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Protein structure prediction is an important problem in the post-genome era, which is one possible way to fill the gap between the rapid-growth sequences and the relative small number of proteins with experimentally determined structures. Despite the structural genomics initiatives and biochemical efforts, the cheapest and fastest way to obtain structural information is through prediction algorithms. Structure prediction, even in the absence of homology, is the first step of the sequence-structure-function paradigm. Great progress has been achieved in protein structure prediction during the last decades. The development of high-quality prediction methods has also been boosted by objective community-wide assessment experiments. However, the ultimate goal of protein structure prediction remains far away to reach. New algorithms, theory and advanced prediction techniques are necessary to facilitate the progress ...
The Biomolecular Structure and Design Graduate Program at the University of Washington accepts students persuing a Ph.D. degree in biochemistry, bioengineering, biological structure, chemistry, or medicinal chemistry. Students typically persue research in biomolecular structure, molecular biophysics, protein design and engineering, protein folding, drug design, and biomolecular interactions using techniques such as xray crystallography, NMR, electron microscopy, and a variety of computational methods.
The IntFOLD-TS method was developed according to the guiding principle that the model quality assessment (QA) would be the most critical stage for our template-based modeling pipeline. Thus, the IntFOLD-TS method firstly generates numerous alternate models, using in-house versions of several different sequence-structure alignment methods, which are then ranked in terms of global quality using our top performing QA method-ModFOLDclust2. In addition to the predicted global quality scores, the predictions of local errors are also provided in the resulting coordinate files, using scores that represent the predicted deviation of each residue in the model from the equivalent residue in the native structure. The IntFOLD-TS method was found to generate high quality 3D models for many of the CASP9 targets, whilst also providing highly accurate predictions of their per-residue errors. This important information may help to make the 3D models that are produced by the IntFOLD-TS method more useful for ...
The YRC PDR provides for the searching of millions of protein descriptions from many databases to find proteins and public experimental data describing those proteins produced by the YRC. The experimental data is in the form of mass spectrometry, yeast two-hybrid, protein structure prediction, light microscopy and protein complex predictions.
Another direction that is being taken is to adapt primary sequence alignment methods to consider secondary and tertiary structure. There are a number of features of proteins integral to their function and interaction with other proteins that are not determined by amino acid sequence alone. Many proteins share functional properties despite vast sequence differences because of the shapes that they fold into. One method of simultaneously quantifying and visualizing these relationships is using a protein structure space map. [¹] Roughly speaking, a Protein structure space map is the result of scoring how well known proteins match, structurally. That score is used as a directional distance used to position families of proteins in relation to each other on a set of axes, closer if they are more similar, distantly if they are more dissimilar. Anyone can look at the structure space map and immediately judge how similar two proteins or protein families are by their proximity on the map.. There are a ...
A procedure for automated protein structure determination is presented that is based on an iterative procedure during which the NOESY peak list assignment and the structure calculation are performed s
Chapter 43. GPU Computing for Protein Structure Prediction Paulius Micikevicius Armstrong Atlantic State University 43.1 Introduction Determining protein 3D structure is one of the greatest challenges in computational biology. Nuclear magnetic resonance (NMR) spectroscopy is the second most popular method (after X-ray crystallography) for structure prediction. Given a
In earlier stage the Tertiary Protein Structure Prediction is unsolved problem in molecular biology. But in nowadays The evolutions in motif identification and side chain modeling present the prospect of nearly automatic model building for a large fraction of newly determined protein sequences. Anyway nice post ...
το κείμενο με τίτλο A composite model assessment score for protein structure prediction σχετίζετε με Τεχνίτη Νοημοσύνη και Ρομποτική
DeepAlign 1.13 :: DESCRIPTION Different from many other tools, DeepAlign aligns two protein structures using evolutionary information and beta strand orientation in addition to geometric similarity. Therefore, DeepAl
Interactions at the molecular level in the cellular environment play a very crucial role in maintaining the physiological functioning of the cell. These molecular interactions exist at varied levels viz. protein-protein interactions, protein-nucleic acid interactions or protein-small molecules interactions. Presently in the field, these interactions and their mechanisms mark intensively studied areas. Molecular interactions can also be studied computationally using the approach named as Molecular Docking. Molecular docking employs search algorithms to predict the possible conformations for interacting partners and then calculates interaction energies. However, docking proposes number of solutions as different docked poses and hence offers a serious challenge to identify the native (or near native) structures from the pool of these docked poses. Here, we propose a rigorous scoring scheme called DockScore which can be used to rank the docked poses and identify the best docked pose out of many as ...
One of the major unsolved problems in molecular biology today is the protein folding problem: given an amino acid sequence, predict the overall three-dimensional structure of the corresponding protein. It has been known since the seminal work of Christian B. Anfinsen in the early seventies that the sequence of a protein encodes its structure, but the exact details of the encoding still remain elusive.. Since the protein folding problem is of enormous practical, theoretical and medical importance - and in addition forms a fascinating intellectual challenge - it is often called the holy grail of bioinformatics. The Statistical Structural Biology group focuses on Bayesian, probabilistic models of protein structure and their application to protein structure prediction, protein design and protein structure determination from experimental data (NMR, SAXS), including data obtained from protein ensembles. Recently, we started working on evolutionary models of protein structure evolution.. We are ...
