Contact and support
Need help, have a question, or want to contact the ResearchHub team?
© 2026 ResearchHub. Built for responsible scholarly connection.
Research graph
References from MEASURING THE SHAPES OF MACROMOLECULES – AND WHY IT MATTERS. Local targets link to admitted publications; unresolved targets remain external evidence.
The Protein Data Bank
10.1093/nar/28.1.235 · 2000 · External reference
Laguerre Voronoi Diagram on the Sphere
2002 · External reference
10.1021/jm1008743
10.1021/jm1008743 · External reference
Exact calculation of the volume and surface-area of fused hard-sphere molecules with unequal atomic radii
10.1080/00268978700102951 · 1987 · External reference
An analytical method for computing atomic contact areas in biomolecules
10.1002/jcc.23111 · 2012 · External reference
10.1002/pro.5560070905
10.1002/pro.5560070905 · External reference
The geometry of biomolecular solvation
2005 · External reference
Interpretation of protein structures: estimation of static accessibility
10.1016/0022-2836(71)90324-x · 1971 · External reference
Interpretation of protein structures: total volume, group volume distributions and packing density
10.1016/0022-2836(74)90570-1 · 1974 · External reference
Areas, volumes, packing, and protein-structure
10.1146/annurev.bb.06.060177.001055 · 1977 · External reference
10.1038/319199a0
10.1038/319199a0 · External reference
Assessing implicit models for nonpolar mean solvation forces: The importance of dispersion and volume terms
2006 · External reference
10.1088/0953-8984/20/03/033101
10.1088/0953-8984/20/03/033101 · External reference
10.1146/annurev-physchem-032210-103458
10.1146/annurev-physchem-032210-103458 · External reference
10.1016/j.cub.2010.11.062
10.1016/j.cub.2010.11.062 · External reference
10.1145/1273440.1250664
10.1145/1273440.1250664 · External reference
10.1002/jcc.20829
10.1002/jcc.20829 · External reference
Recent advances in the development and application of implicit solvent models in biomolecule simulations
10.1016/j.sbi.2004.03.009 · 2004 · External reference
Improving implicit solvent simulations: a Poisson-centric view
10.1016/j.sbi.2005.02.001 · 2005 · External reference
10.1007/s00249-005-0013-y
10.1007/s00249-005-0013-y · External reference
10.1016/j.sbi.2006.03.001
10.1016/j.sbi.2006.03.001 · External reference
10.1146/annurev.physchem.58.032806.104614
10.1146/annurev.physchem.58.032806.104614 · External reference
Application of the accelerated molecular dynamics simulations to the folding of a small protein
10.1063/1.2709639 · 2007 · External reference
10.1039/b714141f
10.1039/b714141f · External reference
Recent advances in implicit solvent-based methods for biomolecular simulations
10.1016/j.sbi.2008.01.003 · 2008 · External reference
Advances in implicit models of water solvent to compute conformational free energy and molecular dynamics of proteins at constant pH
10.1016/b978-0-12-386485-7.00008-9 · 2011 · External reference
10.1517/17460441.2013.749853
10.1517/17460441.2013.749853 · External reference
Molecular models of amino acids, peptides and proteins
10.1063/1.1770803 · 1953 · External reference
Precision space-filling atomic models
10.1002/bip.360030606 · 1965 · External reference
10.1145/1236246.1236288
10.1145/1236246.1236288 · External reference
A generalization of algebraic surface drawing
10.1145/357306.357310 · 1982 · External reference
10.1007/b98879
10.1007/b98879 · 2003 · External reference
10.1016/j.jmgm.2006.02.012
10.1016/j.jmgm.2006.02.012 · External reference
Adepth: new representation and its implications for atomic depths of macromolecules
10.1093/nar/gkt299 · 2013 · External reference
A Gaussian description of molecular shape
10.1021/j100011a016 · 1995 · External reference
New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations
10.1002/jcc.10272 · 2003 · External reference
10.1002/jcc.20796
10.1002/jcc.20796 · External reference
10.1145/267734.267787
10.1145/267734.267787 · External reference
10.1109/38.7748
10.1109/38.7748 · External reference
10.1002/bip.360330204
10.1002/bip.360330204 · External reference
10.1002/bip.360330205
10.1002/bip.360330205 · External reference
Unresolved reference
2001 · External reference
10.1002/prot.22030
10.1002/prot.22030 · External reference
Protein-protein docking using region-based 3D Zernike descriptors
10.1186/1471-2105-10-407 · 2009 · External reference
Molecular surface representation using 3D Zernike descriptors for protein shape comparison and docking
10.2174/138920311796957612 · 2011 · External reference
10.1016/0022-2836(73)90011-9
10.1016/0022-2836(73)90011-9 · External reference
