Search Results - "Heringa, J"

PRALINE: a multiple sequence alignment toolbox that integrates homology-extended and secondary structure information by Simossis, V. A., Heringa, J.

“…PRofile ALIgNEment (PRALINE) is a fully customizable multiple sequence alignment application. In addition to a number of available alignment strategies,…”
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The characteristics of molten globule states and folding pathways strongly depend on the sequence of a protein by Dijkstra, M.J.J., Fokkink, W.J., Heringa, J., van Dijk, E., Abeln, S.

“…The majority of proteins perform their cellular function after folding into a specific and stable native structure. Additionally, for many proteins less…”
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Homology-extended sequence alignment by Simossis, V. A., Kleinjung, J., Heringa, J.

“…We present a profile–profile multiple alignment strategy that uses database searching to collect homologues for each sequence in a given set, in order to…”
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Multi-Harmony: detecting functional specificity from sequence alignment by Brandt, Bernd W, Feenstra, K. Anton, Heringa, Jaap

“…Many protein families contain sub-families with functional specialization, such as binding different ligands or being involved in different protein-protein…”
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RNA structure prediction from evolutionary patterns of nucleotide composition by Smit, S, Knight, R, Heringa, J

“…Structural elements in RNA molecules have a distinct nucleotide composition, which changes gradually over evolutionary time. We discovered certain features of…”
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Integrating protein secondary structure prediction and multiple sequence alignment by Simossis, V A, Heringa, J

“…Modern protein secondary structure prediction methods are based on exploiting evolutionary information contained in multiple sequence alignments. Critical…”
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Scooby-domain: prediction of globular domains in protein sequence by George, Richard A., Lin, Kuang, Heringa, Jaap

“…Scooby-domain (sequence hydrophobicity predicts domains) is a fast and simple method to identify globular domains in protein sequence, based on the observed…”
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SEQATOMS: a web tool for identifying missing regions in PDB in sequence context by Brandt, B.W, Heringa, J, Leunissen, J.A.M

“…With over 46 000 proteins, the Protein Data Bank (PDB) is the most important database with structural information of biological macromolecules. PDB files…”
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The PRALINE online server: optimising progressive multiple alignment on the web by Simossis, V.A., Heringa, J.

“…We introduce the online server for PRALINE (http://ibium.cs.vu.nl/programs/pralinewww/), an iterative versatile progressive multiple sequence alignment (MSA)…”
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The influence of gapped positions in multiple sequence alignments on secondary structure prediction methods by Simossis, V.A., Heringa, J.

“…All currently leading protein secondary structure prediction methods use a multiple protein sequence alignment to predict the secondary structure of the top…”
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Measuring non-steady-state metabolic fluxes in starch-converting faecal microbiota in vitro by Binsl, T W, De Graaf, A A, Venema, K, Heringa, J, Maathuis, A, De Waard, P, Van Beek, J H G M

“…This paper explores human gut bacterial metabolism of starch using a combined analytical and computational modelling approach for metabolite and flux analysis…”
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Cluster Monte Carlo: Extending the range by Blöte, H.W.J., Heringa, J.R., Luijten, E.

“…Monte Carlo simulations with local updates tend to become time-consuming when large-scale correlations exist, such as in critical systems. For a limited, but…”
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A simple and fast approach to prediction of protein secondary structure from multiply aligned sequences with accuracy above 70 by Mehta, Perdeep K., Heringa, Jaap, Argos, Patrick

“…To improve secondary structure predictions in protein sequences, the information residing in multiple sequence alignments of substituted but structurally…”
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Measuring non-steady-state metabolic fluxes in starch-converting faecal microbiota in vitro by Binsl, T W, De Graaf, A A, Venema, K, Heringa, J, Maathuis, A, De Waard, P, Van Beek, J H G M

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The FAIR Guiding Principles for scientific data management and stewardship by Wilkinson, Mark D., Dumontier, Michel, Aalbersberg, IJsbrand Jan, Appleton, Gabrielle, Axton, Myles, Baak, Arie, Blomberg, Niklas, Boiten, Jan-Willem, da Silva Santos, Luiz Bonino, Bourne, Philip E., Bouwman, Jildau, Brookes, Anthony J., Clark, Tim, Crosas, Mercè, Dillo, Ingrid, Dumon, Olivier, Edmunds, Scott, Evelo, Chris T., Finkers, Richard, Gonzalez-Beltran, Alejandra, Gray, Alasdair J.G., Groth, Paul, Goble, Carole, Grethe, Jeffrey S., Heringa, Jaap, ’t Hoen, Peter A.C, Hooft, Rob, Kuhn, Tobias, Kok, Ruben, Kok, Joost, Lusher, Scott J., Martone, Maryann E., Mons, Albert, Packer, Abel L., Persson, Bengt, Rocca-Serra, Philippe, Roos, Marco, van Schaik, Rene, Sansone, Susanna-Assunta, Schultes, Erik, Sengstag, Thierry, Slater, Ted, Strawn, George, Swertz, Morris A., Thompson, Mark, van der Lei, Johan, van Mulligen, Erik, Velterop, Jan, Waagmeester, Andra, Wittenburg, Peter, Wolstencroft, Katherine, Zhao, Jun, Mons, Barend

“…There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders—representing academia, industry,…”
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Monte Carlo renormalization of the 3D Ising model: Analyticity and convergence by Blöte, HW, Heringa, JR, Hoogland, A, Meyer, EW, Smit, TS

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Protein secondary structure prediction by Pirovano, Walter, Heringa, Jaap

“…While the prediction of a native protein structure from sequence continues to remain a challenging problem, over the past decades computational methods have…”
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T-Coffee: A novel method for fast and accurate multiple sequence alignment by Notredame, C, Higgins, D G, Heringa, J

“…We describe a new method (T-Coffee) for multiple sequence alignment that provides a dramatic improvement in accuracy with a modest sacrifice in speed as…”
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An analysis of protein domain linkers: their classification and role in protein folding by George, Richard A., Heringa, Jaap

“…Recent advances in protein engineering have come from creating multi-functional chimeric proteins containing modules from various proteins. These modules are…”
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A simple and fast secondary structure prediction method using hidden neural networks by Lin, Kuang, Simossis, Victor A., Taylor, Willam R., Heringa, Jaap

“…Motivation: In this paper, we present a secondary structure prediction method YASPIN that unlike the current state-of-the-art methods utilizes a single neural…”
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