The creation of an automated method for determining 3D protein structure would be invaluable to the eld of biology and presents an interesting challenge to computer science. Unfortunately , given the current level of protein knowledge, a completely automated solution method is not yet feasible; therefore, our group has decided to integrate existing databases and theories to create a software system that assists X-ray crystallographers in specifying a particular protein structure. By breaking the problem of determining overall protein structure into small subproblems, we hope to come closer to solving a novel structure by solving each component. By generating necessary information for structure determination, this method provides the rst step toward designing a program to determine protein conformation automatically. The properties of a protein are largely determined by its three-dimensional structure Voet and Voet 1990]. This statement would seem to simplify the process of understanding proteins and
An investigation into methods for determining the total protein content of cerebrospinal fluid: implications for universal guidelines ...
Scientists from The University of Manchester - part of the Manchester Cancer Research Centre - used a simple protein test that could prove more useful in predicting survival chances for patients with head-and-neck cancer compared to existing methods.. The team, funded by Cancer Research UK, believe the test could allow doctors to choose more appropriate and tailored treatments. Oral cancers, including the tongue and tonsils, are usually associated with tobacco and alcohol intake.. However, increasing numbers of cases are instead linked to human papillomaviruses (HPV) - which occur in younger people and have a different biology and a better prognosis. One approach for detecting HPV-associated oral cancer relies on finding HPV DNA in the tumour sample but these DNA-based tests may not accurately classify the tumour.. Another approach is to use a marker of HPV rather than testing for HPV DNA directly. The p16 protein usually disappears in tumours that are not caused by HPV infection and has been ...
Lexpressió cortical androgen dependent del KAP està afectada en hipotiroïdisme postnatal. La síntesi puntual de T3 a partir del dia 11 postnatal, comença una resposta cortical feble de KAP que va augmentant cap als dies 15-16, que és quan es produeix un pic fisiològic de T4 i el desenvolupament puberal dels ratolins. Donat que les CCAAT/Enhancer-Binding Proteins (C/EBPs) participen en respostes mitjançades per T3 i que en el promotor del KAP existeixen quatre elements de resposta consens per a C/EBPs, hem analitzat la seva participació en la resposta androgènica de KAP mitjançada per T3. La detecció de p42C/EBPa y p35C/EBPb es troba correlacionada amb lexpressió del KAP, apareixent en extractes renal nuclears de ratolins masles control i hipotiroïdals induïts amb T3 durant els dies 7-21 postnatals, però no en els hipotiroïdals no tractats. Mitjançant transfeccions transitòries es mostrava com C/EBPa i C/EBPb eren capaces dinduir respostes màximes del promotor del KAP i que ...
Considering the significant development and relevance of the structural biology, this course is designed to give students the bases to learn and understand the principles and practise of the most important methods to determine the structure, the conformational stability and dynamics of biomolecules in solution. Attending the course, that is based on theoretical lectures and laboratory practicals, will allow the students to verify their learning skills.. ...
本文描述了通过自组装的自发过程中形成高度有序的基于肽的结构。该方法利用市售的肽和普通的实验室设备。这一技术可以应用到大量的各种肽,并可能导致新的基于肽的装配体的发现。...
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Understanding the function of complex biomacromolecular assemblies requires detailed knowledge of the structure and dynamics of the individual molecular components as well as of their interactions within complexes. Fluorescence based methods offer the possibility to measure protein properties and interactions with a high sensitivity and selectivity. The advent of bright and more photo-stable fluorescent dyes and an enormous methodical and technical improvement of high resolution fluorescence spectroscopy and microscopy enabled studies on proteins even at a single molecule level. Due to the fact that single molecule techniques provide information on the distribution of parameters characterizing the biological macromolecule, these methods are often the approach of choice to clarify and better understand the structure and function of proteins.. ...
... The section deals broadly with proteins as the cells and organs work horses, trying to understand the biological processes and systems from a molecular understanding of the proteins properties. We analyse the proteins physical and chemical structures and their functions under physiologically relevant conditions. Specific areas include: Research areas and projects:. ...
The YRC PDR provides for the searching of millions of protein descriptions from many databases to find proteins and public experimental data describing those proteins produced by the YRC. The experimental data is in the form of mass spectrometry, yeast two-hybrid, protein structure prediction, light microscopy and protein complex predictions.
The VA Tech blurb is silly. Dogs fed unprocessed food derive a majority of their energy from fats. Dogs fed meat, fat, bones, organs, fish, eggs, etc have no lack of either fat or high-quality protein in their diet. No one is suggesting dogs (or puppies) be starved of energy producing nutrients or high-quality protein. And the fact remains that carbohydrate metabolism leads directly to a spike in blood glycogen followed by a crash. Which is exactly what one who plans to go out for 2 or 3 day should seek to avoid ...
The foundation of TPS is our prestigious journal, Protein Science. With a storied history that includes past Editors in Chief: Hans Neurath, Mark Hermodson, and current editor, Brian Matthews, and a reputation for featuring leading-edge protein research through innovative means, the Journal has grown to become the premier platform for scientists all around the world with a trans-disciplinary focus on proteins. Subject matter encompasses protein structure, function, design, and applications, exploring proteins critical roles in molecular and cell biology, genetics, proteomics, evolution, and more.. ...
