CONCORD: a consensus method for protein secondary structure prediction via mixed integer linear optimization

Abstract

Most of the protein structure prediction methods use a multi-step process, which often includes secondary structure prediction, contact prediction, fragment generation, clustering, etc. For many years, secondary structure prediction has been the workhorse for numerous methods aimed at predicting protein structure and function. This paper presents a new mixed integer linear optimization (MILP)-based consensus method: a Consensus scheme based On a mixed integer liNear optimization method for seCOndary stRucture preDiction (CONCORD). Based on seven secondary structure prediction methods, SSpro, DSC, PROF, PROFphd, PSIPRED, Predator and GorIV, the MILPbased consensus method combines the strengths of different methods, maximizes the number of correctly predicted amino acids and achieves a better prediction accuracy. The method is shown to perform well compared with the seven individual methods when tested on the PDBselect25 training protein set using sixfold cross validation. It also performs well compared with another set of 10 online secondary structure prediction servers (including several recent ones) when tested on the CASP9 targets (http://predictioncenter.org/casp9/). The average Q3 prediction accuracy is 83.04 per cent for the sixfold cross validation of the PDBselect25 set and 82.3 per cent for the CASP9 targets. We have developed a MILP-based consensus method for protein secondary structure prediction. A web server, CONCORD, is available to the scientific community at http://helios.princeton.edu/CONCORD.

Structural and functional characterization of the <em>Helicobacter pylori </em>cytidine 5&#39;-monophosphate-pseudaminic acid synthase PseF: molecular insight into substrate recognition and catalysis mechanism

“…The computed physicochemical parameters included molecular mass, isoelectric point, extinction coefficient, instability index, aliphatic index and grand average of hydropathicity (GRAVY). The CYS_REC tool from SoftBerry and the CONCORD26 server were used to predict the existence of disulfide bridges and secondary structural components of HpPseF, respectively.…”

Protein WISDOM: A Workbench for <em>In silico</em> <em>De novo</em> Design of BioMolecules

“…The first approach was implemented by Klepeis et al 15,16 This approach utilizes the protein structure prediction framework ASTRO-FOLD, 26,27,[31][32][33][34][35][36][37][38][39][40][41][42][43][44][45][46][47] which is based on deterministic global optimization. This approach is not currently used in the implementation of Protein WISDOM since it is very computationally demanding.…”

COMSAT: Residue contact prediction of transmembrane proteins based on support vector machines and mixed integer linear programming

“…A tight distance bound corresponding to false predictions can potentially mislead the conformational search. The predicted contacts from COMSAT are used as distance restraints in tandem with protein 3D structure prediction method, ASTRO‐FOLD . In order to be consistent with the previous works, a contact definition of 14 Å between Cα‐Cα atoms for membrane proteins is used in this article.…”