WHAT IF: a molecular modeling and drug design program.

By G. Vriend. 1990

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Citations in the corpus

Measurement of Areas on a Sphere Using Fibonacci and Latitude–Longitude Lattices (2009, methodology): “ The ﬁrst graphs of spherical Fibonacci lattices used, as here, the golden ratio and a Fermat spiral [15, 16, 17]. A version based on the Fibonacci ratio is used in the modelling of complex molecules [71, 65, 42]. In this case 5 Figure 3: Spherical Fibonacci lattices in Nature – an oblique view of t”
Identification, Cloning, and Characterization of a Lactococcus lactis Branched-Chain α-Keto Acid Decarboxylase Involved in Flavor Formation (2005, unknown): “(39) by using the structure of yeast pyruvate decarboxylase (PDB code 1QPB) as a template.”
Application of DEN refinement and automated model building to a difficult case of molecular-replacement phasing: the structure of a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum (2012, methodology): “…which verifies the stereochemical quality of the model using AutoDepInputTool (Yang et al., 2004), MolProbity (Chen et al., 2010) and WHAT IF v.5.0 (Vriend, 1990); the agreement between the atomic model and the data using SFCHECK v.4.0 (Vaguine et al., 1999) and RESOLVE (Terwilliger, 2000); the…”
Molecular Simulations of Cotranslational Protein Folding: Fragment Stabilities, Folding Cooperativity, and Trapping in the Ribosome (2006, unknown): “5 Å of each other after hydrogens had been added to the structures using WHAT IF [83].”
GPCRdb: an information system for G protein-coupled receptors (2015, methodology): “Multiple sequence alignments are performed with WHAT IF ( 11 ) using an iterative sequence-based profile (12).”
Objectively judging the quality of a protein structure from a Ramachandran plot (1997, methodology): “The Ramachandran Z-score procedure was implemented as a procedure in the WHAT IF program (Vriend, 1990).”
Diffusion, Crowding & Protein Stability in a Dynamic Molecular Model of the Bacterial Cytoplasm (2010, methodology): “Any sidechains missing from a structure were built in using the molecular modeling program WHATIF [83].”
QM/MM Methods for Biological Systems (2006, methodology): “Examples include charmm [180, 704], what if [409, 721], or Reduce [406, 407]; an assessment of such procedures has recently appeared [410].”
Statistical potentials for fold assessment (2002, unknown): “These criteria include deviation from standard bond lengths, bond angles, and dihedral angles (Vriend 1990; Engh and Huber 1991; Morris et al. 1992; Laskowski et al. 1993, 1998) residue or atom packing density (Gregoret and Cohen 1991), molecular mechanics energy functions (Novotny et al. 1984,…”