Reactome is pathway database which provides intuitive bioinformatics tools for the visualisation, interpretation and analysis of pathway knowledge.
Finding the ends of a protein chain is easy for a human being. But writing code to find the ends of the protein chains in any PDB file in a general manner seems challenging. I have procrastinated dealing with this for years because of its seeming complexity. Here I lay out my ideas about how to do this. If anyone has other ideas, especially simpler methods, please let me know! Why? I would like to have buttons in FirstGlance that zoom in on the terminal residues (with coordinates) of a protein chain for any PDB entry displayed. Also, in the /Charge/ view in FirstGlance, I would like to show whether the terminal amino and carboxy residues that have coordinates are charged -- that is, whether they are the termini of the experimental protein, or whether the actual terminal amino acids are missing coordinates. Or whether the terminal amino acids are blocked. I prefer to rely on sequence numbers as LITTLE as possible because they are not required to increase monotonically between the N and C termini, ...
3. Dry legumes and legume products (concluded) - Légumineuses et produits dérivés (fin) - Legumbres secas y productos de legumbres (conclusión) ...
Protein Science & Mass Spec | The Tecan Journal is published several times a year, and contains articles featuring users of Tecan instruments, as well as information about latest products and global Tecan activities.
NKCXQMYPWXSLIZ-PSRDDEIFSA-N (2S)-2-[[(2S)-1-[(2S)-5-amino-2-[[2-[[(2S)-6-amino-2-[[2-[[(2S)-2-[[(2S)-4-amino-2-[[(2S)-2-[[(2S,3R)-2-[[(2S)-2-[[(2S,3R)-2-amino-3-hydroxybutanoyl]amino]-3-(1H-indol-3-yl)propanoyl]amino]-3-hydroxybutanoyl]amino]propanoyl]amino]-4-oxobutanoyl]amino]-3-m Chemical compound ...
This page is no longer being maintained. The [[http://​www.fpvis.org/​,interactive graph of fluorescent protein properties]] and [[http://​www.fpvis.org/​PSFP.html,interactive graph of photoswitchable fluorescent protein properties]] pages should be viewed instead ...
The SCOP help-file at http://scop.mrc-lmb.cam.ac.uk/scop/help.html Has the following to say: The number in parenthesis after an entry shows how many children will be found there. So for example the TIM b/a barrel Fold ----- TIM beta/alpha-barrel [51350] (31) has 31 superfamilies and its Ribulose-phosphate binding barrel ---------- Ribulose-phoshate binding barrel [51366] (4) has 4 families. Hope this is what you were looking for Boris ========================================== On 6 Oct 2005, at 13:46, paul wrote: , Hi Folks, , , Quick question. Does anyone know by any chance know how I can find the , number of individual proteins within , each superfamily and family of the SCOP database to get an idea of , which , folds are the most , common and which are very rare? , , Any help much appreciated. , , Best Regards, , , Paul , , -----Original Message----- , From: bio_bulletin_board-bounces , +p.curley=wmin.ac.uk at bioinformatics.org , [mailto:bio_bulletin_board-bounces , +p.curley=wmin.ac.uk at ...
The publication AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. is placed in the Top 10000 of the best publications in CiteWeb. Also in the category Chemistry it is included to the Top 1000. Additionally, the publicaiton AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. is placed in the Top 1000 among other scientific works published in 1996 ...
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Please cite: Karplus, K. and Karchin, R. and Barrett, C. and Tu, S. and Cline, M. and Diekhans, M. and Grate, L. and Casper, J. and Hughey, R. ``What is the value added by human intervention in protein structure prediction? Proteins: Structure Function and Genetics 45(S5):86-91,2001 ...
Please cite: Karplus, K. and Karchin, R. and Barrett, C. and Tu, S. and Cline, M. and Diekhans, M. and Grate, L. and Casper, J. and Hughey, R. ``What is the value added by human intervention in protein structure prediction? Proteins: Structure Function and Genetics 45(S5):86-91,2001 ...
The AccuSizer FX Nano SIS system is specifically designed to measure protein aggregation. The instrument meets and/or exceeds all requirements described in USP
Working out tears down your muscles, which makes high-quality protein essential for your body. Well review the incredibly convenient Body Fortress Protein Shot.
Cellular survival relies crucially on the ability to receive and communicate signals from and to the outside world. A major part of this regulation and communication is performed by proteins within the membrane of a cell.
All Proteins are long linear, unbranched polypeptides and as caloric nutrients built, usually built from strings of about 20 different alpha-amino acid
Protein structures adopt1 many different folds - or shapes. These can be protein classification|classified under various schemes, but it is sometimes di...
Abacus - ABaCUS is a no-frills program developed to investigate the significance of the putative correspondence between exons and units of protein structure ...
