Positioning hydrogen atoms by optimizing hydrogen‐bond networks in protein structures

By Rob W. W. Hooft, Christopher Sander, G. Vriend. 1996

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Citations in the corpus

Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. (1999, background): “WhatIf ( Hooft et al., 1996 ) deals with both aspects of the problem, including even the assignment of H positions for all crystallographically located water molecules with occupancy >0.5; it builds in crystal symmetry, and has a penalty bias against flips in marginal cases.”
The determinants of α-amylase pH–activity profiles (2001, methodology): “The routines apply the hydrogen-bond optimization procedure of Hooft et al. ( Hooft et al., 1996 ) in order to model each of the protein protonation states accurately.”
A New Generation of Crystallographic Validation Tools for the Protein Data Bank (2011, methodology): “New Crystallographic Validation Tools for the PDB NH 3 , and even side-chain amides need to be optimized within entire (local) H-bond networks, including their interactions with nonpolar as well as polar atoms and with ordered waters (Hooft et al., 1996b; Word et al., 1999b).”
Making optimal use of empirical energy functions: Force‐field parameterization in crystal space (2004, methodology): “18 Then YASARA was used to predict the pKa values of the ionizable groups in the crystal, assign their protonation states based on the pH at which the crystal was solved (retrieved from literature if not speciﬁed in the PDB ﬁle) and ﬁll the cell with water.”
SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model. (1999, methodology): “Packages such as PROCHECK (Laskowski, MacArthur et al., 1993) and WHAT-IF (Hooft et al., 1996), often used in the crystallographic community, focus on the validation of geometric and stereochemical parameters of the molecular models (e.g. covalent bonds and angles, main-chain and sidechain dihedral ”
MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes (2004, background): “Traditional clash analysis tools (5,6) do not use the hydrogens, which are especially revealing in this case.”
MolProbity: all-atom structure validation for macromolecular crystallography (2009, unknown): “The percentage of incorrect Asn/ Gln/His flips also remained level or rose slightly prior to 2003, despite the availability of a hydrogen-bond-based system in WHAT IF (Hooft et al., 1996), and even while refinement methods, automation and Ramachandran and rotamer quality all improved.”
PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations (2004, methodology): “The procedure is similar in purpose to the work of Hooft et al. ( 18 ) and Nielsen et al. (10) but uses a newer algorithm and implementation.”
PRODRG: a tool for high-throughput crystallography of protein-ligand complexes. (2004, methodology): “Particularly useful is the topology for the molecular-modelling program WHAT IF (Vriend, 1990), which allows the precise and automatic determination of protein±ligand hydrogen bonding geometry with WHAT IF's HB2 algorithm (Hooft et al., 1996; Rao et al., 2003).”