses using interactive molecular dynamics in virtual realityAug 20 2019Using molecular dynamics (MD) to simulate drug binding & unbinding is a challenge. Because it requires sampling rugged energy landscapes that separate bound and unbound states, it has a high cost and consumes significant computational resources. Here, ... More
$θ$-curves in proteinsAug 16 2019Apart from the knots formed by the main-chain, the proteins can form numerous topological structures, when included the covalent and ion-mediated interactions. In this work, we define the protein non-trivial $\theta$-curves and identify 7 different topologies ... More
Using schematic models to understand the microscopic basis for inverted solubility in $γ$D-crystallinAug 15 2019Inverted solubility--a crystal melting upon cooling--is observed in a handful of proteins, such as carbomonoxy hemoglobin and $\gamma$D-crystallin. In human $\gamma$D-crystallin, the phenomenon is associated with the mutation of the 23$^\mathrm{rd}$ residue, ... More
Random sequential adsorption of spheres on a cylinderAug 14 2019Inspired by observations of beads packed on a thin string in such systems as sea-grapes and dental plaque, we study the random sequential adsorption of spheres on a cylinder. We determine the asymptotic fractional coverage of the cylinder as a function ... More
A minimum set of stable blocks for rational design of polypeptide chains Running head: A set of stable blocks for protein rational designAug 14 2019The aim of this work was to find a minimal set of structurally stable pentapeptides, which allows forming a polypeptide chain of a required 3D structure. To search for factors that ensure structural stability of the pentapeptide, we generated peptide ... More
Investigation of the impact of PTMs on the protein backbone conformationAug 14 2019Post-Translational Modifications (PTMs) are known to play a critical role in the regulation of the protein functions. Their impact on protein structures, and their link to disorder regions have already been spotted on the past decade. Nonetheless, the ... More
In silico prediction of protein flexibility with local structure approachAug 14 2019Flexibility is an intrinsic essential feature of protein structures, directly linked to their functions. To this day, most of the prediction methods use the crystallographic data (namely B-factors) as the only indicator of protein's inner flexibility ... More
Cross-Modal Fusion Between Data in SAXS and Cryo-EM for Biomolecular Structure DeterminationAug 09 2019Cryo-Electron Microscopy (cryo-EM) has become an extremely powerful method for resolving structural details of large biomolecular complexes. However, challenging problems in single-particle methods remain open because of (1) the low signal-to-noise ratio ... More
Resource-Efficient Quantum Algorithm for Protein FoldingAug 06 2019Predicting the three-dimensional (3D) structure of a protein from its primary sequence of amino acids is known as the protein folding (PF) problem. Due to the central role of proteins' 3D structures in chemistry, biology and medicine applications (e.g., ... More
Cross-validation tests for cryo-EM maps using an independent particle setAug 02 2019Cryo-electron microscopy is a revolutionary technique that can provide 3D density maps at near-atomic resolution. However, map validation is still an open issue in the field. Despite several efforts from the community, it is possible to overfit the reconstructions ... More
Universal Transforming Geometric NetworkAug 02 2019The recurrent geometric network (RGN), the first end-to-end differentiable neural architecture for protein structure prediction, is a competitive alternative to existing models. However, the RGN's use of recurrent neural networks (RNNs) as internal representations ... More
The de Rham-Hodge analysis and modeling of biomoleculesAug 01 2019Recent years have witnessed a trend that advanced mathematical tools, such as algebraic topology, differential geometry, graph theory, and partial differential equations, have been developed for describing biological macromolecules. These tools have considerably ... More
Deep Generative Model Driven Protein Folding SimulationAug 01 2019Significant progress in computer hardware and software have enabled molecular dynamics (MD) simulations to model complex biological phenomena such as protein folding. However, enabling MD simulations to access biologically relevant timescales (e.g., beyond ... More
Proteins: the physics of amorphous evolving matterJul 31 2019Proteins are a matter of dual nature. As a physical object, a protein molecule is a folded chain of amino acids with multifarious biochemistry. But it is also an instantiation along an evolutionary trajectory determined by the function performed by the ... More
Investigating the Role of Non-Covalent Interactions in Conformation and Assembly of Triazine-Based Sequence-Defined PolymersJul 30 2019Grate and co-workers at Pacific Northwest National Laboratory recently developed high information content triazine-based sequence-defined polymers that are robust by not having hydrolyzable bonds and can encode structure and functionality by having various ... More