PF2 protein structure and epitope tagging. (A) Diagrammatic representation of the domain structure of the PF2 polypeptide. Indicated are predicted coiled-coil d
Scheme for predicting the tolerated sequences for a protein fold or interaction.The input is at least one protein structure from the protein structure databank
Can anyone advise me on whether it is possible to search any databank with the the SIZE of a protein as well as other more usual information. I would (ideally) like to try to reduce the number of possibilities that are thrown up by disregarding proteins that are too small or too large. What database is best ? I would be very obliged for any advise on i/ what to try and ii/ how to go about it Thanks in advance dtoroser at unity.ncsu.edu ...
CiteSeerX - Document Details (Isaac Councill, Lee Giles, Pradeep Teregowda): Background The protein structure prediction problem is one of the most challenging problems in biological sciences. Many approaches have been proposed using database information and/or simplified protein models. The protein structure prediction problem can be cast in the form of an optimization problem. Notwithstanding its importance, the problem has very seldom been tackled by Constraint Logic Programming, a declarative programming paradigm suitable for solving combinatorial optimization problems. Results Constraint Logic Programming techniques have been applied to the protein structure prediction problem on the face-centered cube lattice model. Molecular dynamics techniques, endowed with the notion of constraint, have been also exploited. Even using a very simplified model, Constraint Logic Programming on the face-centered cube lattice model allowed us to obtain acceptable results for a few small proteins. As a test
Review Graduate Program details of Biomolecular Structure and Biophysics - Master in West Lafayette Indiana United States from Purdue University. Biomolecular Structure and Biophysics is part of the Purdue University Interdisciplinary Life Science Program (PULSe). Some of the highlights of PULSe include: PULSe offers...
To gain a better understanding of how proteins function a process known as protein structure prediction (PSP) is carried out. However, experimental PSP methods, such as X-ray crystallography and Nuclear Magnetic Resonance (NMR), can be time-consuming and inaccurate. This has given rise to numerous computational PSP approaches to try and elicit a proteins three-dimensional conformation. A popular PSP search strategy is Genetic Algorithms (GA). GAs allow for a generic search approach, which can provide a generic improvement to alleviate the need to redefine the search strategies for separate sequences. Though GAs working principles are remarkable, a serious problem that is inherent in the GA search process is the growth of twins or identical chromosomes. Therefore, enhanced twin removal strategies are crucial for any GA search solving hard-optimisation problems like PSP. In this paper we explain our high-resolution GA feature-based resampling PSP approach and propose a twin removal strategy to ...
Tetracycline-responsive transcriptional activator driven by the liver-specific mouse major urinary protein promoter (MUP-tTA).. The E. Coli tetracycline operon regulatory system was used to generate a liver-specific transcription activation system that was inhibited by tetracycline. The transcription activator was a fused protein consisting of a tetracycline repressor gene (tetR) that was only active in the presence of tetracycline and a herpes simplex virus protein (VP-16) transcription activating domain (Tet-Off). Transcription was induced only in the absence of tetracycline (Tet-Off). A liver-specific promoter such as the mouse major urinary protein (MUP) promoter determined that the tetracycline-regulated transcriptional activator (tTA) would be expressed specifically in liver. To study the effect of the transcription activator on a target gene (for example, beta-galactosidase, LacZ) specifically in liver, MUP-tTA mice would be mated with transgenic mice in which the TAg Target gene was ...
Computational protein structure prediction has made great progress in the last three decades [1, 2]. Protein inter-residue contact prediction is one of the problems being actively studied in the structure prediction community. Recent CASP (Critical Assessment of Techniques for Protein Structure Prediction) [3-7] events have demonstrated that a few true contacts, extracted from template-based models, can provide very important information for protein structure refinement, especially on targets without good templates in PDB [8]. For example, Misura et al. [9] have revised the widely-used ab initio folding program, Rosetta [10], by incorporating inter-residue contact information as a component of Rosettas energy function, and shown that the revised Rosetta exhibits not only a better computational efficiency, but also a better prediction accuracy. For some test proteins, the models built by this revised Rosetta are more accurate than their template-based counterparts, which is rarely seen before ...
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Protein three-dimensional structure prediction directly from amino acid sequence is an important issue in bioinformatics. An intermediate approach to this problem is to predict the so-called one-dimensional structural properties of proteins. The solvent accessibility or accessible surface area (ASA) of an amino acid residue in a protein structure is one such property and the knowledge of this property can significantly enhance the overall structure and function prediction of proteins [1, 2]. Given an amino acid sequence, the goal of such prediction is to estimate the ASA of each residue making use of previously observed ASA values taken from known protein structures. The knowledge from previously observed structures is modeled using machine learning and other methods [3-16]. Various methods of predicting ASA from sequence or sequence-derived evolutionary information have been developed such as neural networks [8-12], Bayesian analysis [13], information theory [14, 15], multiple linear ...
... A: Left, crystal structure of the MarA transcription factor bound to DNA; right, our best submitted model in CASP3. Despite many incorrect details, the overall fold is predicted with sufficient accuracy to allow insights into the mode of DNA binding. B: Left, the crystal structure of bacteriocin AS-48; middle, our best submitted model in CASP4; right, a structurally and functionally related protein (NK-lysin) identified using this model in a structure-based search of the Protein Data Bank (PDB). The structural and functional similarity is not recognizable using sequence comparison methods (the identity between the two sequences is only 5 percent). C: Left, crystal structure of the second domain of MutS; middle, our best submitted model for this domain in CASP4; right, a structurally related protein (RuvC) with a related function recognized using the model in a structure-based search of the PDB. The similarity was not recognized using ...
