DOI: 10.1016/s0959-440x(97)80029-2. Empirical potentials and functions for protein folding and binding

Empirical potentials and functions for protein folding and binding

10.1016/s0959-440x(97)80029-2

Crossref journal-article

Elsevier BV

Current Opinion in Structural Biology (78)

Bibliography

Vajda, S., Sippl, M., & Novotny, J. (1997). Empirical potentials and functions for protein folding and binding. Current Opinion in Structural Biology, 7(2), 222â228.

Authors 3

Sandor Vajda (first)
Manfred Sippl (additional)
Jiri Novotny (additional)

References 71 Referenced 113

10.1002/prot.340040105 / Proteins / Criteria that discriminate between native proteins and incorrectly folded models by Novotny (1988)
10.1016/0022-2836(91)80222-G / J Mol Biol / Protein docking and complementarity by Shoichet (1991)
10.1006/jmbi.1995.0600 / J Mol Biol / Decomposition of interaction free energies in proteins and other complex systems by Brady (1995)
10.1021/bi00437a034 / Biochemistry / On the attribution of binding energy in the antigen—antibody complexes McPC 603, D1.3 and HyHEL-5 by Novotny (1989)
10.1021/bi00251a004 / Biochemistry / Effect of conformational flexibility and solvation on receptor-ligand binding free energies by Vajda (1994)
10.1126/science.7761829 / Science / Classical electrostatics in biology and chemistry by Honig (1995)
10.1002/pro.5560040401 / Protein Sci / Principles of protein folding — a perspective from simple exact models by Dill (1995)
10.1006/jmbi.1994.1110 / J Mol Biol / Kinetics of protein folding: a lattice model study of the requirements for folding to the native state by Sali (1994)
10.1006/jmbi.1996.0114 / J Mol Biol / Residue—residue potentials with a favorable contact pair term and unfavorable high packing density term, for simulation and threading by Miyazava (1996)
10.1002/(SICI)1097-0134(199603)24:3<335::AID-PROT6>3.0.CO;2-F / Proteins / Comparing folding codes for proteins and polymers by Chan (1996)
10.1006/jmbi.1996.0375 / J Mol Biol / Local interactions dominate folding in a simple protein model by Unger (1996)
10.1006/jmbi.1995.0511 / J Mol Biol / Impact of local and non-local interactions on thermodynamics and kinetics of protein folding by Abkevics (1995)
10.1002/jcc.540141009 / J Comp Chem / Lattice representations of globular proteins: how good are they? by Godzik (1993)
10.1002/(SICI)1096-987X(199606)17:8<1025::AID-JCC11>3.0.CO;2-D / J Comp Chem / Lattice modeling: accuracy of energy calculations by Reva (1996)
10.1016/S1359-0278(96)00005-3 / Fold Des / Adding backbone to protein folding: why proteins are polypeptides? by Honig (1996)
10.1038/253694a0 / Nature / Computer simulations of protein folding by Levitt (1975)
10.1073/pnas.75.2.554 / Proc Natl Acad Sci USA / On the formation of protein tertiary structure by Hagler (1978)
10.1016/0022-2836(76)90347-8 / J Mol Biol / Calculation of protein tertiary structure by Kuntz (1976)
10.1073/pnas.91.10.4436 / Proc Natl Acad Sci USA / An evolutionary approach to folding small alpha-helical proteins that uses sequence information and an empirical guiding fitness function by Bowie (1994)
10.1073/pnas.91.11.5027 / Proc Natl Acad Sci USA / An algorithm to generate low-resolution tertiary structures from knowledge of secondary structure by Monge (1994)
10.1016/0263-7855(95)00052-6 / J Mol Graph / Simulating the folding of small proteins by use of the local minimum energy and the free solvation energy yields native-like structures by Brasseur (1995)
10.1002/prot.340060208 / Proteins / A computer model to dynamically simulate protein folding: studies with crambin by Wilson (1989)
10.1002/pro.5560050607 / Protein Sci / Self-consistently optimized statistical mechanical energy functions for sequence structure alignment by Koretke (1996)
10.1016/0141-8130(95)01036-X / Int J Biol Macromol / Ab initio tertiary-fold prediction of helical and non-helical protein chains using a genetic algorithm by Dandekar (1996)
10.1002/prot.340180405 / Proteins / Monte-Carlo simulations of protein folding. 1. Lattice model and interaction scheme by Kolinski (1994)