Estimation of Protein-Ligand Unbinding Kinetics Using Non-Equilibrium Targeted Molecular Dynamics SimulationsJul 25 2019We here report on non-equilibrium targeted Molecular Dynamics simulations as tool for the estimation of protein-ligand unbinding kinetics. With this method, we furthermore investigate the molecular basis determining unbinding rates, correlating simulations ... More
Approximate calculation of the binding energy between 17$β$-estradiol and human estrogen receptor alphaJul 25 2019Estrogen receptors (ERs) are a group of proteins activated by 17$\beta$-estradiol. The endocrine-disrupting chemicals (EDCs) mimic estrogen action by bind directly to the ligand binding domain of ER. From this perspective, ER represent a good model for ... More
Approximate Numerical Integration of the Chemical Master Equation for Stochastic Reaction NetworksJul 24 2019Numerical solution of the chemical master equation for stochastic reaction networks typically suffers from the state space explosion problem due to the curse of dimensionality and from stiffness due to multiple time scales. The dimension of the state ... More
Enhanced Diffusion and Chemotaxis of EnzymesJul 21 2019Jul 23 2019Many enzymes appear to diffuse faster in the presence of substrate and to drift either up or down a concentration gradient of their substrate. Observations of these phenomena, termed enhanced enzyme diffusion (EED) and enzyme chemotaxis, respectively, ... More
Enhanced Diffusion and Chemotaxis of EnzymesJul 21 2019Jul 27 2019Many enzymes appear to diffuse faster in the presence of substrate and to drift either up or down a concentration gradient of their substrate. Observations of these phenomena, termed enhanced enzyme diffusion (EED) and enzyme chemotaxis, respectively, ... More
Analyses of protein cores reveal fundamental differences between solution and crystal structuresJul 18 2019There have been several studies suggesting that protein structures solved by NMR spectroscopy and x-ray crystallography show significant differences. To understand the origin of these differences, we assembled a database of high-quality protein structures ... More
The Marginal Stability of Proteins: How Jiggling and Wiggling of Atoms are Connected to Neutral EvolutionJul 17 2019Experimental evidence indicates that proteins are marginally stable. Unlike all previous proposals here we suggest, on a statistical thermodynamics basis, that the upper bound of the marginal stability of proteins also belongs to biomacromolecular complexes ... More
Perturbation Potentials to Overcome Order/Disorder Transitions in Alchemical Binding Free Energy CalculationsJul 14 2019We investigate the role of order/disorder transitions in alchemical simulations of protein-ligand absolute binding free energies. We show, in the context of a potential of mean force description, that for a benchmarking system (the complex between the ... More
Perturbation Potentials to Overcome Order/Disorder Transitions in Alchemical Binding Free Energy CalculationsJul 14 2019Aug 02 2019We investigate the role of order/disorder transitions in alchemical simulations of protein-ligand absolute binding free energies. We show, in the context of a potential of mean force description, that for a benchmarking system (the complex between the ... More
Weighted persistent homology for osmolyte molecular aggregation and hydrogen-bonding network analysisJul 14 2019It has long been observed that trimethylamin N-oxide (TMAO) and urea demonstrate dramatically different properties in a protein folding process. Even with the enormous theoretical and experimental research work of the two osmolytes, various aspects of ... More
The possibility of blocking the process of DNA base pairs opening by hydrogen peroxideJul 12 2019One of the most progressive methods of cancer treatment is ion beam therapy. The simulations of water radiolysis show that in the cell medium the most long-living species are hydrogen peroxide (H$_2$O$_2$) molecules. But up to the present time the role ... More
The possibility of blocking the process of DNA base pairs opening by hydrogen peroxideJul 12 2019Aug 07 2019One of the most progressive methods of cancer treatment is ion beam therapy. The simulations of water radiolysis show that in the cell medium the most long-living species are hydrogen peroxide (H$_2$O$_2$) molecules. But up to the present time the role ... More
Method of moments for 3-D single particle ab initio modeling with non-uniform distribution of viewing anglesJul 11 2019Single-particle reconstruction in cryo-electron microscopy (cryo-EM) is an increasingly popular technique for determining the 3-D structure of a molecule from several noisy 2-D projections images taken at unknown viewing angles. Most reconstruction algorithms ... More
Multiscale Visual Drilldown for the Analysis of Large Ensembles of Multi-Body Protein ComplexesJul 09 2019When studying multi-body protein complexes, biochemists use computational tools that can suggest hundreds or thousands of their possible spatial configurations. However, it is not feasible to experimentally verify more than only a very small subset of ... More