Free Online Library: Analysis of an immune algorithm for protein structure prediction.(Report) by Informatica; Computers and office automation Algorithms Usage Mutation Research Mutation (Biology) Protein folding Methods Models Protein structure Proteins Structure Simulation Simulation methods
Understanding the link between protein structure and protein function is a fundamental problem that underlies diverse application areas including drug target identification, protein function prediction, and structure-based evolutionary analysis. The specific few amino acids that mediate the drug-binding affinity of targeted binding sites are an example of a substructure within a protein. The catalytic substructures of enzymatic proteins are intrinsically linked to enzyme function [1-4], and establishing a mechanistic understanding of how specific structural features affect protein function is a central problem in structural genomics [5]. The analysis of the physico-chemical properties of the few amino acids constituting these substructures, common to families of functionally related proteins, can provide direct insight to the structural features that dictate a particular enzymatic function [2]. For example, the family of serine proteases is a well-established case of a common functional ...
A Two-Layer Learning Architecture for Multi-Class Protein Folds Classification: 10.4018/978-1-4666-3604-0.ch041: Classification of protein folds plays a very important role in the protein structure discovery process, especially when traditional sequence alignment methods
RF-Phos, Dukka KC, Random Forest, RF, computational biology, machine learning, hydroxylation site, protein classification, general phosphosite, phosphorylation site prediction, post-translational modification, Protein Structure Prediction, Protein Side Chain Packing, symmetry in protein, multi-domain protein structure prediction, North Carolina A&T State University, RFNR, Feature Extraction, Protein
To determine the effect of GenotropinTM on whole body protein turnover (WBPT), IGF-1 levels and cytokines. Utilizing the stable isotope 1-[13C] leucine, we will measure WBPT. Measurements of WBPT will be correlated with LBM and changes in height and weight velocity. This data will be compared to that from age matched normal children (archival data maintained by the PI). We will measure IGF-1 and the cytokines TNF-α, IL-6 and IL-10 at baseline and very six months. These measures will be correlated with height and weight velocity and IGF-1 levels. Cytokine levels will also be correlated with protein catabolism. This specific aim tests the hypothesis that chronically ill children have increased catabolism, caused by high levels of circulating cytokines and low levels of IGF-1, and that these abnormalities improve with GenotropinTM ...
We have shown that chronic metabolic acidosis in awake rats accelerates whole body protein turnover using stochastic modeling and a continuous infusion of L-[1-13C] leucine. To delineate the role that glucocorticoids play in mediating these catabolic responses, we measured protein turnover in awake,...
Protein domain superfamilies in CATH-Gene3D have been subclassified into functional families (or FunFams), which are groups of protein sequences and structures with a high probability of sharing the same function(s). Therefore, the functionally important residues in a family are also expected to be highly conserved.. Information on conserved positions in CATH-Gene3D FunFam alignments is shown through the Alignment tab of the FunFam webpages. Conservation scores have been calculated using Scorecons and columns in the alignment are coloured using a rainbow colour scheme, where the highly conserved residues are shown in red through to positions that are not conserved at all, shown in blue. The conservation scores are also mapped onto a representative protein domain structure.. To investigate putative conserved sites for your protein sequence, run a sequence search against the FunFams and click on the FunFam match Alignment page.. ...
Abstract: Despite impressive successes in protein design, designing a well-folded protein of more 100 amino acids de novo remains a formidable challenge. Exploiting the promising biophysical features of the artificial protein Octarellin V, we improved this protein by directed evolution, thus creating a more stable and soluble protein: Octarellin V.1. Next, we obtained crystals of Octarellin V.1 in complex with crystallization chaperons and determined the tertiary structure. The experimental structure of Octarellin V.1 differs from its in silico design: the (αβα) sandwich architecture bears some resemblance to a Rossman-like fold instead of the intended TIM-barrel fold. This surprising result gave us a unique and attractive opportunity to test the state of the art in protein structure prediction, using this artificial protein free of any natural selection. We tested 13 automated webservers for protein structure prediction and found none of them to predict the actual structure. More than 50% of ...
