Search Results

There are 9015 results for: content related to: CyClus: A fast, comprehensive cylindrical interface approximation clustering/reranking method for rigid-body protein–protein docking decoys

  1. You have free access to this content
    On the analysis of protein–protein interactions via knowledge-based potentials for the prediction of protein–protein docking

    Protein Science

    Volume 20, Issue 3, March 2011, Pages: 529–541, Elisenda Feliu, Patrick Aloy and Baldo Oliva

    Article first published online : 24 FEB 2011, DOI: 10.1002/pro.585

  2. A large decoy set of protein–protein complexes produced by flexible docking

    Journal of Computational Chemistry

    Volume 32, Issue 1, 15 January 2011, Pages: 106–120, Guillaume Launay and Thomas Simonson

    Article first published online : 17 NOV 2010, DOI: 10.1002/jcc.21604

  3. How different from random are docking predictions when ranked by scoring functions?

    Proteins: Structure, Function, and Bioinformatics

    Volume 78, Issue 16, December 2010, Pages: 3376–3385, Elisenda Feliu and Baldomero Oliva

    Article first published online : 16 SEP 2010, DOI: 10.1002/prot.22844

  4. PROCOS: Computational analysis of protein–protein complexes

    Journal of Computational Chemistry

    Volume 32, Issue 12, September 2011, Pages: 2575–2586, Florian Fink, Jochen Hochrein, Vincent Wolowski, Rainer Merkl and Wolfram Gronwald

    Article first published online : 31 MAY 2011, DOI: 10.1002/jcc.21837

  5. Comparison of two optimization methods to derive energy parameters for protein folding: Perceptron and Z score

    Proteins: Structure, Function, and Bioinformatics

    Volume 41, Issue 2, 1 November 2000, Pages: 192–201, Michele Vendruscolo, Leonid A. Mirny, Eugene I. Shakhnovich and Eytan Domany

    Article first published online : 17 AUG 2000, DOI: 10.1002/1097-0134(20001101)41:2<192::AID-PROT40>3.0.CO;2-3

  6. Sampling and scoring: A marriage made in heaven

    Proteins: Structure, Function, and Bioinformatics

    Volume 81, Issue 11, November 2013, Pages: 1874–1884, Sandor Vajda, David R. Hall and Dima Kozakov

    Article first published online : 18 AUG 2013, DOI: 10.1002/prot.24343

  7. Coarse- and fine-grained models for proteins: Evaluation by decoy discrimination

    Proteins: Structure, Function, and Bioinformatics

    Volume 81, Issue 5, May 2013, Pages: 754–773, Chris Kauffman and George Karypis

    Article first published online : 27 FEB 2013, DOI: 10.1002/prot.24222

  8. Structure refinement of protein model decoys requires accurate side-chain placement

    Proteins: Structure, Function, and Bioinformatics

    Volume 81, Issue 3, March 2013, Pages: 469–478, Mark A. Olson and Michael S. Lee

    Article first published online : 12 NOV 2012, DOI: 10.1002/prot.24204

  9. Consensus scoring for enriching near-native structures from protein–protein docking decoys

    Proteins: Structure, Function, and Bioinformatics

    Volume 75, Issue 2, 1 May 2009, Pages: 397–403, Shide Liang, Samy O. Meroueh, Guangce Wang, Chao Qiu and Yaoqi Zhou

    Article first published online : 2 SEP 2008, DOI: 10.1002/prot.22252

  10. A discriminative Ramachandran potential of mean force aimed at minimizing secondary structure bias

    Journal of Computational Chemistry

    Volume 33, Issue 7, 15 March 2012, Pages: 791–799, Sampath Koppole and Michael Schaefer

    Article first published online : 6 JAN 2012, DOI: 10.1002/jcc.22908

  11. Predicting protein complex geometries with a neural network

    Proteins: Structure, Function, and Bioinformatics

    Volume 78, Issue 4, March 2010, Pages: 1026–1039, Myong-Ho Chae, Florian Krull, Stephan Lorenzen and Ernst-Walter Knapp

    Article first published online : 8 OCT 2009, DOI: 10.1002/prot.22626

  12. Scoring protein interaction decoys using exposed residues (SPIDER): A novel multibody interaction scoring function based on frequent geometric patterns of interfacial residues

    Proteins: Structure, Function, and Bioinformatics

    Volume 80, Issue 9, August 2012, Pages: 2207–2217, Raed Khashan, Weifan Zheng and Alexander Tropsha

    Article first published online : 7 JUN 2012, DOI: 10.1002/prot.24110

  13. Distance dependency and minimum amino acid alphabets for decoy scoring potentials

    Journal of Computational Chemistry

    Volume 34, Issue 1, 5 January 2013, Pages: 10–20, Susanne Pape, Franziska Hoffgaard, Mirjam Dür and Kay Hamacher

    Article first published online : 1 SEP 2012, DOI: 10.1002/jcc.23099

  14. You have free access to this content
    An accurate, residue-level, pair potential of mean force for folding and binding based on the distance-scaled, ideal-gas reference state

    Protein Science

    Volume 13, Issue 2, February 2004, Pages: 400–411, Chi Zhang, Song Liu, Hongyi Zhou and Yaoqi Zhou

    Article first published online : 1 JAN 2009, DOI: 10.1110/ps.03348304

  15. You have free access to this content
    Cues used by the black fly, Simulium annulus, for attraction to the common loon (Gavia immer)

    Journal of Vector Ecology

    Volume 37, Issue 2, December 2012, Pages: 359–364, Meggin L. Weinandt, Michael Meyer, Mac Strand and Alec R. Lindsay

    Article first published online : 26 NOV 2012, DOI: 10.1111/j.1948-7134.2012.00239.x

  16. LABORATORY EXPERIMENTS ON GREGARIOUS BEHAVIOUR IN OVIPOSITING FEMALES OF THE DESERT LOCUST, (SCHISTOCERCA GREGARIA (FORSK.))

    Entomologia Experimentalis et Applicata

    Volume 6, Issue 4, December 1963, Pages: 279–303, MAUD J. NORRIS and Mrs. O. W. RICHARDS

    Article first published online : 5 APR 2011, DOI: 10.1111/j.1570-7458.1963.tb00628.x

  17. Optimized distance-dependent atom-pair-based potential DOOP for protein structure prediction

    Proteins: Structure, Function, and Bioinformatics

    Volume 83, Issue 5, May 2015, Pages: 881–890, Myong-Ho Chae, Florian Krull and Ernst-Walter Knapp

    Article first published online : 25 MAR 2015, DOI: 10.1002/prot.24782

  18. Multi-LZerD: Multiple protein docking for asymmetric complexes

    Proteins: Structure, Function, and Bioinformatics

    Volume 80, Issue 7, July 2012, Pages: 1818–1833, Juan Esquivel-Rodríguez, Yifeng David Yang and Daisuke Kihara

    Article first published online : 8 MAY 2012, DOI: 10.1002/prot.24079

  19. You have free access to this content
    Design of an optimal Chebyshev-expanded discrimination function for globular proteins

    Protein Science

    Volume 11, Issue 8, August 2002, Pages: 2010–2021, Boris Fain, Yu Xia and Michael Levitt

    Article first published online : 13 APR 2009, DOI: 10.1110/ps.0200702

  20. Detecting local residue environment similarity for recognizing near-native structure models

    Proteins: Structure, Function, and Bioinformatics

    Volume 82, Issue 12, December 2014, Pages: 3255–3272, Hyungrae Kim and Daisuke Kihara

    Article first published online : 30 OCT 2014, DOI: 10.1002/prot.24658