An evaluation of computational strategies for use in the determination of protein structure from distance constraints obtained by nuclear magnetic resonance
TF Havel - Progress in biophysics and molecular biology, 1991 - Elsevier
Methods of calculating the conformations of biological (macro) molecules from constraints
upon the possible values of their interatomic distances, together with planarity and chirality …
upon the possible values of their interatomic distances, together with planarity and chirality …
Determination of three-dimensional structures of proteins and nucleic acids in solution by nuclear magnetic resonance spectroscop
GM Clore, AM Gronenborn - Critical reviews in biochemistry and …, 1989 - Taylor & Francis
Over the last decade, modem molecular biology, and in particular recombinant DNA
technology, has had a major impact on a large number of biological disciplines. If one …
technology, has had a major impact on a large number of biological disciplines. If one …
Learning subpocket prototypes for generalizable structure-based drug design
Generating molecules with high binding affinities to target proteins (aka structure-based
drug design) is a fundamental and challenging task in drug discovery. Recently, deep …
drug design) is a fundamental and challenging task in drug discovery. Recently, deep …
Antibody-antigen docking and design via hierarchical structure refinement
Computational antibody design seeks to automatically create an antibody that binds to an
antigen. The binding affinity is governed by the 3D binding interface where antibody …
antigen. The binding affinity is governed by the 3D binding interface where antibody …
Molecule generation for target protein binding with structural motifs
Designing ligand molecules that bind to specific protein binding sites is a fundamental
problem in structure-based drug design. Although deep generative models and geometric …
problem in structure-based drug design. Although deep generative models and geometric …
Data visualization with multidimensional scaling
We discuss methodology for multidimensional scaling (MDS) and its implementation in two
software systems, GGvis and XGvis. MDS is a visualization technique for proximity data, that …
software systems, GGvis and XGvis. MDS is a visualization technique for proximity data, that …
Determination of three-dimensional structures of proteins from interproton distance data by hybrid distance geometry-dynamical simulated annealing calculations
A new hybrid distance space-real space method for determining three-dimensional
structures of proteins on the basis of interproton distance restraints is presented. It involves …
structures of proteins on the basis of interproton distance restraints is presented. It involves …
Conformation of β-hairpins in protein structures: A systematic classification with applications to modelling by homology, electron density fitting and protein engineering
BL Sibanda, TL Blundell, JM Thornton - Journal of molecular biology, 1989 - Elsevier
A systematic classification of β-hairpin structures which takes into account the polypeptide
chain length and hydrogen bonding between the two antiparallel β-strands is described. We …
chain length and hydrogen bonding between the two antiparallel β-strands is described. We …
The theory and practice of distance geometry
TF Havel, ID Kuntz, GM Crippen - Bulletin of Mathematical Biology, 1983 - Elsevier
The mathematics of distance geometry constitutes the basis of a group of algorithms for
revealing the structural consequences of diverse forms of information about a …
revealing the structural consequences of diverse forms of information about a …
Structures of larger proteins in solution: three-and four-dimensional heteronuclear NMR spectroscopy
GM Clore, AM Gronenborn - Science, 1991 - science.org
Three-and four-dimensional heteronuclear nuclear magnetic resonance (NMR)
spectroscopy offers dramatic improvements in spectral resolution by spreading through …
spectroscopy offers dramatic improvements in spectral resolution by spreading through …