Specific binding between proteins plays a crucial role in molecular functions and biological processes. Protein binding interfaces and their atomic contacts are typically defined by simple criteria, such as distance-based definitions that only use some threshold of spatial distance in previous studies. These definitions neglect the nearby atomic organization of contact atoms, and thus detect predominant contacts which are interrupted by other atoms. It is questionable whether such kinds of interrupted contacts are as important as other contacts in protein binding. To tackle this challenge, we propose a new definition called beta (β) atomic contacts. Our definition, founded on the β-skeletons in computational geometry, requires that there is no other atom in the contact spheres defined by two contact atoms; this sphere is similar to the van der Waals spheres of atoms. The statistical analysis on a large dataset shows that β contacts are only a small fraction of conventional distance-based contacts. To
Zhou, R., He, Y. & Xiao, Y. (2011). Multi-nucleation and vectorial folding pathways of large helix protein. Computational Biology And Chemistry 35, 169-173.. Zhao, Y. J., Gong, Z. & Xiao, Y. (2011). Improvements of the Hierarchical Approach for Predicting RNA Tertiary Structure. Journal Of Biomolecular Structure & Dynamics 28, 815-826.. Li, L., Guo, D. C., Huang, Y. Y., Liu, S. Y. & Xiao, Y. (2011). ASPDock: protein-protein docking algorithm using atomic solvation parameters model. Bmc Bioinformatics 12.. Lei, H. X., Chen, C. J., Xiao, Y. & Duan, Y. (2011). The protein folding network indicates that the ultrafast folding mutant of villin headpiece subdomain has a deeper folding funnel. Journal Of Chemical Physics 134.. Gong, Z., Zhao, Y. J., Chen, C. J. & Xiao, Y. (2011). Role of Ligand Binding in Structural Organization of Add A-riboswitch Aptamer: A Molecular Dynamics Simulation. Journal Of Biomolecular Structure & Dynamics 29, 403-416.. Fleishman, S. J., Whitehead, T. A., Strauch, E. M., ...
Ghosh, Arindam and Bansal, M (2003) A glossary of DNA structures from A to Z. In: Acta Crystallographica Section D Biological Crystallography, 59 (4). pp. 620-626. Olson , WK and Bansal , M and Burley , SK and Dickerson, Richard E (2001) A standard reference frame for the description of Nucleic Acid Base-Pair Geometry. In: Journal of Molecular Biology, 313 (1). 229-237 . Chowdhury, S and Bansal , M (2001) A nanosecond molecular dynamics study of antiparallel d(G)(7) quadruplex structures: Effect of the coordinated cations. In: Journal of Biomolecular Structure & Dynamics, 18 (5). pp. 647-669. Kumar, S and Bansal, M (1998) Dissecting alpha-helices: Position-specific analysis of alpha-helices in globular proteins. In: Proteins: Structure, Funcaction, and Bioinformatics, 31 (4). pp. 460-470. Kiran, MR and Bansal, M (1997) Sequence Independent Recombination Triple Helices: A Molecular Dynamics Study. In: Journal of Biomolecular Structure & Dynamics, 15 (2). pp. 333-345. Kiran, MR and Mohanty, D and ...
Recent progress in DNA-sequencing technologies has ushered in an era of rapid and cost-effective genome sequencing, enabling clinical applications [1] and the potential for personalized systems medicine [2] through the understanding of an individuals genetic risks and by integration with longitudinal phenotype measurements [3].The detailed knowledge of an individuals genotype poses a significant interpretation challenge: while genetic variants disrupting transcript structure and protein-coding sequences (for example, nonsense mutations) have long been considered "low hanging fruit" relative to variants in non-coding sequences, the field still struggles with interpreting missense mutations, which are more common, and more frequently associated with disease [4]. This has led to an increasing number of variants of uncertain significance (VUS). To address the resulting annotation and reporting challenges [5, 6], the American College for Genetics and Genomics (ACMG) and the Association for ...
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TY - JOUR. T1 - Histidine-rich glycoprotein as an excellent biomarker for sepsis and beyond. AU - Nishibori, Masahiro. AU - Wake, Hidenori. AU - Morimatsu, Hiroshi. PY - 2018/8/17. Y1 - 2018/8/17. N2 - Sepsis remains a critical problem with high morbidity and mortality worldwide. One of the problems we have in critical care is the need to find a good biomarker of sepsis to determine the existence of bacterial infection and the severity of patients. This would enable us to start appropriate treatment at an earlier stage of the disease course. We propose that decreases in the plasma protein histidine-rich glycoprotein (HRG) is an excellent biomarker of sepsis compared with the current markers. Based on the novel pathophysiological roles of HRG in the cascade of events during sepsis, we also discuss the potential for supplemental therapy with purified HRG.. AB - Sepsis remains a critical problem with high morbidity and mortality worldwide. One of the problems we have in critical care is the need to ...
Energy functions are used in a variety of roles in protein modelling. An energy function precise enough to always discriminate the native protein structure from all possible decoys would not only simplify the protein structure prediction problem considerably. It would also increase our understanding of the protein folding process itself. If feasible, one would like to use quantum mechanical models, being the most detailed representation, to calculate the energy of a protein. It can theoretically be done by solving the Schrödinger equation. This equation can be solved exactly for the hydrogen atom, but is no longer trivial for three or more particles. In recent years it has become possible to approximately solve the Schrödinger equation for systems up to hundred atoms with the Hartree-Fock or self-consistent field approximations. Their main idea is that the many-body interactions are reduced to several two-body interactions. Energy functions are important to all aspects of protein structure ...
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Despite the diversity of protein superfamilies, sequence space is extremely sparsely populated by functional proteins. Most random protein sequences have no fold or function.[8] Enzyme superfamilies, therefore, exist as tiny clusters of active proteins in a vast empty space of non-functional sequence.[9][10] The density of functional proteins in sequence space, and the proximity of different functions to one another is a key determinant in understanding evolvability.[11] The degree of interpenetration of two neutral networks of different activities in sequence space will determine how easy it is to evolve from one activity to another. The more overlap between different activities in sequence space, the more cryptic variation for promiscuous activity will be.[12] Protein sequence space has been compared to the Library of Babel a theoretical library containing all possible books that are 410 pages long.[13][14] In the Library of Babel, finding any book that made sense was impossible due to the ...
