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Exact and efficient analytical calculation of the accessible surface areas and their gradients for macromolecules
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54/54 checkable references clean · checked 2026-07-23
Every reference with a DOI in the deposited reference list resolved to a known work in Crossref or DataCite at the dated check, and none carried a retraction, withdrawal, or removal notice.
5 without a DOI — not checked. A reference deposited without a DOI is never matched by title or guessed at; it stays outside the checked set, and this line discloses that.
The 54 checked references that resolve
resolves10.1016/0022-2836(71)90324-X
The interpretation of protein structures: Estimation of static accessibility
resolves10.1073/pnas.84.10.3086
Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides.
resolves10.1073/pnas.87.8.3240
Protein model structure evaluation using the solvation free energy of folding.
resolves10.1093/protein/7.2.221
A method for rapidly assessing and refining simple solvent treatments in molecular modelling. Example studies on the antigen-combining loop H2 from FAB fragment McPC603
resolves10.1002/pro.5560040714
A new computational model for protein folding based on atomic solvation
resolves10.1016/0263-7855(90)80059-O
Molecular volumes and surfaces of biomacromolecules via GEPOL: A fast and efficient algorithm
resolves10.1002/jcc.540140503
Minimization of empirical energy functions in proteins including hydrophobic surface area effects
resolves10.1002/jcc.540141103
Improved strategy in analytic surface calculation for molecular systems: Handling of singularities and computational efficiency
resolves10.1002/jcc.540150504
On the analytical calculation of van der Waals surfaces and volumes: Some numerical aspects
resolves10.1002/jcc.540160303
The double cubic lattice method: Efficient approaches to numerical integration of surface area and volume and to dot surface contouring of molecular assemblies
resolves10.1002/(SICI)1096-987X(19960115)17:1<57::AID-JCC6>3.0.CO;2-#
Analytical first derivatives of molecular surfaces with respect to nuclear coordinates
resolves10.1016/0898-5529(88)90015-2
A rapid approximation to the solvent accessible surface areas of atoms
resolves10.1021/ja00172a038
Semianalytical treatment of solvation for molecular mechanics and dynamics
resolves10.1002/jcc.540130102
MSEED: A program for the rapid analytical determination of accessible surface areas and their derivatives
resolves10.1002/jcc.540160810
A rapid method for calculating derivatives of solvent accessible surface areas of molecules
resolves10.1002/(SICI)1097-0282(199601)38:1<69::AID-BIP6>3.0.CO;2-U
New theoretical methodology for elucidating the solution structure of peptides from NMR data. II. free energy of dominant microstates of Leu-enkephalin and population-weighted average nuclear Overhauser effects intensities
resolves10.1111/j.1399-3011.1996.tb01351.x
Monte‐Carlo calculations of the solvent effects on the conformation of angiotensin II
resolves10.1002/prot.340140112
Empirical solvation models in the context of conformational energy searches: Application to bovine pancreatic trypsin inhibitor
resolves10.1007/s008940050001
Folding of Globular Proteins by Energy Minimization and Monte Carlo Simulations with Hydrophobic Surface Area Potentials
resolves10.1002/pro.5560010204
Atomic solvation parameters applied to molecular dynamics of proteins in solution
resolves10.1080/08927029308022162
Protein Structure Prediction with a Combined Solvation Free Energy-Molecular Mechanics Force Field
resolves10.1006/jmbi.1996.0139
An Efficient Mean Solvation Force Model for Use in Molecular Dynamics Simulations of Proteins in Aqueous Solution
resolves10.1002/pro.5560041014
Atomic solvation parameters in the analysis of protein‐protein docking results
resolves10.1002/bip.360290403
The program FANTOM for energy refinement of polypeptides and proteins using a Newton – Raphson minimizer in torsion angle space
resolves10.1016/0022-2836(85)90134-2
Calculation of protein conformations by proton-proton distance constraints
resolves10.1016/0010-4655(89)90125-2
Vectorized link cell Fortran code for molecular dynamics simulations for a large number of particles
resolves10.1073/pnas.78.7.4175
X-ray analysis (1. 4-Å resolution) of avian pancreatic polypeptide: Small globular protein hormone
resolves10.1016/S0022-2836(77)80200-3
The protein data bank: A computer-based archival file for macromolecular structures
resolves10.1016/0022-2836(91)90754-T
Efficient computation of three-dimensional protein structures in solution from nuclear magnetic resonance data using the program DIANA and the supporting programs CALIBA, HABAS and GLOMSA
resolves10.1016/0014-5793(94)00366-1
Pattern recognition and self‐correcting distance geometry calculations applied to myohemerythrin
resolves10.1073/pnas.84.19.6611
Monte Carlo-minimization approach to the multiple-minima problem in protein folding.
resolves10.1002/jcc.540120904
Efficient search for all low energy conformations of polypeptides by Monte Carlo methods
resolves10.1016/0022-2836(73)90011-9
Environment and exposure to solvent of protein atoms. Lysozyme and insulin
resolves10.1002/prot.340100305
Empirical solvation models can be used to differentiate native from near‐native conformations of bovine pancreatic trypsin inhibitor
resolves10.1021/bi00550a017
Conformation and association of pancreatic polypeptide from three species
resolves10.1002/bip.360220138
Conformational flexibility in a small globular hormone: X‐ray analysis of avian pancreatic polypeptide at 0.98‐Å resolution
resolves10.1021/j100589a006
Energy parameters in polypeptides. VII. Geometric parameters, partial atomic charges, nonbonded interactions, hydrogen bond interactions, and intrinsic torsional potentials for the naturally occurring amino acids
resolves10.1021/j100234a011
Energy parameters in polypeptides. 9. Updating of geometrical parameters, nonbonded interactions, and hydrogen bond interactions for the naturally occurring amino acids
resolves10.1006/jmbi.1996.0256
Energy Functions that Discriminate X-ray and Near-native Folds from Well-constructed Decoys
resolves10.1002/pro.5560021016
Prediction of protein conformation on the basis of a search for compact structures: Test on avian pancreatic polypeptide
resolves10.1016/0263-7855(96)00009-4
MOLMOL: A program for display and analysis of macromolecular structures
The 5 references without a DOI — listed, not checked
no DOI — not checkedIn Computer Simulation of Biomolecular Systems, Vol., 3, and Eds., ESCOM, Leiden, 1996.
no DOI — not checked10.1002/(SICI)1096-987X(199802)19:3<319::AID-JCC6>3.0.CO;2-W-BIB23.2
no DOI — not checkedDifferential Geometry of Curves and Surfaces, Prentice-Hall, Englewood Cliffs, NJ, 1976.
no DOI — not checkedInformation on how to obtain the new version of FANTOM can be found on the web page http://www. scsb.utmb.edu/fantom/fm_home.html or by e-mail request to werner@nmr.utmb.edu.
no DOI — not checkedComputational Geometry in C, Cambridge University Press, New York, 1993.
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