Rapid approximation to molecular-surface area via the use of Boolean logic and look-up tables
10.1002/jcc.540140309 · 1993 · External reference
A vectorized algorithm for calculating the accessible surface area of macromolecules
10.1002/jcc.540120712 · 1991 · External reference
Efficient parallel algorithms for solvent accessible surface area of proteins
10.1109/tpds.2002.1011399 · 2004 · External reference
The triplet distribution function in a fluid of hard spheres
10.1080/00268976300100581 · 1963 · External reference
A method to compute the volume of a molecule
10.1016/0097-8485(82)80006-5 · 1982 · External reference
The calculation of molecular volumes and the use of volume analysis in the investigation of structured media and of solid-state organic reactivity
10.1021/ja00354a007 · 1983 · External reference
10.1007/s00894-009-0541-y
10.1007/s00894-009-0541-y · External reference
10.1145/220279.220324
10.1145/220279.220324 · External reference
Analytical approximation to the accessible surface-area of proteins
10.1073/pnas.77.4.1736 · 1980 · External reference
10.1016/0898-5529(88)90015-2
10.1016/0898-5529(88)90015-2 · External reference
POPS: a fast algorithm for solvent accessible surface areas at atomic and residue level
10.1093/nar/gkg601 · 2003 · External reference
10.1016/s1359-0278(98)00036-4
10.1016/s1359-0278(98)00036-4 · External reference
Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO)
10.1002/(sici)1096-987x(19990130)20:2<217::aid-jcc4>3.0.co;2-a · 1999 · External reference
CUSA and CUDE: GPU-accelerated methods for estimating solvent accessible surface area and desolvation
10.1089/cmb.2008.0157 · 2009 · External reference
Solvent accessible surface-area and excluded volume in proteins. Analytical equations for overlapping spheres and implications for the hydrophobic effect
10.1016/0022-2836(84)90231-6 · 1984 · External reference
Computation of molecular volume
10.1021/ja00291a006 · 1985 · External reference
Analytical treatment of the volume and surface area of molecules formed by an arbitrary collection of unequal spheres intersected by planes
10.1080/00268979100100941 · 1991 · External reference
On the analytical calculation of van-der-Waals surfaces and volumes: some numerical aspects
10.1002/jcc.540150504 · 1994 · External reference
An elegant algorithm of the analytical calculation for the volume of fused spheres with different radii
10.1016/0010-4655(96)00082-3 · 1996 · External reference
Area of intersection of n equal circular disks
10.1088/0305-4470/11/6/006 · 1978 · External reference
The union of balls and its dual shape
10.1007/bf02574053 · 1995 · External reference
Algorithms for calculating excluded volume and its derivatives as a function of molecular-conformation and their use in energy minimization
10.1002/jcc.540120314 · 1991 · External reference
Implementation of solvent effect in molecular mechanics. Part 3. The first and second-order analytical derivatives of excluded volume
10.1016/s0166-1280(09)80068-7 · 1994 · External reference
An improved algorithm for the analytical computation of solvent-excluded volume. The treatment of singularities in solvent-accessible surface-area and volume functions
10.1002/jcc.540160703 · 1995 · External reference
Analytical first derivatives of molecular surfaces with respect to nuclear coordinates
10.1002/(sici)1096-987x(19960115)17:1<57::aid-jcc6>3.0.co;2-# · 1996 · External reference
The weighted-volume derivative of a space-filling diagram
10.1073/pnas.0537830100 · 2003 · External reference
10.1007/s00454-004-1099-1
10.1007/s00454-004-1099-1 · External reference
10.1002/jcc.540130102
10.1002/jcc.540130102 · External reference
A rapid method for calculating derivatives of solvent accessible surface areas of molecules
10.1002/jcc.540160810 · 1994 · External reference
10.1016/0263-7855(92)80074-n
10.1016/0263-7855(92)80074-n · External reference
10.1016/s1093-3263(98)00002-3
10.1016/s1093-3263(98)00002-3 · External reference
LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites
10.1016/s1093-3263(02)00164-x · 2003 · External reference
PocketPicker: analysis of ligand binding-sites with shape descriptors
10.1186/1752-153x-1-7 · 2007 · External reference
SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions
10.1016/0263-7855(95)00073-9 · 1995 · External reference
10.1023/a:1008124202956
10.1023/a:1008124202956 · External reference
10.1002/prot.21283
10.1002/prot.21283 · External reference
Roll: A new algorithm for the detection of protein pockets and cavities with a rolling probe sphere
10.1093/bioinformatics/btp599 · 2010 · External reference
10.1002/(sici)1097-0134(19981001)33:1<18::aid-prot2>3.0.co;2-h