Dahl, H M.; Truelsen, E; and Blair, G E., "The purification and properties of two low-molecular-weight proteins required for the initiation of translation in ascites tumour cells." (1977). Subject Strain Bibliography 1977. 1411 ...
Discriminative Subgraph Mining for Protein Classification: 10.4018/978-1-4666-1785-8.ch016: Protein classification can be performed by representing 3-D protein structures by graphs and then classifying the corresponding graphs. One effective way to
The functions of biological systems emerge from the structures of macromolecules, their conformational dynamics, and their higher order assembly. Determination of biomolecular structures and an understanding of their conformational changes and assembly properties provide great insights into biological mechanisms. Much of the research in structural biology at the Weizmann Institute is carried out in the Faculty of Chemistry, using a diverse set of cutting-edge research tools and methods. Investigators in the Structural Biology Department rely on the primary techniques for experimental structure determination, namely X-ray crystallography, NMR, and electron microscopy, but they also employ a variety of other specialized and emerging spectroscopic methods combined with creative molecular engineering to explore macromolecular structures, energetics, and dynamics. Experimental strategies are complemented by computational and theoretical approaches. Among the specific subjects of research in the ...
Ghosh, Sambit and Gadiyaram, Vasundhara and Vishveshwara, Saraswathi (2017) Validation of protein structure models using network similarity score. In: PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 85 (9). pp. 1759-1776. Chandran, Aneesh and Vishveshwara, Saraswathi (2016) Exploration of the conformational landscape in pregnane X receptor reveals a new binding pocket. In: PROTEIN SCIENCE, 25 (11). pp. 1989-2005. Dighe, Anasuya and Chandra, Nagasuma and Vishveshwara, Saraswathi and Ananthasuresh, GK (2015) Dissecting Ligand Binding Sites : A Layer at a Time. In: BIOPHYSICAL JOURNAL, 108 (2, 1). 216A. Ghosh, Soma and Chandra, Nagasuma and Vishveshwara, Saraswathi (2015) Influence of iron on iron dependent repressor (IdeR) activation and DNA binding. In: JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 33 (1). p. 8. Ghosh, Soma and Chandra, Nagasuma and Vishveshwara, Saraswathi (2015) Investigating the Mechanism of Iron Dependent Repressor (IDER) Activation and DNA Binding. In: BIOPHYSICAL JOURNAL, ...
An intricate new three-dimensional protein structure is providing a detailed look into how brain cells communicate rapidly.. By visualizing how three neural proteins interact with one another, researchers have revealed how they help groups of brain cells release chemical messages at the same time.. The work describes a surprising new cooperation among the three proteins, and could offer insight into other processes where cells secrete molecules, including insulin and airway mucus.. When a group of neurons receives an electrical signal, the cells release chemicals called neurotransmitters nearly instantaneously - within less than one thousandth of a second. Neurons hold neurotransmitters in bubble-like structures called synaptic vesicles. These structures rest inside the end of long, thin projections that point toward neighboring cells. To free neurotransmitters from their bubbles, neurons must fuse vesicle membranes with the outer membrane of the projections. This opens the bubbles and dumps ...
Since the structure of proteins is more conserved than the sequence, the identification of conserved three-dimensional (3D) patterns among a set of proteins, can be important for protein function prediction, protein clustering, drug discovery and the establishment of evolutionary relationships. Thus, several computational applications to identify, describe and compare 3D patterns (or motifs) have been developed. Often, these tools consider a 3D pattern as that described by the residues surrounding co-crystallized/docked ligands available from X-ray crystal structures or homology models. Nevertheless, many of the protein structures stored in public databases do not provide information about the location and characteristics of ligand binding sites and/or other important 3D patterns such as allosteric sites, enzyme-cofactor interaction motifs, etc. This makes necessary the development of new ligand-independent methods to search and compare 3D patterns in all available protein structures. Here we introduce
Knowledge-based protocols for protein structure prediction : from protein threading to solvent accessibility prediction and back to protein structure prediction by threading. Jarek Meller Division of Biomedical Informatics, Slideshow 5415171 by pippa
Profacgen, a US-based biotech company, has added one additional molecular modeling service, protein structure modeling, to its existing custom protein services.. The three-dimensional structure of a protein provides essential information about its biological function and facilitates the design of therapeutic drugs that specifically bind to the protein target. Recent years have witnessed a tremendous increase in the number of experimentally determined protein structures. It is, however, still generally tedious and time-consuming to solve protein structures with experimental approaches. Therefore, computational approaches represent an alternative and supplement to experimental methods to obtain three-dimensional structure of a protein.. By taking advantages of computational modeling methods, Profacgen is able to predict the three-dimensional structure of proteins of its customers interest. Over the years, Profacgen has accumulated abundant experience with the modeling of various kinds of ...
