Numerical criteria for the evaluation of ab initio predictions of protein structure

Keywords

Validator, Computer science, Scripting language, Set (abstract data type), Data mining

References

• Protein Secondary Structure PredictionStanley R. Krystek, William J. Metzler, Jiří Novotný — 1995
• A local alignment method for protein structure motifs.Christine Orengo, William R. Taylor — 1993
• Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical featuresWolfgang Kabsch, Christian Sander — 1983
• A large‐scale experiment to assess protein structure prediction methodsJohn Moult, Jan T. Pedersen, Richard Judson — 1995
• Systematic representation of protein folding patterns.Arthur M. Lesk — 1995
• Rigid domains in proteins: An algorithmic approach to their identificationWilliam L. Nichols, George D. Rose, Lynn F. Ten Eyck — 1995
• Protein structure comparison by alignment of distance matrices.Liisa Holm, Chris Sander — 1993
• A program to produce both detailed and schematic plots of protein structuresP. Kraulis — 1991
• Redefining the goals of protein secondary structure prediction.Burkhard Rost, Chris Sander, Reinhard Schneider — 1994
• A fast algorithm for rendering space-filling molecule picturesDavid Bacon, WayneF. Anderson — 1988
• Common spatial arrangements of backbone fragments in homologous and non-homologous proteins.Nickolai Alexandrov, Katsutoshi Takahashi, Nobuhiro Gō — 1992
• Raster3D Version 2.0. A program for photorealistic molecular graphics.E.A. Merritt, M.E.P. Murphy — 1994
• Fast and simple monte carlo algorithm for side chain optimization in proteins: Application to model building by homologyLiisa Holm, Chris Sander — 1992
• Database of homology‐derived protein structures and the structural meaning of sequence alignmentChris Sander, Reinhard Schneider — 1991
• PHD - an automatic mail server for protein secondary structure predictionBurkhard Rost, Chris Sander, Reinhard Schneider — 1994
• Knowledge‐based protein secondary structure assignmentDmitrij Frishman, Patrick Argos — 1995
• A modified definition of Sov, a segment‐based measure for protein secondary structure prediction assessmentAdam Zemła, ?eslovas Venclovas, Krzysztof Fidelis — 1999
• Contact area difference (CAD): a robust measure to evaluate accuracy of protein models.Ruben Abagyan, Maxim Totrov — 1997
• Evaluation of current techniques for Ab initio protein structure predictionTom Defay, Fred E. Cohen — 1995
• The Limits of Protein Secondary Structure Prediction Accuracy from Multiple Sequence AlignmentRobert B. Russell, Geoffrey J. Barton — 1993

Cited by

• A physical approach to protein structure prediction.Rieza Ardiningsih — 2001
• A comparison of computational methods for the maximum contact map overlap of protein pairs.Giuseppe Lancia, Natalio Krasnogor, Robert D. Carr — 2003
• SPI – Structure Predictability Index for Protein SequencesMichał Bryliński, Leszek Konieczny, Irena Roterman — 2005
• Improved modeling of side‐chains in proteins with rotamer‐based methods: A flexible rotamer modelJoaquim Mendes, António M. Baptista, M.A. Carrondo — 1999
• Ab initio protein structure prediction of CASP III targets using ROSETTAKim T. Simons, Rich Bonneau, Ingo Ruczinski — 1999
• Processing and analysis of CASP3 protein structure predictionsAdam Zemła, Česlovas Venclovas, John Moult — 1999
• Are predicted structures good enough to preserve functional sites?Liping Wei, Enoch S. Huang, Russ B. Altman — 1999
• RMS/Coverage graphs: A qualitative method for comparing three‐dimensional protein structure predictionsTim Hubbard — 1999
• Déjà vu all over again: finding and analyzing protein structure similarities.Michael Sierk, Gerard J. Kleywegt — 2004
• Analysis and assessment of ab initio three‐dimensional prediction, secondary structure, and contacts predictionChristine Orengo, James E. Bray, Tim Hubbard — 1999
• A guide to template based structure prediction.Xiaotao Qu, Rosemarie Swanson, Ryan Day — 2009
• Assessment of novel fold targets in CASP4: Predictions of three‐dimensional structures, secondary structures, and interresidue contactsArthur M. Lesk, Loredana Lo Conte, Tim Hubbard — 2001
• Detection and reduction of evolutionary noise in correlated mutation analysis.Orly Noivirt, Miriam Eisenstein, Amnon Horovitz — 2005
• Refinement of protein structure homology models via long, all‐atom molecular dynamics simulationsAlpan Raval, Stefano Piana, Michael P. Eastwood — 2012
• Using multiple templates to improve quality of homology models in automated homology modelingPer Larsson, Björn Wallner, Erik Lindahl — 2008
• LGA: a method for finding 3D similarities in protein structuresAdam Zemła — 2003
• Detecting local structural similarity in proteins by maximizing number of equivalent residuesDaron M. Standley, Hiroyuki Toh, Haruki Nakamura — 2004
• Processing and evaluation of predictions in CASP4Adam Zemła, ?eslovas Venclovas, John Moult — 2001
• Mapping the Conformational Dynamics and Pathways of Spontaneous Steric Zipper Peptide OligomerizationDirk Matthes, Vytautas Gapsys, Venita Daebel — 2011
• System for accepting server predictions in CASP6Volker A. Eyrich, Andriy Kryshtafovych, Maciej Miłostan — 2005

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