Protein structure alignment by incremental combinatorial extension (CE) of the optimal path.

By Ilya N. Shindyalov, Philip E. Bourne. 1998

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

Citations in the corpus

RUPEE: A fast and accurate purely geometric protein structure search (2018, background): “46 For pairwise alignment, Combinatorial Extensions (CE) [8] and FATCAT [9] are 47”
TM-align: a protein structure alignment algorithm based on the TM-score (2005, neutral): “TM-align is also faster than two other often-used algorithms, CE (17) and DALI (38), and yet provides structure alignments of higher TM-score (which is not surprising since maximization of the TMscore is the goal of the TM-align objective function).”
The RCSB Protein Data Bank: redesigned web site and web services (2010, methodology): “This tool utilizes new Java implementations of the CE (13) and FATCAT (14) structure-alignment algorithms and provides references to external structure alignment servers.”
DeepTracer ID: De Novo Protein Identification from Cryo-EM Maps (2022, methodology): “We use three different approaches, PyMOL-align 21 , PyMOL-cealign 22 and FATCAT 23 , to align the AlphaFold2 predicted structures to the backbone model traced directly from the cryo-EM map (Fig.”
MM-align: a quick algorithm for aligning multiple-chain protein complex structures using iterative dynamic programming (2009, methodology): “A simple treatment might be to join the multiple chains into an artificial monomer and then align the two ‘monomers’ using existing programs such as Dali (9), CE (10) or TM-align (11).”
MUSCLE: multiple sequence alignment with high accuracy and high throughput. (2004, methodology): “We re-aligned each pair of structures using the CE aligner (29), and retained only those pairs for which FSSP and CE agreed on 50 or more positions.”
SP5: Improving Protein Fold Recognition by Using Torsion Angle Profiles and Profile-Based Gap Penalty Model (2008, methodology): “We use PREFAB because its reference alignment is made from the consensus of two separate structural alignment programs (CE [40] and FSSP [41]) rather than one in Prosup.”
Fast overlapping of protein contact maps by alignment of eigenvectors (2010, methodology): “CE (Shindyalov and Bourne, 1998), DaliLite (Holm and Park, 2000) and TM-align (Zhang and Skolnick, 2005) are structural alignment methods.”
A novel method to compare protein structures using local descriptors (2011, background): “The major approaches to structure superposition, including comparing intramolecular inter-residue distances (SSAP [8], DALI [9], PAUL [10]), matching main-chain fragments (CE [11]), or Secondary Structure Elements (SSEs) (VAST [12], SARF [13], MATRAS [14], GANGSTA [15]), handle the limitations impos”
A topology‐constrained distance network algorithm for protein structure determination from NOESY data (2005, unknown): “0 Å.(66) These good agreements demonstrate the robustness and reliability of the program AutoStructure.”