10.1002/prot.340180406 / Proteins / Monte-Carlo simulations of protein folding. 2. Application to protein-A, ROP, and crambin by Kolinski (1994)
10.1002/prot.340220202 / Protein Sci / LINUS: a hierarchical procedure to predict the fold of a protein by Srinivasan (1995)
10.1093/protein/8.8.769 / Protein Eng / A simple protein folding algorithm using binary code and secondary structure constraints by Sun (1995)
10.1002/pro.5560050209 / Protein Sci / Folding proteins with a simple energy function and extensive conformational searching by Yue (1996)
10.1096/fasebj.10.1.8566532 / FASEB J / Protein folding by a biased Monte Carlo procedure in the dihedral angle space by Lee (1996)
10.1016/S0006-3495(95)80259-6 / Biophys J / Folding simulations of alanine-based peptides with lysin residues by Sung (1995)
10.1073/pnas.87.8.3240 / Proc Natl Acad Sci USA / Protein model structure evaluation using the solvation free energy of folding by Chiche (1990)
10.1002/prot.340230314 / Proteins / Homology modeling by the ICM method by Cardozo (1995)
10.1016/S0006-3495(95)79906-4 / Biophys J / A genetic algorithm that seeks native states of peptides and proteins by Sun (1995)
10.1006/jmbi.1996.0139 / J Mol Biol / An efficient mean solvation force model for use in molecular dynamics simulations of proteins in aqueous solution by Fraternali (1996)
Second meeting on the critical assessment of techniques for protein prediction on World Wide Web URL: http://iris4.carb.nist.gov/casp2
10.1006/jmbi.1996.0226 / J Mol Biol / Stability changes upon mutation of solvent-accessible residues in proteins evaluated by database-derived potentials by Gilis (1996)
10.1016/S1359-0278(96)00042-9 / Fold Des / Helmholtz free energy of atom pair interactions in proteins by Sippl (1996)
10.1016/S0022-2836(05)80269-4 / J Mol Biol / Calculation of conformational ensembles from potentials of the main force by Sippl (1990)
10.1006/jmbi.1996.0427 / J Mol Biol / Helmholtz free energy of peptide hydrogen bonds in proteins by Sippl (1996)
10.1016/S0959-440X(96)80075-3 / Curr Opin Struct Biol / Structure-derived potentials and protein simulations by Jernigan (1996)
10.1006/jmbi.1996.0175 / J Mol Biol / Statistical potentials extracted from protein structures: how accurate are they? by Thomas (1996)
10.1073/pnas.93.21.11628 / Proc Natl Acad Sci USA / An iterative method for extracting energy-like quantities from protein structures by Thomas (1996)
10.1006/jmbi.1996.0859 / J Mol Biol / Determination of atomic desolvation energies from the structures of crystallised proteins by Zhang (1997)
10.1093/protein/9.8.637 / Protein Eng / Evaluation of atomic level mean force potentials via inverse refinement of protein structures: atomic burial position and pairwise non-bonded interactions by DeBolt (1996)
10.1002/(SICI)1099-1352(199603)9:2<175::AID-JMR260>3.0.CO;2-D / J Mol Recog / Molecular docking toward drug design by Gschwend (1996)
10.1006/jmbi.1995.0493 / J Mol Biol / Molecular surface complementarity at protein-protein interfaces — the critical role played by surface normals at well placed, sparse points in docking by Norel (1995)
10.1002/(SICI)1097-0282(199609)39:3<455::AID-BIP16>3.0.CO;2-A / Biopolymers / Low-resolution docking: prediction of complexes for undetermined structures by Vakser (1996)
10.1002/pro.5560050406 / Protein Sci / Prediction of complexes using empirical free energy functions by Weng (1996)
10.1021/jm00026a001 / J Med Chem / Computational methods to predict binding free energy in ligand—receptor complexes by Ajay (1995)
10.1002/pro.5560010117 / Protein Sci / Calculation of the free energy of association for protein complexes by Horton (1992)
10.1002/pro.5560040711 / Protein Sci / Solvent accessibility as a predictive tool for the free energy of inhibitor binding to the HIV-1 protease by Nauchitel (1995)
10.1021/jm940778t / J Med Chem / An approach to rapid estimation of relative binding affinities of enzyme inhibitors: application to peptidomimetic inhibitors of the human immunodeficiency virus type 1 protease by Viswanadhan (1996)
