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Exploring protein functions from structural flexibility using CABS‐flex modeling.
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- Protein Science: A Publication of the Protein Society, 2024, v. 33, n. 9, p. 1, doi. 10.1002/pro.5090
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- Article
HCPM—program for hierarchical clustering of protein models.
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- Bioinformatics, 2005, v. 21, n. 14, p. 3179, doi. 10.1093/bioinformatics/bti450
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- Article
Modeling of loops in proteins: a multi-method approach.
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- BMC Structural Biology, 2010, v. 10, p. 5, doi. 10.1186/1472-6807-10-5
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- Article
Contact prediction in protein modeling: Scoring, folding and refinement of coarse-grained models.
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- BMC Structural Biology, 2008, v. 8, p. 1, doi. 10.1186/1472-6807-8-36
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- Article
Integrative modeling of diverse protein-peptide systems using CABS-dock.
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- PLoS Computational Biology, 2023, v. 19, n. 7, p. 1, doi. 10.1371/journal.pcbi.1011275
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- Article
Role of Resultant Dipole Moment in Mechanical Dissociation of Biological Complexes.
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- Molecules, 2018, v. 23, n. 8, p. 1995, doi. 10.3390/molecules23081995
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- Article
Coarse-Grained Modeling of Peptide Docking Associated with Large Conformation Transitions of the Binding Protein: Troponin I Fragment–Troponin C System.
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- Molecules, 2015, v. 20, n. 6, p. 10763, doi. 10.3390/molecules200610763
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- Article
Hierarchical modeling of protein interactions.
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- Journal of Molecular Modeling, 2007, v. 13, n. 6/7, p. 691, doi. 10.1007/s00894-007-0177-8
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- Article
Protein–Protein Docking with Large-Scale Backbone Flexibility Using Coarse-Grained Monte-Carlo Simulations.
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- International Journal of Molecular Sciences, 2021, v. 22, n. 14, p. 7341, doi. 10.3390/ijms22147341
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- Article
Modeling of Disordered Protein Structures Using Monte Carlo Simulations and Knowledge-Based Statistical Force Fields.
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- International Journal of Molecular Sciences, 2019, v. 20, n. 3, p. 606, doi. 10.3390/ijms20030606
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- Article
Modeling of Protein Structural Flexibility and Large-Scale Dynamics: Coarse-Grained Simulations and Elastic Network Models.
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- International Journal of Molecular Sciences, 2018, v. 19, n. 11, p. 3496, doi. 10.3390/ijms19113496
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- Article
Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics.
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- International Journal of Molecular Sciences, 2013, v. 14, n. 5, p. 9893, doi. 10.3390/ijms14059893
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- Article
BioShell-Threading: versatile Monte Carlo package for protein 3D threading.
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- BMC Bioinformatics, 2014, v. 15, n. 1, p. 2, doi. 10.1186/1471-2105-15-22
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- Article
ClusCo: clustering and comparison of protein models.
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- BMC Bioinformatics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2105-14-62
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- Article
Protein Folding with a Reduced Model and Inaccurate Short-Range Restraints.
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- Macromolecular Theory & Simulations, 2005, v. 14, n. 7, p. 444, doi. 10.1002/mats.200500020
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- Article
Helix-coil and beta sheet-coil transitions in a simplified, yet realistic protein model.
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- Macromolecular Theory & Simulations, 2000, v. 9, n. 8, p. 523, doi. 10.1002/1521-3919(20001101)9:8<523::AID-MATS523>3.0.CO;2-I
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- Article
Dynamics of star branched polymers in a matrix of linear chains - a Monte Carlo study.
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- Macromolecular Theory & Simulations, 1994, v. 3, n. 4, p. 715, doi. 10.1002/mats.1994.040030407
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- Article
Fast and accurate methods for predicting short-range constraints in protein models.
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- Journal of Computer-Aided Molecular Design, 2008, v. 22, n. 11, p. 783, doi. 10.1007/s10822-008-9213-8
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- Article
Protein structure prediction by tempering spatial constraints.
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- Journal of Computer-Aided Molecular Design, 2005, v. 19, n. 8, p. 603, doi. 10.1007/s10822-005-9016-0
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- Article
Use of residual dipolar couplings as restraints in ab initio protein structure prediction.
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- Biopolymers, 2003, v. 70, n. 4, p. 548, doi. 10.1002/bip.10511
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- Article
A simple lattice model that exhibits a protein-like cooperative all-or-none folding transition.
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- Biopolymers, 2003, v. 69, n. 3, p. 399, doi. 10.1002/bip.10385
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- Article
Collapse transitions in protein-like lattice polymers: The effect of sequence patterns.
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- Biopolymers, 1997, v. 42, n. 5, p. 537, doi. 10.1002/(SICI)1097-0282(19971015)42:5<537::AID-BIP4>3.0.CO;2-R
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- Article
PHENOMENOLOGICAL THEORY OF POLYMER MELT DYNAMICS.
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- International Journal of Modern Physics B: Condensed Matter Physics; Statistical Physics; Applied Physics, 1989, v. 3, n. 1, p. 33, doi. 10.1142/S0217979289000038
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- Article
Flexible docking of peptides to proteins using CABS‐dock.
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- Protein Science: A Publication of the Protein Society, 2020, v. 29, n. 1, p. 211, doi. 10.1002/pro.3771
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- Article
Protein secondary structure prediction using a small training set (compact model) combined with a Complex-valued neural network approach.
