title: Stochastic Proximity Embedding: Methods and Applications.
abstract: Since its inception in 1996, the stochastic proximity embedding (SPE) algorithm and its variants have been applied to a wide range of problems in computational chemistry and biology with notable success. At its core, SPE attempts to generate Euclidean coordinates for a set of points so that they satisfy a prescribed set of geometric constraints. The algorithm's appeal rests on three factors: 1) its conceptual and programmatic simplicity; 2) its superior speed and scaling properties; and 3) its broad applicability. Here, we review some of the key applications, outline known limitations and ways to circumvent them, and highlight additional problem domains where the use of this technique could lead to significant breakthroughs.
authors.affiliation: Johnson & Johnson Pharmaceutical Research & Development, L.L.C., Welsh & McKean Roads, Spring House, PA 19477, USA tel: (215) 628-6814. dagrafio@its.jnj.com.
authors.forename: Dimitris K
authors.initials: DK
authors.lastname: Agrafiotis
authors.affiliation: Current address: D. E. Shaw Research & Development, 120 West 45th Street, New York, NY 10036, USA.
authors.forename: Huafeng
authors.initials: H
authors.lastname: Xu
authors.affiliation: Current address: NIDDK, National Institutes of Health, Building 5, Room 137A, Bethesda, MD 20892, USA.
authors.forename: Fangqiang
authors.initials: F
authors.lastname: Zhu
authors.affiliation: Current address: GlaxoSmithKline, 1250 S. Collegeville Road, Code UP12-210, Collegeville, PA 19426, USA.
authors.forename: Deepak
authors.initials: D
authors.lastname: Bandyopadhyay
authors.affiliation: Johnson & Johnson Pharmaceutical Research & Development, L.L.C., Welsh & McKean Roads, Spring House, PA 19477, USA tel: (215) 628-6814.
authors.forename: Pu
authors.initials: P
authors.lastname: Liu
keywords: Alignment; Boosting; Conformational analysis; Dimensionality reduction; Docking; Loop modeling; Manifold learning; Nonlinear mapping; Pharmacophore; Protein loop; Self-organizing superposition; Stochastic proximity embedding; Stochastic search; Structure depiction; Systematic search