A5072753313- Protein Structure and Dynamics
- Machine Learning in Bioinformatics
- Enzyme Structure and Function
- RNA and protein synthesis mechanisms
- Mass Spectrometry Techniques and Applications
- Computational Drug Discovery Methods
- Plant and animal studies
- Genomics and Phylogenetic Studies
- Microbial Metabolic Engineering and Bioproduction
- Biochemical and Structural Characterization
- Toxin Mechanisms and Immunotoxins
- Insect and Arachnid Ecology and Behavior
- Peptidase Inhibition and Analysis
- Glycosylation and Glycoproteins Research
- Insect and Pesticide Research
- Species Distribution and Climate Change
- Signaling Pathways in Disease
- Machine Learning in Materials Science
- Bioinformatics and Genomic Networks
- Cell Image Analysis Techniques
- Advanced Data Processing Techniques
- Turtle Biology and Conservation
- Machine Learning and Algorithms
- vaccines and immunoinformatics approaches
- Fuzzy Logic and Control Systems
Ben-Gurion University of the Negev
2013-2024
Stanford University
1998-2014
Carmel (Israel)
2014
University of Haifa
2014
Stanford Medicine
2003
Scripps Research Institute
1998
Hebrew University of Jerusalem
1997
Institute of Life Sciences
1995
A package of computer programs for molecular dynamics simulations-MOIL-is described. flexible data structure enables the study macromolecules with potentials consistent AMBER/OPLS force field. The supplied parameter set has proteins in mind. In addition to 'wide spread' applications such as energy, energy minimization, normal modes, and free calculations code is also provided pursue less common applications. This includes reaction path (in condensed phases), uses mean field approach enhanced...
A Gene for Early Acceptance One of the fundamental properties immune system is ability to distinguish self- from nonself–histocompatibility. To gain insight into evolution and molecular basis histocompatibility, Voskoboynik et al. (p. 384 ) sought determine genetic a natural transplantation reaction that occurs in Botryllus schlosseri , colonial urochordate. Compatibility allows vascular fusion among individuals, whereas incompatibility results an inflammatory rejection response. single gene...
The protein structure prediction problem continues to elude scientists. Despite the introduction of many methods, only modest gains were made over last decade for certain classes targets. To address this challenge, a social-media based worldwide collaborative effort, named WeFold, was undertaken by 13 labs. During collaboration, laboratories simultaneously competing with each other. Here, we present first attempt at "coopetition" in scientific research applied and refinement problems....
Significance Bioinformatic analysis revealed that approximately 40% of human messenger RNAs contain upstream open reading frames (uORFs) in their 5′ untranslated regions. Some these sequences are translated, but the function encoded peptides remains unknown. Our study a uORF encoding for peptide exhibiting kinase inhibitory activity. This uORF, PKC family member, possess typical pseudosubstrate motif, which autoinhibits catalytic activity all PKCs. Using mouse models and cells, we show this...
Ecology documents and interprets the abundance distribution of organisms. Ecoinformatics addresses this challenge by analyzing databases observational data. insects has high scientific applied importance, as are abundant, speciose, involved in many ecosystem functions. They also crucially impact human well-being, activities dramatically affect insect demography phenology. Hazards, such pollinator declines, outbreaks agricultural pests spread insect-borne diseases, raise an urgent need to...
The function of a protein is determined by its structure, which creates need for efficient methods structure determination to advance scientific and medical research. Because current experimental carry high price tag, computational predictions are highly desirable. Given sequence, produce numerous 3D structures known as decoys. Selection the best quality decoys both challenging essential end users can handle only few ones. Therefore, scoring functions central decoy selection. They combine...
Abstract Methods to reliably estimate the quality of 3D models proteins are essential drivers for wide adoption and serious acceptance protein structure predictions by life scientists. In this article, most successful groups in CASP12 describe their latest methods estimates model accuracy (EMA). We show that pure single estimation have shown clear progress since CASP11; 3 top (MESHI, ProQ3, SVMQA) all perform better than method CASP11 (ProQ2). Although outperform quasi‐single (ModFOLD6...
Abstract Critical Assessment of Structure Prediction (CASP) is an organization aimed at advancing the state art in computing protein structure from sequence. In spring 2020, CASP launched a community project to compute structures most structurally challenging proteins coded for SARS‐CoV‐2 genome. Forty‐seven research groups submitted over 3000 three‐dimensional models and 700 sets accuracy estimates on 10 proteins. The resulting were released public. members also worked together provide...