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- BMC Bioinformatics, 2016, v. 17, p. 1, doi. 10.1186/s12859-016-1209-0
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- Article
Protein–peptide docking using CABS-dock and contact information.
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- Briefings in Bioinformatics, 2019, v. 20, n. 6, p. 2299, doi. 10.1093/bib/bby080
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- Article
Three-dimensional modeling of the I-TevI homing endonuclease catalytic domain, a GIY–YIG superfamily member, using NMR restraints and Monte Carlo dynamics.
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- Protein Engineering, 2001, v. 14, n. 10, p. 717, doi. 10.1093/protein/14.10.717
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- Article
Does a backwardly read protein sequence have a unique native state?
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- Protein Engineering, 1996, v. 9, n. 1, p. 5, doi. 10.1093/protein/9.1.5
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- Article
Structural genomics and its importance for gene function analysis.
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- Nature Biotechnology, 2000, v. 18, n. 3, p. 283, doi. 10.1038/73723
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- Article
CABS-dock standalone: a toolbox for flexible protein–peptide docking.
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- Bioinformatics, 2019, v. 35, n. 20, p. 4170, doi. 10.1093/bioinformatics/btz185
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- Article
CABS-flex standalone: a simulation environment for fast modeling of protein flexibility.
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- Bioinformatics, 2019, v. 35, n. 4, p. 694, doi. 10.1093/bioinformatics/bty685
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- Article
Optimization of protein models.
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- WIREs: Computational Molecular Science, 2012, v. 2, n. 3, p. 479, doi. 10.1002/wcms.1090
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- Publication type:
- Article
Protein-peptide molecular docking with large-scale conformational changes: the p53-MDM2 interaction.
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- Scientific Reports, 2016, p. 37532, doi. 10.1038/srep37532
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- Publication type:
- Article
CABS-NMR-De novo tool for rapid global fold determination from chemical shifts, residual dipolar couplings and sparse methyl-methyl noes.
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- Journal of Computational Chemistry, 2011, v. 32, n. 3, p. 536, doi. 10.1002/jcc.21640
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- Article
Protein structure prediction: Combining de novo modeling with sparse experimental data.
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- Journal of Computational Chemistry, 2007, v. 28, n. 10, p. 1668, doi. 10.1002/jcc.20657
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- Article
Backbone building from quadrilaterals: A fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinates.
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- Journal of Computational Chemistry, 2007, v. 28, n. 9, p. 1593, doi. 10.1002/jcc.20624
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- Article
Assessing energy functions for flexible docking.
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- Journal of Computational Chemistry, 1998, v. 19, n. 14, p. 1612, doi. 10.1002/(SICI)1096-987X(19981115)19:14<1612::AID-JCC7>3.0.CO;2-M
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- Publication type:
- Article
Algorithm for rapid reconstruction of protein backbone from alpha carbon coordinates.
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- Journal of Computational Chemistry, 1997, v. 18, n. 1, p. 80, doi. 10.1002/(SICI)1096-987X(19970115)18:1<80::AID-JCC8>3.0.CO;2-W
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- Article
Lattice representations of globular proteins: How good are they?
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- Journal of Computational Chemistry, 1993, v. 14, n. 10, p. 1194, doi. 10.1002/jcc.540141009
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- Publication type:
- Article
Multibody coarse-grained potentials for native structure recognition and quality assessment of protein models.
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- Proteins, 2014, v. 82, n. 7, p. 1549, doi. 10.1002/prot.24578
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- Article
Structural features that predict real-value fluctuations of globular proteins.
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- Proteins, 2012, v. 80, n. 5, p. 1425, doi. 10.1002/prot.24040
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- Article
How noise in force fields can affect the structural refinement of protein models?
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- Proteins, 2012, v. 80, n. 2, p. 335, doi. 10.1002/prot.23240
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- Publication type:
- Article
Multibody coarse-grained potentials for native structure recognition and quality assessment of protein models.
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- Proteins, 2011, v. 79, n. 6, p. 1923, doi. 10.1002/prot.23015
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- Article
Ideal amino acid exchange forms for approximating substitution matrices.
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- Proteins, 2007, v. 69, n. 2, p. 379, doi. 10.1002/prot.21509
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- Article
Generalized protein structure prediction based on combination of fold-recognition with de novo folding and evaluation of models.
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- Proteins, 2005, v. 61, n. S7, p. 84, doi. 10.1002/prot.20723
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- Article
Inferring ideal amino acid interaction forms from statistical protein contact potentials.
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- Proteins, 2005, v. 59, n. 1, p. 49, doi. 10.1002/prot.20380
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- Article
TOUCHSTONEX: Protein structure prediction with sparse NMR data.
- Published in:
- Proteins, 2003, v. 53, n. 2, p. 290, doi. 10.1002/prot.10499
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- Article
TOUCHSTONE: A unified approach to protein structure prediction.
- Published in:
- Proteins, 2003, v. 53, n. S6, p. 469, doi. 10.1002/prot.10551
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- Publication type:
- Article
CABS-flex 2.0: a web server for fast simulations of flexibility of protein structures.
- Published in:
- Nucleic Acids Research, 2018, v. 46, n. W1, p. W338, doi. 10.1093/nar/gky356
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- Publication type:
- Article
CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site.
- Published in:
- Nucleic Acids Research, 2015, v. 43, n. W1, p. W419, doi. 10.1093/nar/gkv456
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- Article