Biochemistry is a rich source of important computational problems that should be of interest to mathematicians, computer scientists and engineers. The dramatic drop in the cost of sequencing DNA as well as progress in several structural genomics initiatives have created many new and exciting opportunities. ...
Biomolecules are the prime information processing elements of living matter. Most of these inanimate systems are polymers that compute their own structures and dynamics using as input seemingly random character strings of their sequence, following which they coalesce and perform integrated cellular functions. In large computational systems with finite interaction-codes, the appearance of conflicting goals is inevitable. Simple conflicting forces can lead to quite complex structures and behaviors, leading to the concept of frustration in condensed matter. We present here some basic ideas about frustration in biomolecules and how the frustration concept leads to a better appreciation of many aspects of the architecture of biomolecules, and especially how biomolecular structure connects to function by means of localized frustration. These ideas are simultaneously both seductively simple and perilously subtle to grasp completely. The energy landscape theory of protein folding provides a framework ...
A laser technique that can measure interactions between proteins tangled in a cells membrane is expected to help in the discovery of new drugs.
Abstract:. Biomolecules are the prime information processing elements of living matter. Most of these inanimate systems are polymers that compute their own structures and dynamics using as input seemingly random character strings of their sequence, following which they coalesce and perform integrated cellular functions. In large computational systems with finite interaction-codes, the appearance of conflicting goals is inevitable. Simple conflicting forces can lead to quite complex structures and behaviors, leading to the concept of frustration in condensed matter. We present here some basic ideas about frustration in biomolecules and how the frustration concept leads to a better appreciation of many aspects of the architecture of biomolecules, and especially how biomolecular structure connects to function by means of localized frustration. These ideas are simultaneously both seductively simple and perilously subtle to grasp completely. The energy landscape theory of protein folding provides a ...
Sens. Blumenthal and Murphy sent a letter to the CDC director Tuesday asking the agency to buy 250,000 FluBlok doses in January from Protein Sciences Corp., for this season.
Protein structure prediction techniques proceed in two steps, namely the generation of many structural models for the protein of interest, followed by an evaluation of all these models to identify those that are native-like. In theory, the second ste
How protein structure is established is a fascinating question and a field that is actively studied by prominent labs around the world. Protein folding is the process of a chain of amino acids curling into its final shape, and how this process occurs is complex and not completely understood. In general proteins fold depending on their environment (exposed to water or not, for example) and with the help of other proteins, called chaperones. Protein chaperones help to establish a proteins structure as well as maintain it during times of stress. Further, modifications on proteins can change their structures, such as when p53, a protein that is involved in regulating many processes within the cell, is phosphorylated - its structure and, consequently, its function is altered slightly ...
Scan Pocket Surface This option will try a single residue side-chain mutation at each position in the protein that is in contact with the receptor ...
Protein structures are stabilized using noncovalent interactions. In addition to the traditional noncovalent interactions, newer types of interactions are thought to be present in proteins. One such interaction, an anion-p pair, in which the positively charged edge of an aromatic ring interacts with an anion, forming a favorable anion-quadrupole interaction, has been previously proposed [Jackson, M. R., et al. (2007) J. Phys. Chem. B111, 8242?8249]. To study the role of anion-? interactions in stabilizing
Users can interactively analyze protein-small ligand binding modes with statistically determined interaction patterns rather than relying on a priori knowledge of the users.
Free practice questions for High School Biology - Understanding Proteins and Nucleic Acids. Includes full solutions and score reporting.
Buy our Pescadillo 293T transfected lysate (positive control). ab94282 has been validated in western blot. Abcam now offers a 12-month guarantee.
APSnet Feature. July, 2002... Jan E. LeachDepartment of Plant PathologyKansas State UniversityManhattan, KS [email protected] Scott GoldDepartment of Plant PathologyUniversity of GeorgiaAthens, GA [email protected] Sue A. TolinDept of Plant Path, Physiology, & Weed SciVirginia Pol...
SCOPe: Structural Classification of Proteins - extended database, and ASTRAL compendium for protein structure and sequence analysis
SCOPe: Structural Classification of Proteins - extended database, and ASTRAL compendium for protein structure and sequence analysis
Bacterial protein structures can expedite the development of novel antibiotics. Here is the latest research on bacterial proteins and the resolution of their structures. ...
Quanta will calculate hydrogen bonds and then analyze the secondary structure in its Protein Design Module, but it seems like a rather large investment if all you want to do is determine the secondary structure......... ........Tom Branham ...
Secondary structure of proteins refers to local and repetitive conformations, such as α‐helices and β‐strands, which occur in protein structures
We want to understand how evolution works at the molecular level. To this end, we study evolution of HIV within individual patients. The HIV genome changes substantially in the course of the infection and its evolution can be directly observed by sequencing frozen serial blood samples taken every couple of month. Using this data, we can trace how viral proteins change over time in response to immune selection and drug treatment. We complement the sequence data with theoretical modeling, as well as with data on protein function and measurements of viral fitness. The detailed understanding of HIV biology and the availability of time series genotype data make HIV a unique model system for evolution ...
Protein structure and function prediction (see my [http://www.sbc.su.se/~maccallr/ former homepage] for predictors of protein disorder, residue-residue contacts and nuclear localisation ...