Deflation reveals dynamical structure in nondominant reaction coordinatesJul 09 2019The output of molecular dynamics simulations is high-dimensional, and the degrees of freedom among the atoms are related in intricate ways. Therefore, a variety of analysis frameworks have been introduced in order to distill complex motions into lower-dimensional ... More
Gelation impairs small molecule migration in polymer mixturesJul 09 2019Surface segregation of the low-molecular weight component in a polymeric mixture leads to degradation of industrial formulations. We report a simultaneous phase separation and surface migration phenomena in oligomer-polymer and oligomer-gel systems following ... More
4D Liquid-phase Electron Microscopy of Ferritin by Brownian Single Particle AnalysisJul 07 2019Protein function and activity are a consequence of its three-dimensional structure. Single particle analysis of cryogenic electron micrographs has radically changed structural biology allowing atomic reconstruction of almost any type of proteins. While ... More
The Application of Information Spectrum Method on Small Molecules and Target RecognitionJul 05 2019Current methods for investigation of receptor - ligand interactions in drug discovery are based on three-dimensional complementarity of receptor and ligand surfaces, and they include pharmacophore modelling, QSAR, molecular docking etc. Those methods ... More
Strongly bent double-stranded DNA: reconciling theory and experimentJul 02 2019The strong bending of polymers is poorly understood. We propose a general quantitative framework of polymer bending that includes both the weak and strong bending regimes on the same footing, based on a single general physical principle. As the bending ... More
Molecular activity prediction using graph convolutional deep neural network considering distance on a molecular graphJul 02 2019Machine learning is often used in virtual screening to find compounds that are pharmacologically active on a target protein. The weave module is a type of graph convolutional deep neural network that uses not only features focusing on atoms alone (atom ... More
Molecular activity prediction using graph convolutional deep neural network considering distance on a molecular graphJul 02 2019Jul 04 2019Machine learning is often used in virtual screening to find compounds that are pharmacologically active on a target protein. The weave module is a type of graph convolutional deep neural network that uses not only features focusing on atoms alone (atom ... More
Prediction of Small Molecule Kinase Inhibitors for Chemotherapy Using Deep LearningJun 30 2019The current state of cancer therapeutics has been moving away from one-size-fits-all cytotoxic chemotherapy, and towards a more individualized and specific approach involving the targeting of each tumor's genetic vulnerabilities. Different tumors, even ... More
Hierarchical domain model explains multifractal scaling of chromosome contact mapsJun 28 2019Modern experimental techniques such as Hi--C make it possible to measure the probability that different chromosomal regions are close in space. Usually, these measurements are characterized by the scaling of the contact probability as a function of the ... More
Purification of total flavonoids from Aurea Helianthus flowers and In Vitro Hypolipidemic EffectJun 28 2019The effects of purification methods and its hypolipidemic function on the total flavonoids of Aurea Helianthus flower were investigated. Liquid-liquid extraction of ethanol extract from Aurea Helianthus flower was carried out by using different polar ... More
Effect of different polarity solvents on total phenols and flavonoids content, and In-vitro antioxidant properties of flowers extract from Aurea HelianthusJun 28 2019The total phenols and flavonoids content of different polar solvent extracts from Aurea Helianthus flowers, and their antioxidant activity were determined. The ethanol extract of Aurea Helianthus flowers were suspended in water and fractionated using ... More
Structure and dynamics of dynorphin peptide and its receptorJun 27 2019Dynorphin is a neuropeptide involved in pain, addiction and mood regulation. It exerts its activity by binding to the kappa opioid receptor (KOP) which belongs to the large family of G-protein coupled receptors. The dynorphin peptide was discovered in ... More
Improving RNA secondary structure prediction via state inference with deep recurrent neural networksJun 26 2019The problem of determining which nucleotides of an RNA sequence are paired or unpaired in the secondary structure of an RNA, which we call RNA state inference, can be studied by different machine learning techniques. Successful state inference of RNA ... More
Quantified uncertainty of flexible protein-protein docking algorithmsJun 24 2019The strength or weakness of an algorithm is ultimately governed by the confidence of its result. When the domain of the problem is large (e.g. traversal of a high-dimensional space), a perfect solution cannot be obtained, so approximations must be made. ... More