Insects are highly abundant and diverse, play major roles in ecosystem functions. Monitoring of insect populations is key to their sustainable management. However, the labor expertise needed identify insects, challenges archiving wealth data collected monitoring programs, often limit these efforts. We describe a pipeline reduce barriers associated with curating mining big biodiversity. The pipeline, STARdbi, includes capturing flying insects sticky traps, scanning storing trap-images public...
Transfer of the green algae Chlamydomonas reinhardtii from low light to high generated an oxidative stress that led a dramatic arrest in synthesis large subunit (LSU) ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). The translational correlated with transient changes intracellular levels reactive oxygen species and shifting glutathione pool toward its oxidized form (Irihimovitch, V., Shapira, M. (2000) J. Biol. Chem. 275, 16289–16295). Here we examined how redox potential affected...
All eukaryotic mRNAs possess a 5′-cap (m 7 GpppN) that is recognized by family of cap-binding proteins. These participate in various processes, such as RNA transport and stabilization, well assembly the translation initiation complex. The trypanosomatids complex; addition to 7-methyl guanosine, it includes unique modifications on first four transcribed nucleotides, thus denoted cap-4. Here we analyze protein Leishmania , an attempt understand structural features promote its binding this...
Abstract Rotatable torsion angles are the major degrees of freedom in proteins. Adjacent highly correlated and energy terms that rely on these correlations intensively used molecular modeling. However, utility based is not yet fully exploited. Many do capture full scale correlations. Other terms, which lookup tables, cannot be context force‐driven algorithms because they differentiable. This study aims to extend usability by presenting a set high‐dimensional fully‐differentiable derived from...
Abstract Motivation: The roughness of energy landscapes is a major obstacle to protein structure prediction, since it forces conformational searches spend much time struggling escape numerous traps. Specifically, beta-sheet formation prone stray, many possible combinations hydrogen bonds are dead ends in terms assembly. It has been shown that cooperative for backbone ease this problem by augmenting bond patterns consistent with beta sheets. Here, we present novel hydrogen-bond term both...
The structural reorganization of the actin cytoskeleton is facilitated through action motor proteins that crosslink filaments and transport them relative to each other. Here, we present a combined experimental-computational study probes dynamic evolution mixtures clusters myosin motors. While on small spatial temporal scales system behaves in very noisy manner, larger it evolves into several well distinct patterns such as bundles, asters networks. These are characterized by junctions with...
Abstract Every two years groups worldwide participate in the Critical Assessment of Protein Structure Prediction (CASP) experiment to blindly test strengths and weaknesses their computational methods. CASP has significantly advanced field but many hurdles still remain, which may require new ideas collaborations. In 2012 a web-based effort called WeFold, was initiated promote collaboration within community attract researchers from other fields contribute CASP. Members WeFold coopetition...
We tackle the problem of protein secondary structure prediction using a common task framework. This lead to introduction multiple ideas for neural architectures based on state art building blocks, used in this first time. take principled machine learning approach, which provides genuine, unbiased performance measures, correcting longstanding errors application domain. focus Q8 resolution structure, an active area continuously improving methods. use ensemble strong predictors achieve accuracy...
Recent advancements in machine learning techniques for protein structure prediction motivate better results its inverse problem-protein design. In this work we introduce a new graph mimetic neural network, MimNet, and show that it is possible to build reversible architecture solves the design problems tandem, allowing improve backbone when estimated. We use ProteinNet data set state of art can be met even improved, given recent architectures folding.
Summary: Adapting a modular and object-oriented approach in the design of molecular modeling packages may reduce software development barrier between ideas their programed applications. Towards this goal we developed MESHI, new, strictly object-oriented, suite written Java. MESHI provides comprehensive library extendable classes for all essential components modeling: geometry elements, energy functions optimization methods.
The inverse protein folding problem, also known as sequence design, seeks to predict an amino acid that folds into a specific structure and performs function. Recent advancements in machine learning techniques have been successful generating functional sequences, outperforming previous energy function-based methods. However, these methods are limited their interoperability robustness, especially when designing proteins must function under non-ambient conditions, such high temperature,...
Motivation: Structural knowledge, extracted from the Protein Data Bank (PDB), underlies numerous potential functions and prediction methods. The PDB, however, is highly biased: many proteins have more than one entry, while entire protein families are represented by a single structure, or even not at all. standard solution to this problem limit studies non-redundant subsets of PDB. While alleviating biases, hides many-to-many relations between sequences structures. That is, datasets conceal...
Deep mutational scanning provides unprecedented wealth of quantitative data regarding the functional outcome mutations in proteins. A single experiment may measure properties (eg, structural stability) numerous protein variants. Leveraging experimental to gain insights about unexplored regions landscape is a major computational challenge. Such facilitate further work and accelerate development novel variants with beneficial therapeutic or industrially relevant properties. Here we present...