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wouterboomsma protein-structure [68 articles]

Recent papers added to wouterboomsma library classified by the tag protein-structure. You can also see everyone's protein-structure.
  • P-SEA: a new efficient assignment of secondary structure from C alpha trace of proteins
    Comput. Appl. Biosci., Vol. 13, No. 3. (1 June 1997), pp. 291-295.
    by G Labesse, N Colloc'h, J Pothier, Jp Mornon
    posted to protein-structure secondary-structure by wouterboomsma on 2007-10-03 15:16:01 as ** along with 2 people thamelry j3xucite
  • Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features.
    Biopolymers, Vol. 22, No. 12. (December 1983), pp. 2577-2637.
    by W Kabsch, C Sander
    posted to protein-structure secondary-structure by wouterboomsma on 2007-09-05 13:09:57 as ** along with 14 people mschofie kaarsinogen lna chad_davis penka ffranca dgront choonpeng leelarcombe rabio gisle medic0747 martainn chgjb
  • Protein secondary structure prediction based on position-specific scoring matrices.
    J Mol Biol, Vol. 292, No. 2. (17 September 1999), pp. 195-202.
    by DT Jones
    posted to protein-structure secondary-structure by wouterboomsma on 2007-09-05 12:57:13 as ** along with 8 people saunders dandaman chad_davis j3xucite dgront leelarcombe rabio rph
  • Stereochemistry of polypeptide chain configurations.
    J Mol Biol, Vol. 7 (July 1963), pp. 95-99.
    by GN RAMACHANDRAN, C RAMAKRISHNAN, V SASISEKHARAN
    posted to protein-structure by wouterboomsma on 2007-09-05 12:26:46 as ** along with 2 people Diego_Prada jwm
  • Dissecting contact potentials for proteins: Relative contributions of individual amino acids.
    Proteins (19 July 2007)
    by N-V V Buchete, J E E Straub, D Thirumalai
    posted to energy-function protein-structure by wouterboomsma on 2007-07-30 09:22:06 as ** along with 1 person RamuAnandakrishnan
  • Characterization of protein-folding pathways by reduced-space modeling.
    Proc Natl Acad Sci U S A, Vol. 104, No. 30. (24 July 2007), pp. 12330-12335.
    by S Kmiecik, A Kolinski
    posted to folding-pathways protein-structure by wouterboomsma on 2007-07-30 09:20:45 as ** along with 3 people mkurc sekmi nh
  • Protein folding by zipping and assembly.
    Proc Natl Acad Sci U S A, Vol. 104, No. 29. (17 July 2007), pp. 11987-11992.
    by SB Ozkan, GA Wu, JD Chodera, KA Dill
    posted to protein-structure by wouterboomsma on 2007-07-30 09:15:33 as *** along with 2 people aqeel cdeane
  • Towards high-resolution protein structure prediction. Fast refinement of reduced models with all-atom force field
    BMC Structural Biology, Vol. 7 (29 June 2007), 43.
    by Sebastian Kmiecik, Dominik Gront, Andrzej Kolinski
    posted to protein-structure by wouterboomsma on 2007-07-09 10:56:24 as ** along with 2 people rabio sekmi
  • A coarse-grained protein force field for folding and structure prediction.
    Proteins (28 June 2007)
    by Julien Maupetit, P Tuffery, Philippe Derreumaux
    posted to energy-function protein-structure by wouterboomsma on 2007-07-09 10:54:21 as ** along with 1 person choonpeng
  • Biopolymer structure simulation and optimization via fragment regrowth Monte Carlo.
    J Chem Phys, Vol. 126, No. 22. (14 June 2007)
    by J Zhang, SC Kou, JS Liu
    posted to mcmc protein-structure by wouterboomsma on 2007-07-09 10:51:36 as ** along with 1 person huyun110
  • The protein folding problem: when will it be solved?
    Curr Opin Struct Biol (13 June 2007)
    by Ken A A Dill, S Banu B Ozkan, Thomas R R Weikl, John D D Chodera, Vincent A A Voelz
    posted to protein-structure review by wouterboomsma on 2007-07-09 10:49:08 as read along with 6 people cat_worth cactus Jporci cdeane kalicuta sebk
  • ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins.