Cooperativity, Absolute Interaction, and Algebraic OptimizationJun 24 2019We consider a measure of cooperativity based on the minimal absolute interaction required to generate an observed titration behavior. We describe the corresponding algebraic optimization problem and show how it can be solved using the nonlinear algebra ... More
Inter-residue, inter-protein and inter-family coevolution: bridging the scalesJun 24 2019Interacting proteins coevolve at multiple but interconnected scales, from the residue-residue over the protein-protein up to the family-family level. The recent accumulation of enormous amounts of sequence data allows for the development of novel, data-driven ... More
Intrinsic noise, Delta-Notch signalling and delayed reactions promote sustained, coherent, synchronised oscillations in the presomitic mesodermJun 21 2019Using a stochastic individual-based modelling approach, we examine the role that Delta-Notch signalling plays in the regulation of a robust and reliable somite segmentation clock. We find that not only can Delta-Notch signalling synchronise noisy cycles ... More
Knotted Proteins: Tie Etiquette in Structural BiologyJun 20 2019A small fraction of all protein structures characterized so far are entangled. The challenge of understanding the properties of these knotted proteins, and the why and the how of their natural folding process, has been taken up in the past decade with ... More
Key biology you should have learned in physics class: Using ideal-gas mixtures to understand biomolecular machinesJun 19 2019The biological cell exhibits a fantastic range of behaviors, but ultimately these are governed by a handful of physical and chemical principles. Here we explore simple theory, known for decades and based on the simple thermodynamics of mixtures of ideal ... More
Evaluating Protein Transfer Learning with TAPEJun 19 2019Protein modeling is an increasingly popular area of machine learning research. Semi-supervised learning has emerged as an important paradigm in protein modeling due to the high cost of acquiring supervised protein labels, but the current literature is ... More
Molecular free energy profiles from force spectroscopy experiments by inversion of observed committorsJun 19 2019In single-molecule force spectroscopy experiments, a biomolecule is attached to a force probe via polymer linkers, and the total extension -- of molecule plus apparatus -- is monitored as a function of time. In a typical unfolding experiment at constant ... More
Sensitivity Comparison of Macro- and Micro-electrochemical Biosensors for Human Chorionic Gonadotropin Biomarker DetectionJun 13 2019Selectivity and sensitivity are important figures of merit in the design and optimization of electrochemical biosensors. The efficiency of the fabricated immunosensing surface can easily be influenced by several factors, such as detection limit, non-specific ... More
The hydrophobic effect characterises the thermodynamic signature of amyloid fibril growthJun 13 2019Many proteins have the potential to aggregate into amyloid fibrils, which are associated with a wide range of human disorders including Alzheimer's and Parkinson's disease. In contrast to that of folded proteins, the thermodynamic stability of amyloid ... More
Simulated Epidemics in 3D Protein Structures to Detect Functional PropertiesJun 12 2019The outcome of an epidemic is closely related to the network of interactions between the individuals. Likewise, protein functions depend on the 3D arrangement of their residues and on the underlying energetic interaction network. Borrowing ideas from ... More
In silico evidence that protein unfolding is as a precursor of the protein aggregationJun 12 2019We present a computational study on the folding and aggregation of proteins in aqueous environment, as function of its concentration. We show how the increase of the concentration of individual protein species can induce a partial unfolding of the native ... More
High-resolution Markov state models for the dynamics of Trp-cage miniprotein constructed over slow folding modes identified by state-free reversible VAMPnetsJun 12 2019State-free reversible VAMPnets (SRVs) are a neural network-based framework capable of learning the leading eigenfunctions of the transfer operator of a dynamical system from trajectory data. In molecular dynamics simulations, these data-driven collective ... More
Protein contact map prediction using bi-directional recurrent neural networkJun 11 2019Given native 2D contact map, protein 3D structure could be reconstructed with accuracy of 2A or better, and such reconstruction is a feasible computational approach for protein folding problem. The prediction accuracy from traditional methods is generally ... More
Phylogenetic correlations can suffice to infer protein partners from sequencesJun 10 2019Determining which proteins interact together is crucial to a systems-level understanding of the cell. Recently, algorithms based on Direct Coupling Analysis (DCA) pairwise maximum-entropy models have allowed to identify interaction partners among the ... More
