Search Results - "Wodak, S. J."

CYGD: the Comprehensive Yeast Genome Database by Guldener, U, Munsterkotter, M, Kastenmuller, G, Strack, N, Helden, J. van, Lemer, C, Richelles, J, Wodak, S.J, Garcia-Martinez, J, Perez-Ortin, J.E

“…The Comprehensive Yeast Genome Database (CYGD) compiles a comprehensive data resource for information on the cellular functions of the yeast Saccharomyces…”
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Analysis of zinc binding sites in protein crystal structures by Alberts, Ian L., Nadassy, Katalin, Wodak, Shoshana J.

“…The geometrical properties of zinc binding sites in a dataset of high quality protein crystal structures deposited in the Protein Data Bank have been examined…”
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Metabolic PathFinding: inferring relevant pathways in biochemical networks by Croes, Didier, Couche, Fabian, Wodak, Shoshana J., van Helden, Jacques

“…Our knowledge of metabolism can be represented as a network comprising several thousands of nodes (compounds and reactions). Several groups applied graph…”
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SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model by Vaguine, Alexei A., Richelle, Jean, Wodak, S. J.

“…In this paper we present SFCHECK, a stand‐alone software package that features a unified set of procedures for evaluating the structure‐factor data obtained…”
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Combining pattern discovery and discriminant analysis to predict gene co-regulation by Simonis, N., Wodak, S. J., Cohen, G. N., van Helden, J.

“…Motivation: Several pattern discovery methods have been proposed to detect over-represented motifs in upstream sequences of co-regulated genes, and are for…”
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NMR Sequential Assignments and Solution Structure of Chlorotoxin, a Small Scorpion Toxin That Blocks Chloride Channels by Lippens, G, Najib, J, Wodak, S. J, Tartar, A

“…The solution structure of chlorotoxin, a small toxin purified from the venom of the Leiurus quinquestriatus scorpion, has been determined using 2D 1H NMR…”
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Representing and analysing molecular and cellular function using the computer by van Helden, J, Naim, A, Mancuso, R, Eldridge, M, Wernisch, L, Gilbert, D, Wodak, S J

“…Determining the biological function of a myriad of genes, and understanding how they interact to yield a living cell, is the major challenge of the post…”
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Contribution of the Hydrophobic Effect to Protein Stability: Analysis Based on Simulations of the Ile-96 → Ala Mutation in Barnase by Prevost, Martine, Wodak, Shoshana J., Tidor, Bruce, Karplus, Martin

“…Molecular dynamics simulations have been used to compute the difference in the unfolding free energy between wild-type barnase and the mutant in which Ile-96…”
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Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches by Kocher, J P, Rooman, M J, Wodak, S J

“…Several types of potentials are derived from a dataset of known protein structures by computing statistical relations between amino acid sequence and different…”
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Structural Features of Protein−Nucleic Acid Recognition Sites by Nadassy, Katalin, Wodak, Shoshana J, Janin, Joël

“…We analyzed the atomic models of 75 X-ray structures of protein−nucleic acid complexes with the aim of uncovering common properties. The interface area…”
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Deviations from Standard Atomic Volumes as a Quality Measure for Protein Crystal Structures by Pontius, Joan, Richelle, Jean, Wodak, Shoshana J.

“…Standard ranges of atomic and residue volumes are computed in 64 highly resolved and well-refined protein crystal structures using the classical Voronoi…”
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DAnCER: disease-annotated chromatin epigenetics resource by Turinsky, Andrei L, Turner, Brian, Borja, Rosanne C, Gleeson, James A, Heath, Michael, Pu, Shuye, Switzer, Thomas, Dong, Dong, Gong, Yunchen, On, Tuan, Xiong, Xuejian, Emili, Andrew, Greenblatt, Jack, Parkinson, John, Zhang, Zhaolei, Wodak, Shoshana J

“…Chromatin modification (CM) is a set of epigenetic processes that govern many aspects of DNA replication, transcription and repair. CM is carried out by groups…”
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Extracting information on folding from the amino acid sequence: Accurate predictions for protein regions with preferred conformation in the absence of tertiary interactions by Rooman, Marianne J, Kocher, Jean Pierre A, Wodak, Shoshana J

“…A recently developed procedure to predict backbone structure from the amino acid sequence [Rooman, M., Kocher, J. P., & Wodak, S. (1991) J. Mol. Biol, 221,…”
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Inferring Meaningful Pathways in Weighted Metabolic Networks by Croes, Didier, Couche, Fabian, Wodak, Shoshana J., van Helden, Jacques

“…An approach is presented for computing meaningful pathways in the network of small molecule metabolism comprising the chemical reactions characterized in all…”
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Structural Principles of Parallel β -Barrels in Proteins by Lasters, Ignace, Wodak, Shoshana J., Alard, Philippe, Van Cutsem, Eric

“…Eight-stranded β -sheets in nine protein structures containing ``TIM (triose phosphate isomerase) barrels'' are shown to be fitted satisfactorily by…”
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Automatic procedures for protein design by Jaramillo, A, Wernisch, L, Hery, S, Wodak, S J

“…This review describes computational procedures for deriving the amino acid sequences that are compatible with a given protein backbone structure. Such…”
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Are database-derived potentials valid for scoring both forward and inverted protein folding? by Rooman, M J, Wodak, S J

“…Database-derived potentials, compiled from frequencies of sequence and structure features, are often used for scoring the compatibility of protein sequences…”
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Checking nucleic acid crystal structures by Das, Ujjwal, Chen, Shengfeng, Fuxreiter, Monika, Vaguine, Alexei A., Richelle, Jean, Berman, Helen M., Wodak, Shoshana J.

“…The program SFCHECK [Vaguine et al. (1999), Acta Cryst. D55, 191–205] is used to survey the quality of the structure‐factor data and the agreement of those…”
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Optimal protein structure alignments by multiple linkage clustering: application to distantly related proteins by Boutonnet, N S, Rooman, M J, Ochagavia, M E, Richelle, J, Wodak, S J

“…A fully automatic procedure for aligning two protein structures is presented. It uses as sole structural similarity measure the root mean square (r.m.s.)…”
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Automatic protein design with all atom force-fields by exact and heuristic optimization by Wernisch, L, Hery, S, Wodak, S J

“…A fully automatic procedure for predicting the amino acid sequences compatible with a given target structure is described. It is based on the CHARMM package,…”
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