    Nucleic Acids Res (21 May 2007)
    by Markus Wiederstein, Manfred J J Sippl
    posted to error-detection protein-structure by wouterboomsma on 2007-07-09 10:37:44 as ***
  • Ab initio protein structure prediction using chunk-TASSER.
    Biophys J (11 May 2007)
    by Hongyi Zhou, Jeffrey Skolnick
    posted to protein-structure by wouterboomsma on 2007-07-09 10:33:23 as ** along with 1 person huyun110
  • "Pinning strategy": a novel approach for predicting the backbone structure in terms of protein blocks from sequence.
    J Biosci, Vol. 32, No. 1. (January 2007), pp. 51-70.
    by AG De Brevern, C Etchebest, C Benros, S Hazout
    posted to local-structure protein-structure by wouterboomsma on 2007-05-15 11:03:00 as ** along with 1 person j3xucite
  • Protein structure prediction aided by geometrical and probabilistic constraints.
    J Comput Chem (20 April 2007)
    by Gaurav Porwal, Swapnil Jain, S Dhilly D Babu, Deepak Singh, Hemant Nanavati, Santosh Noronha
    posted to protein-structure by wouterboomsma on 2007-05-15 11:02:40 as **
  • Protein structure prediction: Combining de novo modeling with sparse experimental data.
    J Comput Chem (6 March 2007)
    by Dorota Latek, Dariusz Ekonomiuk, Andrzej Kolinski
    posted to experimental-data protein-structure by wouterboomsma on 2007-05-15 10:53:27 as **
  • Backbone building from quadrilaterals: A fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinates.
    J Comput Chem, Vol. 28, No. 9. (15 July 2007), pp. 1593-1597.
    by D Gront, S Kmiecik, A Kolinski
    posted to protein-structure representation by wouterboomsma on 2007-05-15 10:52:30 as ** along with 4 people j3xucite dgront sekmi mijam
  • HMMSTR: a hidden Markov model for local sequence-structure correlations in proteins.
    J Mol Biol, Vol. 301, No. 1. (4 August 2000), pp. 173-190.
    by C Bystroff, V Thorsson, D Baker
    posted to fragments protein-structure by wouterboomsma on 2007-02-27 14:03:55 as read along with 4 people and 1 group wenhan j3xucite dgront rabio MBLAB
  • Shaping up the protein folding funnel by local interaction: Lesson from a structure prediction study
    PNAS, Vol. 103, No. 9. (28 February 2006), pp. 3141-3146.
    by George Chikenji, Yoshimi Fujitsuka, Shoji Takada
    posted to fragments protein-structure by wouterboomsma on 2007-02-26 18:13:08 as read along with 4 people eckart_bindewald sotaro rsantana saunders
  • Monte Carlo simulations of protein folding. II. Application to protein A, ROP, and crambin.
    Proteins, Vol. 18, No. 4. (April 1994), pp. 353-366.
    by A Kolinski, J Skolnick
    posted to lattice protein-structure by wouterboomsma on 2007-02-26 17:33:07 as read
  • Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme.
    Proteins, Vol. 18, No. 4. (April 1994), pp. 338-352.
    by A Kolinski, J Skolnick
    posted to lattice protein-structure by wouterboomsma on 2007-02-26 17:28:38 as read along with 2 people dgront iantunbridge
  • An evolutionary approach to folding small alpha-helical proteins that uses sequence information and an empirical guiding fitness function.
    Proc Natl Acad Sci U S A, Vol. 91, No. 10. (10 May 1994), pp. 4436-4440.
    by JU Bowie, D Eisenberg
    posted to fragments protein-structure by wouterboomsma on 2007-02-26 13:11:30 as read
  • Folding proteins with a simple energy function and extensive conformational searching.
    Protein Sci, Vol. 5, No. 2. (February 1996), pp. 254-261.
    by K Yue, KA Dill
    posted to protein-structure by wouterboomsma on 2007-02-26 12:35:49 as read
  • Determination of the conformation of folding initiation sites in proteins by computer simulation.