Critical phenomena in the temperature-pressure-crowding phase diagram of a proteinJun 09 2019In the cell, proteins fold and perform complex functions through global structural rearrangements. Function requires a protein to be at the brink of stability to be susceptible to small environmental fluctuations, yet stable enough to maintain structural ... More
Seq-SetNet: Exploring Sequence Sets for Inferring StructuresJun 06 2019Sequence set is a widely-used type of data source in a large variety of fields. A typical example is protein structure prediction, which takes an multiple sequence alignment (MSA) as input and aims to infer structural information from it. Almost all of ... More
OnionNet: a multiple-layer inter-molecular contact based convolutional neural network for protein-ligand binding affinity predictionJun 06 2019Computational drug discovery provides an efficient tool helping large scale lead molecules screening. One of the major tasks of lead discovery is identifying molecules with promising binding affinities towards a target, a protein in general. The accuracies ... More
Enhancing the performance of DNA surface-hybridization biosensors through target depletionJun 04 2019DNA surface-hybridization biosensors utilize the selective hybridization of target sequences in solution to surface-immobilized probes. In this process, the target is usually assumed to be in excess, so that its concentration does not significantly vary ... More
Energy landscapes and dynamics of xylo-nucleic acidsJun 03 2019Artificial analogues of the natural nucleic acids have attracted recent interest as a diverse class of information storage molecules capable of self-replication. In the present study, we use the computational potential energy landscape framework to investigate ... More
Scaffold-based molecular design using graph generative modelMay 31 2019Searching new molecules in areas like drug discovery often starts from the core structures of candidate molecules to optimize the properties of interest. The way as such has called for a strategy of designing molecules retaining a particular scaffold ... More
Current enhancement in solid-state nanopores depends on three-dimensional DNA structureMay 31 2019The translocation of double-stranded DNA through a solid-state nanopore may either decrease or increase the ionic current depending on the ionic concentration of the surrounding solution. Below a certain crossover ionic concentration, the current change ... More
Anionic nanoparticle-lipid membrane interactions: the protonation of anionic ligands at the membrane surface reduces membrane disruptionMay 30 2019Monolayer-protected gold nanoparticles (Au NPs) are promising biomedical tools with applications to diagnosis and therapy, thanks to their biocompatibility and versatility. Here we show how the NP surface functionalization can drive the mechanism of interaction ... More
Collective-variable selection and generative Hopfield-Potts models for protein-sequence familiesMay 28 2019Statistical models for families of evolutionary related proteins have recently gained interest: in particular pairwise Potts models, as those inferred by the Direct-Coupling Analysis, have been able to extract information about the three-dimensional structure ... More
Persistent homology analysis of osmolyte molecular aggregation and their hydrogen-bonding networksMay 28 2019Two types of osmolytes, i.e., trimethylamin N-oxide (TMAO) and urea, demonstrate dramatically different properties in a protein folding process. Even with the great progresses in revealing the potential underlying mechanism of these two osmolyte systems, ... More
Role of Ligand Conformation on Nanoparticle-Protein InteractionsMay 28 2019Engineered biomedical nanoparticles (NP) administered via intravenous routes are prone to associate to serum proteins. The protein corona can mask the NP surface functionalization and hamper the delivery of the NP to its biological target. The design ... More
AmoebaContact and GDFold: a new pipeline for rapid prediction of protein structuresMay 28 2019Native contacts between residues could be predicted from the amino acid sequence of proteins, and the predicted contact information could assist the de novo protein structure prediction. Here, we present a novel pipeline of a residue contact predictor ... More
Towards Interpretable Sparse Graph Representation Learning with Laplacian PoolingMay 28 2019Recent work in graph neural networks (GNNs) has lead to improvements in molecular activity and property prediction tasks. However, GNNs lack interpretability as they fail to capture the relative importance of various molecular substructures due to the ... More
Investigation of HIV-1 Gag binding with RNAs and Lipids using Atomic Force MicroscopyMay 27 2019Atomic Force Microscopy was utilized to study the morphology of Gag, {\Psi}RNA, and their binding complexes with lipids in a solution environment with 0.1{\AA} vertical and 1nm lateral resolution. TARpolyA RNA was used as a RNA control. The lipid used ... More