10.1002/pro.5560040923 / Protein Sci / A preference-based free energy parameterization of enzyme-inhibitor binding. Applications to HIV-1 protease inhibitor design by Wallqvist (1995)
10.1002/(SICI)1097-0134(199608)25:4<403::AID-PROT1>3.0.CO;2-E / Proteins / Docking enzyme—inhibitor complexes using a preference-based free energy surface by Wallquist (1996)
10.1021/ja960751u / J Am Chem Soc / SMoG: De novo design method based on simple, fast, an accurate free energy estimates. 1. Methodology and supporting evidence by DeWitte (1996)
10.1007/BF00126743 / J Comp Aid Mol Des / The development of a simple empirical scoring function to estimate the binding constant for a protein ligand complex of known three-dimensional structure by Bohm (1994)
10.1006/jmbi.1996.0311 / J Mol Biol / X-SITE — use of empirically derived atomic packing preferences to identify favourable interaction regions in the binding sites of proteins by Laskowski (1996)
10.1093/protein/8.7.677 / Protein Eng / Empirical free energy calculations of ligand—protein crystallographic complexes. 1. Knowledge-based ligand—protein interaction potentials applied to the prediction of human immunodeficiency virus 1 protease binding affinity by Verkhivker (1995)
10.1021/jm00002a012 / J Med Chem / A priori predictions of activity for HIV-1 protease inhibitors employing energy minimization in the active site by Holloway (1995)
10.1021/ja9539002 / J Am Chem Soc / VALIDATE: a new method for receptor-based prediction of binding affinities of novel ligands by Head (1996)
10.1002/pro.5560050219 / Protein Sci / Computational method for relative binding energies of enzyme substrate complexes by Zhang (1996)
10.1006/jmbi.1995.0375 / J Mol Biol / A continuum model for protein—protein interactions: application to the docking problem by Jackson (1995)
10.1002/pro.5560041014 / Protein Sci / Atomic solvation parameters in the analysis of protein—protein docking results by Cummings (1995)
10.1002/pro.5560041206 / Protein Sci / Comparison of atomic solvation parametric sets: applicability and limitations in protein folding and binding by Juffer (1995)
10.1093/protein/8.11.1081 / Protein Eng / Extracting hydrophobicity parameters from solute partition and protein mutation/unfolding experiments by Vajda (1995)
10.1002/(SICI)1096-987X(19970130)18:2<268::AID-JCC11>3.0.CO;2-E / J Comp Chem / Finite difference Poisson—Boltzmann electrostatic calculations: increased accuracy achieved by harmonic dielectric smoothing and charge antialiasing by Bruccoleri (1997)
10.1006/jmbi.1997.0961 / J Mol Biol / Empirical free energy calculations: a blind test and further improvements to the method by Novotny (1997)
10.1126/science.7754388 / Science / Models of protein folding by Smith (1995)
10.1002/bip.360260114 / Biopolymers / Prediction of folding of short polypeptide segments by uniform conformational sampling by Bruccoleri (1987)
10.1080/08927029308022163 / Mol Simulat / Application of systematic conformational search to protein modeling by Bruccoleri (1993)

Dates

Type	When
Created	23 years, 1 month ago (July 25, 2002, 6:37 a.m.)
Deposited	1 year, 10 months ago (Oct. 30, 2023, 6:47 p.m.)
Indexed	4 weeks ago (Aug. 2, 2025, 1:09 a.m.)
Issued	28 years, 4 months ago (April 1, 1997)
Published	28 years, 4 months ago (April 1, 1997)
Published Print	28 years, 4 months ago (April 1, 1997)

Funders 0

None

BibTeX

@article{Vajda_1997, title={Empirical potentials and functions for protein folding and binding}, volume={7}, ISSN={0959-440X}, url={http://dx.doi.org/10.1016/s0959-440x(97)80029-2}, DOI={10.1016/s0959-440x(97)80029-2}, number={2}, journal={Current Opinion in Structural Biology}, publisher={Elsevier BV}, author={Vajda, Sandor and Sippl, Manfred and Novotny, Jiri}, year={1997}, month=apr, pages={222–228} }

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      "author": "Ajay",
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      "author": "Horton",
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      "author": "Viswanadhan",
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      "author": "Bohm",
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