    Proteins, Vol. 23, No. 2. (October 1995), pp. 129-141.
    by F Avbelj, J Moult
    posted to protein-structure by wouterboomsma on 2007-02-26 11:57:08 as read
  • Automated structure prediction of weakly homologous proteins on a genomic scale
    PNAS, Vol. 101, No. 20. (18 May 2004), pp. 7594-7599.
    by Yang Zhang, Jeffrey Skolnick
    posted to protein-structure by wouterboomsma on 2007-02-26 10:45:29 as read along with 3 people nigham j3xucite mirzazadeh
  • LINUS: a hierarchic procedure to predict the fold of a protein.
    Proteins, Vol. 22, No. 2. (June 1995), pp. 81-99.
    by R Srinivasan, GD Rose
    posted to local-structure protein-structure by wouterboomsma on 2007-02-23 19:53:51 as read
  • Blind predictions of local protein structure in CASP2 targets using the I-sites library.
    Proteins, Vol. Suppl 1 (1997), pp. 167-171.
    by C Bystroff, D Baker
    posted to fragments protein-structure by wouterboomsma on 2007-02-22 20:01:06 as read
  • Some fundamental aspects of building protein structures from fragment libraries.
    Protein Sci, Vol. 13, No. 6. (June 2004), pp. 1636-1650.
    by JB Holmes, J Tsai
    posted to fragments protein-structure by wouterboomsma on 2007-02-22 19:57:29 as read along with 2 people and 2 groups barry eckart_bindewald structural_bioinformatics Bioinformatics
  • Prediction of local structure in proteins using a library of sequence-structure motifs.
    J Mol Biol, Vol. 281, No. 3. (21 August 1998), pp. 565-577.
    by C Bystroff, D Baker
    posted to fragments protein-structure by wouterboomsma on 2007-02-22 19:21:16 as read along with 1 person dgront
  • All-atom ab initio folding of a diverse set of proteins.
    Structure, Vol. 15, No. 1. (January 2007), pp. 53-63.
    by JS Yang, WW Chen, J Skolnick, EI Shakhnovich
    posted to protein-structure energy-function by wouterboomsma on 2007-02-05 11:42:46 as *** along with 1 person choonpeng
  • Prediction of structures of multidomain proteins from structures of the individual domains.
    Protein Sci (22 December 2006)
    by Andrew M M Wollacott, Alexandre Zanghellini, Paul Murphy, David Baker
    posted to protein-structure multi-domain by wouterboomsma on 2007-02-05 11:36:19 as ** along with 4 people choonpeng zwang IrinaMoreira rph
  • Statistical potential for assessment and prediction of protein structures.
    Protein Sci, Vol. 15, No. 11. (November 2006), pp. 2507-2524.
    by MY Shen, A Sali
    posted to energy-function protein-structure by wouterboomsma on 2006-11-09 16:12:15 as ** along with 3 people dimka j3xucite cdeane
  • Bayesian data mining of protein domains gives an efficient predictive algorithm and new insight.
    J Mol Model (Online) (7 October 2006)
    by Rajani R Joshi, Vivekanand V Samant
    posted to domain-finding protein-structure by wouterboomsma on 2006-10-16 17:54:35 as **
  • Novel approach for alpha-helical topology prediction in globular proteins: Generation of interhelical restraints.
    Proteins (6 October 2006)
    by S R R McAllister, B E E Mickus, J L L Klepeis, C A A Floudas
    posted to local-structure protein-structure by wouterboomsma on 2006-10-16 17:53:25 as **
  • Improved beta-protein structure prediction by multilevel optimization of nonlocal strand pairings and local backbone conformation
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2006), NA.
    by Philip Bradley, David Baker
    posted to protein-structure sampling by wouterboomsma on 2006-10-16 17:03:45 as **
  • Prediction of peptide structure: How far are we?
    Proteins (3 October 2006)
    by Annick Thomas, Sébastien Deshayes, Marc Decaffmeyer, Marie Hélène H Van Eyck, Benoit Charloteaux, Robert Brasseur
    posted to protein-structure review by wouterboomsma on 2006-10-09 07:33:28 as **
  • Sampling Realistic Protein Conformations Using Local Structural Bias.
    PLoS Comput Biol, Vol. 2, No. 9. (22 September 2006)
    by Thomas Hamelryck, John T T Kent, Anders Krogh
    posted to protein-structure sampling by wouterboomsma on 2006-10-02 12:43:02 as *** along with 2 people j3xucite hmk
  • Direct correlation between proteins' folding rates and their amino acid compositions: An ab initio folding rate prediction.