A COLD Approach to Generating Optimal SamplesMay 23 2019Optimising discrete data for a desired characteristic using gradient-based methods involves projecting the data into a continuous latent space and carrying out optimisation in this space. Carrying out global optimisation is difficult as optimisers are ... More
Three-dimensional view of ultrafast dynamics in photoexcited bacteriorhodopsinMay 22 2019Bacteriorhodopsin (bR) is a light-driven proton pump. We use time-resolved crystallography at an X-ray free-electron laser to follow the structural changes in multiphoton-excited bR from 250 femtoseconds to 10 picoseconds. Quantum chemistry and ultrafast ... More
Molecular rules for selectivity in lipase-catalysed acylation of lysineMay 21 2019The selectivity of L-lysine acylation by lauric acid catalysed by Candida antarctica lipase B (CALB) was investigated combining experimental and theoretical methodologies. Experiments showed the near-exclusive acylation of lysine $\epsilon$-amino group; ... More
Deep learning to generate in silico chemical property libraries and candidate molecules for small molecule identification in complex samplesMay 21 2019Comprehensive and unambiguous identification of small molecules in complex samples will revolutionize our understanding of the role of metabolites in biological systems. Existing and emerging technologies have enabled measurement of chemical properties ... More
ROMEO: A Plug-and-play Software Platform of Robotics-inspired Algorithms for Modeling Biomolecular Structures and MotionsMay 20 2019Motivation: Due to the central role of protein structure in molecular recognition, great computational efforts are devoted to modeling protein structures and motions that mediate structural rearrangements. The size, dimensionality, and non-linearity of ... More
Transient hydrophobic exposure in the molecular dynamics of Abeta peptide at low water concentrationMay 20 2019Abeta is a disordered peptide central to Alzheimer's Disease. Aggregation of Abeta has been widely explored, but its molecular crowding less so. The synaptic cleft where Abeta locates only holds 60-70 water molecules along its width. We subjected Abeta40 ... More
Predicting 3D structure and stability of RNA pseudoknots in monovalent and divalent ion solutionsMay 19 2019RNA pseudoknots are a kind of minimal RNA tertiary structural motifs, and their three-dimensional (3D) structures and stability play essential roles in a variety of biological functions. Therefore, to predict 3D structures and stability of RNA pseudoknots ... More
Fluctuations of Electric Fields in the Active Site of the Enzyme Ketosteroid IsomeraseMay 18 2019We report the effect of conformational dynamics on the fluctuations of electric fields in the active site of the enzyme Ketosteroid Isomerase (KSI). While KSI is considered rigid with little conformational variation to support different stages of the ... More
Limitations in Predicting Radiation-Induced Pharmaceutical Instability during Long-Duration SpaceflightMay 15 2019As human spaceflight seeks to expand beyond low-Earth orbit, NASA and its international partners face numerous challenges related to ensuring the safety of their astronauts, including the need to provide a safe and effective pharmacy for long-duration ... More
Size and structure of the sequence space of repeat proteinsMay 11 2019The coding space of protein sequences is shaped by evolutionary constraints set by requirements of function and stability. We show that the coding space of a given protein family--the total number of sequences in that family--can be estimated using models ... More
Size and structure of the sequence space of repeat proteinsMay 11 2019Jul 03 2019The coding space of protein sequences is shaped by evolutionary constraints set by requirements of function and stability. We show that the coding space of a given protein family--the total number of sequences in that family--can be estimated using models ... More
Thermal Fracture Kinetics of Heterogeneous Semiflexible PolymersMay 08 2019The fracture and severing of polymer chains plays a critical role in the failure of fibrous materials and the regulated turnover of intracellular filaments. Using continuum wormlike chain models, we investigate the fracture of semiflexible polymers via ... More
Thermal Fracture Kinetics of Heterogeneous Semiflexible PolymersMay 08 2019Aug 12 2019The fracture and severing of polymer chains plays a critical role in the failure of fibrous materials and the regulated turnover of intracellular filaments. Using continuum wormlike chain models, we investigate the fracture of semiflexible polymers via ... More
Parameter-free Clustering of Free Energy Landscapes with Gaussian MixturesMay 08 2019Free energy landscapes provide insights into conformational ensembles of biomolecules. In order to analyze these landscapes and elucidate mechanisms underlying conformational changes, there is a need to extract metastable states with limited noise. This ... More
Allostery and conformational changes upon binding as generic features of proteins: a high-dimension geometrical approachMay 07 2019A growing number of experimental evidence shows that it is general for a ligand binding protein to have a potential for allosteric regulation and for further evolution. In addition, such proteins generically change their conformation upon binding. O. ... More