10.1002/(sici)1097-0134(19981001)33:1<18::aid-prot2>3.0.co;2-h · External reference
10.1016/s0166-218x(98)00067-5
10.1016/s0166-218x(98)00067-5 · External reference
MolAxis: a server for identification of channels in macromolecules
10.1093/nar/gkn223 · 2008 · External reference
10.1002/jcc.21060
10.1002/jcc.21060 · External reference
The Volume of atoms on the protein surface: calculated from simulation, using Voronoi Polyhedra
10.1006/jmbi.1995.0351 · 1995 · External reference
Quantification of protein surfaces, volumes, and atom-atom contacts using a constrained Voronoi procedure
2002 · External reference
Discrimination of native protein structures using atom-atom contact scoring
10.1073/pnas.0535768100 · 2003 · External reference
A novel evaluation of residue and protein volumes by means of Laguerre tessellation
10.1021/ci9004892 · 2010 · External reference
10.1021/ci100195t
10.1021/ci100195t · External reference
Interaction interfaces in proteins via the Voronoi diagram of atoms
10.1016/j.cad.2006.07.007 · 2006 · External reference
Voroprot: an interactive tool for the analysis and visualization of complex geometric features of protein structure
10.1093/bioinformatics/btq720 · 2011 · External reference
10.1002/(sici)1097-0134(19981001)33:1<1::aid-prot1>3.0.co;2-o
10.1002/(sici)1097-0134(19981001)33:1<1::aid-prot1>3.0.co;2-o · External reference
10.1002/jcc.21884
10.1002/jcc.21884 · External reference
Inclusion-exclusion-Bonferroni identities and inequalities for discrete tube-like problems via Euler characteristics
1992 · External reference
Surface area of the intersection of three spheres with unequal radii. A simplified formula
10.1080/00268978800100453 · 1988 · External reference
Unresolved reference
1994 · External reference
10.1016/s0969-2126(00)00065-4
10.1016/s0969-2126(00)00065-4 · External reference
10.1093/nar/gkl282
10.1093/nar/gkl282 · External reference
10.1002/prot.340200307
10.1002/prot.340200307 · External reference
10.1016/j.bcp.2005.12.026
10.1016/j.bcp.2005.12.026 · External reference
10.1038/356083a0
10.1038/356083a0 · External reference
Atomic environment energies in proteins defined from statistics of accessible and contact surface areas
10.1006/jmbi.1995.0328 · 1995 · External reference
Unresolved reference
External reference
10.1145/174462.156635
10.1145/174462.156635 · External reference
Computing the volume of union of balls: a certified algorithm
10.1145/2049662.2049665 · 2011 · External reference
A brighter future for protein structure prediction
10.1038/5794 · 1999 · External reference
10.1126/science.1219021
10.1126/science.1219021 · External reference
10.1089/cmb.1996.3.213
10.1089/cmb.1996.3.213 · External reference
10.1007/978-3-642-21551-3_36
10.1007/978-3-642-21551-3_36 · 2012 · External reference
10.1016/j.cagd.2006.03.002
10.1016/j.cagd.2006.03.002 · External reference
Alpha shapes applied to molecular shape characterization exhibit novel properties compared to established shape descriptors
10.1021/ci900190z · 2009 · External reference
Defining and characterizing protein surface using alpha shapes
10.1002/prot.22301 · 2009 · External reference
SplitPocket: identification of protein functional surfaces and characterization of their spatial patterns
10.1093/nar/gkp308 · 2009 · External reference
10.1073/pnas.1119684109
10.1073/pnas.1119684109 · External reference
Structural alignment of proteins by a novel TOPOFIT method, as a superimposition of common volumes at a topomax point
10.1110/ps.04672604 · 2004 · External reference
10.1002/prot.20479
10.1002/prot.20479 · External reference
Fpocket: an open source platform for ligand pocket detection
10.1186/1471-2105-10-168 · 2009 · External reference
Analysis of surface structures of hydrogen bonding in protein-ligand interaction using alpha shape model
10.1016/j.cplett.2012.07.016 · 2012 · External reference
10.1145/1147954.1147957
10.1145/1147954.1147957 · External reference
A discriminatory function for prediction of protein-DNA interactions based on the alpha shape modeling
10.1093/bioinformatics/btq478 · 2010 · External reference
Alpha shape and Delaunay triangulation in studies of protein related interactions
2013 · External reference
10.1371/journal.pone.0040540
10.1371/journal.pone.0040540 · External reference
Molecular dynamics simulations of biomolecules
10.1038/nsb0902-646 · 2002 · External reference
Topological persistence and simplification
10.1007/s00454-002-2885-2 · 2002 · External reference
Persistent voids: a new structural metric for membrane fusion
10.1093/bioinformatics/btm250 · 2007 · External reference
10.1109/biovis.2012.6378599
10.1109/biovis.2012.6378599 · External reference