    Proteins (25 August 2006)
    by Bin-Guang G Ma, Jian-Xiu X Guo, Hong-Yu Y Zhang
    posted to folding-rate protein-structure by wouterboomsma on 2006-08-30 19:05:14 as **
  • A study of fragment-based protein structure prediction: biased fragment replacement for searching low-energy conformation.
    Genome Inform, Vol. 16, No. 2. (2005), pp. 104-113.
    by SJ Park
    posted to fragments protein-structure by wouterboomsma on 2006-08-17 10:13:49 as **
  • Atom-by-atom analysis of global downhill protein folding
    Nature, Vol. 442, No. 7100. (14 June 2006), pp. 317-321.
    by Mourad Sadqi, David Fushman, Victor Muã±oz
    posted to protein-structure by wouterboomsma on 2006-07-31 17:25:53 as ** along with 4 people and 2 groups marcius choonpeng gisle huyun110 BioinfoCIPF SGU-CIPF
  • Atom-wise statistics and prediction of solvent accessibility in proteins.
    Biophys Chem (20 July 2006)
    by Y Hemajit H Singh, M Michael M Gromiha, Akinori Sarai, Shandar Ahmad
    posted to protein-structure solvent-exposure by wouterboomsma on 2006-07-26 11:41:52 as **
  • A contact energy function considering residue hydrophobic environment and its application in protein fold recognition.
    Genomics Proteomics Bioinformatics, Vol. 3, No. 4. (November 2005), pp. 218-224.
    by MJ Duan, YH Zhou
    posted to energy-function protein-structure by wouterboomsma on 2006-07-24 14:46:30 as **
  • Into the fold. Advances in technology and algorithms facilitate great strides in protein structure prediction.
    EMBO Rep, Vol. 7, No. 3. (March 2006), pp. 249-252.
    by P Hunter
    posted to protein-structure review by wouterboomsma on 2006-07-24 14:43:07 as ** along with 1 person chad_davis
  • HARMONY: a server for the assessment of protein structures.
    Nucleic Acids Res, Vol. 34, No. Web Server issue. (1 July 2006)
    by G Pugalenthi, K Shameer, N Srinivasan, R Sowdhamini
    posted to protein-structure quality-assessment servers by wouterboomsma on 2006-07-24 14:39:00 as ** along with 2 people skhadar wilbur
  • The effect of experimental resolution on the performance of knowledge-based discriminatory functions for protein structure selection.
    Protein Eng Des Sel (14 July 2006)
    by Tianyun Liu, Ram Samudrala
    posted to energy-function protein-structure by wouterboomsma on 2006-07-24 14:37:00 as **
  • A model of local-minima distribution on conformational space and its application to protein structure prediction.
    Proteins (12 July 2006)
    by Hongzhi Li
    posted to energy-function protein-structure by wouterboomsma on 2006-07-24 14:29:37 as **
  • Progress in structure prediction of alpha-helical membrane proteins.
    Curr Opin Struct Biol (3 July 2006)
    by Sarel J J Fleishman, Nir Ben-Tal
    posted to protein-structure review by wouterboomsma on 2006-07-24 14:26:30 as ** along with 1 person and 1 group xdeupi LabCompMed
  • Ultra-fast evaluation of protein energies directly from sequence.
    PLoS Comput Biol, Vol. 2, No. 6. (16 June 2006)
    by G Grigorya, F Zhou, SR Lustig, G Ceder, D Morgan, AE Keating
    posted to energy-function protein-structure by wouterboomsma on 2006-07-24 13:56:42 as ** along with 1 person chgjb
  • Advances in homology protein structure modeling.
    Curr Protein Pept Sci, Vol. 7, No. 3. (June 2006), pp. 217-227.
    by Z Xiang
    posted to homology-modeling protein-structure by wouterboomsma on 2006-07-24 13:55:19 as **
  • Potential for assessing quality of protein structure based on contact number prediction.
    Proteins (20 June 2006)
    by Takashi Ishida, Shugo Nakamura, Kentaro Shimizu
    posted to protein-structure quality-assessment by wouterboomsma on 2006-07-24 13:53:32 as **
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