tRNA as stabilizing matrix for fluorescent silver clusters: photophysical properties and IR studyMay 04 2019In this experimental study fluorescent silver clusters on tRNA matrix were synthesized for the first time. Obtained complexes have two emission regions in visible part of spectrum. We have also studied our complexes using FTIR spectroscopy. The possible ... More
tRNA as stabilizing matrix for fluorescent silver clusters: photophysical properties and IR studyMay 04 2019May 18 2019In this experimental study fluorescent silver clusters on tRNA matrix were synthesized for the first time. Obtained complexes have two emission regions in visible part of spectrum. We have also studied our complexes using FTIR spectroscopy. The possible ... More
Comprehensive classification of the plant non-specific lipid transfer protein superfamily towards its Sequence -Structure -Function analysisMay 02 2019Background. Non-specific Lipid Transfer Proteins (nsLTPs) are widely distributed in the plant kingdom and constitute a superfamily of related proteins. More than 800 different sequences have been characterized so far, but their biological functions remain ... More
DNA energy constraints shape biological evolutionary trajectoriesMay 02 2019Most living systems rely on double-stranded DNA (dsDNA) to store their genetic information and perpetrate themselves. Thus, the biological information contained within a dsDNA molecule, in terms of a linear sequence of nucleotides, has been considered ... More
Machine Learning for Classification of Protein Helix Capping MotifsMay 01 2019The biological function of a protein stems from its 3-dimensional structure, which is thermodynamically determined by the energetics of interatomic forces between its amino acid building blocks (the order of amino acids, known as the sequence, defines ... More
A polymer model of bacterial supercoiled DNA including structural transitions of the double helixApr 25 2019DNA supercoiling, the under or overwinding of DNA, is a key physical mechanism both participating to compaction of bacterial genomes and making genomic sequences adopt various structural forms. DNA supercoiling may lead to the formation of braided superstructures ... More
Topology, Landscapes, and Biomolecular Energy TransportApr 25 2019While ubiquitous, energy redistribution remains a poorly understood facet of the nonequilibrium thermodynamics of biomolecules. At the molecular level, finite-size effects, pronounced nonlinearities, and ballistic processes conspire to produce behavior ... More
Backbone chemical shift assignments of human 14-3-3$σ$Apr 24 201914-3-3 proteins are a group of seven dimeric adapter proteins that exert their biological function by interacting with hundreds of phosphorylated proteins, thus influencing their sub-cellular localization, activity or stability in the cell. Due to this ... More
The lubricity of mucin solutions is robust against changes in physiological conditionsApr 18 2019Solutions of manually purified gastric mucins have been shown to be promising lubricants for biomedical purposes, where they can efficiently reduce friction and wear. However, so far, such mucin solutions have been mostly tested in specific settings, ... More
The lubricity of mucin solutions is robust toward changes in physiological conditionsApr 18 2019Jul 18 2019Solutions of manually purified gastric mucins have been shown to be promising lubricants for biomedical purposes, where they can efficiently reduce friction and wear. However, so far, such mucin solutions have been mostly tested in specific settings, ... More
DeepNovoV2: Better de novo peptide sequencing with deep learningApr 17 2019May 22 2019Personalized cancer vaccines are envisioned as the next generation rational cancer immunotherapy. The key step in developing personalized therapeutic cancer vaccines is to identify tumor-specific neoantigens that are on the surface of tumor cells. A promising ... More
DeepNovoV2: Better de novo peptide sequencing with deep learningApr 17 2019We introduce DeepNovoV2, the state-of-the-art neural networks based model for de novo peptide sequencing. Contrary to existing models like DeepNovo or DeepMatch which represents each spectrum as a long sparse vector, in DeepNovoV2, we propose to directly ... More
Cryo-Electron Microscopy Image Analysis Using Multi-Frequency Vector Diffusion MapsApr 16 2019Cryo-electron microscopy (EM) single particle reconstruction is an entirely general technique for 3D structure determination of macromolecular complexes. However, because the images are taken at low electron dose, it is extremely hard to visualize the ... More
Detection of protein-ligand binding sites with 3D segmentationApr 13 2019In recent years machine learning (ML) took bio- and cheminformatics fields by storm, providing new solutions for a vast repertoire of problems related to protein sequence, structure, and interactions analysis. ML techniques, deep neural networks especially, ... More