Articles

Search Articles

Advanced search
Help

Catalogue

Articles

Databases

X
Search Filters
Format Format
Format Format
X
Sort by Item Count (A-Z)
Filter by Count
Journal Article (619) 619
Publication (124) 124
Conference Proceeding (36) 36
Patent (27) 27
Book / eBook (23) 23
Magazine Article (16) 16
Newspaper Article (13) 13
Book Chapter (12) 12
Dissertation (7) 7
Web Resource (3) 3
Book Review (1) 1
Data Set (1) 1
Government Document (1) 1
Journal / eJournal (1) 1
Reference (1) 1
Streaming Video (1) 1
Trade Publication Article (1) 1
more...
Subjects Subjects
Subjects Subjects
X
Sort by Item Count (A-Z)
Filter by Count
index medicus (193) 193
protein folding (129) 129
computer simulation (120) 120
models, molecular (116) 116
proteins (104) 104
kinetics (101) 101
biophysics (91) 91
physics, atomic, molecular & chemical (79) 79
analysis (74) 74
article (74) 74
chemistry, physical (73) 73
molecular dynamics (73) 73
molecular dynamics simulation (72) 72
algorithms (71) 71
thermodynamics (70) 70
markov chains (69) 69
proteins - chemistry (65) 65
protein conformation (62) 62
humans (58) 58
simulation (54) 54
research (53) 53
chemistry, multidisciplinary (49) 49
simulations (46) 46
molecular-dynamics simulations (45) 45
multidisciplinary sciences (45) 45
biochemistry & molecular biology (44) 44
models, chemical (43) 43
physics (38) 38
mutation (37) 37
dynamics (36) 36
models (36) 36
model (35) 35
molecular-dynamics (35) 35
biochemistry (32) 32
protein (32) 32
usage (32) 32
biomolecules (31) 31
chemistry (31) 31
protein structure, secondary (31) 31
water (31) 31
quantitative biology (30) 30
computational biology (29) 29
animals (28) 28
transition (28) 28
software (27) 27
biological sciences (26) 26
pathways (26) 26
protein binding (26) 26
research article (26) 26
water - chemistry (26) 26
mechanism (25) 25
force-field (24) 24
peptides (24) 24
time factors (24) 24
mathematical models (23) 23
distributed computing (22) 22
ligands (22) 22
biology (21) 21
entropy (21) 21
temperature (21) 21
amino acid sequence (20) 20
molecular conformation (20) 20
beta-hairpin (19) 19
biochemical research methods (19) 19
molecules (19) 19
binding sites (18) 18
electricity (18) 18
protein-folding kinetics (18) 18
solvents - chemistry (18) 18
binding (17) 17
female (17) 17
peptides - chemistry (17) 17
protein structure, tertiary (17) 17
chemical properties (16) 16
male (16) 16
quantitative biology - biomolecules (16) 16
design (15) 15
medicine (15) 15
models, statistical (15) 15
nucleic acid conformation (15) 15
probability (15) 15
rna (15) 15
testing (15) 15
trajectories (15) 15
computer science, interdisciplinary applications (14) 14
crystallography, x-ray (14) 14
markov processes (14) 14
models, theoretical (14) 14
molecular biology (14) 14
molecular sequence data (14) 14
organic chemistry (14) 14
peptide (14) 14
science (14) 14
solvents (14) 14
systems (14) 14
activation (13) 13
cell biology (13) 13
free energy (13) 13
genetic aspects (13) 13
hydrogen bonding (13) 13
more...
Library Location Library Location
Library Location Library Location
X
Sort by Item Count (A-Z)
Filter by Count
Robarts - Stacks (12) 12
Online Resources - Online (3) 3
UTL at Downsview - May be requested (3) 3
Earth Sciences (Noranda) - Stacks (2) 2
UofT at Mississauga - Stacks (2) 2
Gerstein Science - Stacks (1) 1
Mathematical Sciences - Stacks (1) 1
Music - Stacks (1) 1
Robarts - May be requested in 6-10 wks (1) 1
Royal Ontario Museum - Far Eastern (1) 1
more...
Language Language
Language Language
X
Sort by Item Count (A-Z)
Filter by Count
English (741) 741
French (14) 14
German (7) 7
Sanskrit (3) 3
Chinese (1) 1
Hindi (1) 1
Portuguese (1) 1
more...
Publication Date Publication Date
Click on a bar to filter by decade
Slide to change publication date range


1. An introduction to Markov state models and their application to long timescale molecular simulation
by Bowman, Gregory R., editor of compilation and Pande, Vijay, editor of compilation and Noé, Frank, editor of compilation
2014, Advances in experimental medicine and biology, ISBN 9400776055, Volume 797., xii, 139 pages
"The aim of this book volume is to explain the importance of Markov state models to molecular simulation, how they work, and how they can be applied to a range... 
Time Factors | Markov processes | Models, Molecular | Markov chains | Biology | Mathematical models | Molecular Dynamics Simulation | Biology-Mathematical models | Molecular dynamics
Book
Details down arrow
2. Full Text Markov State Models: From an Art to a Science
by Husic, Brooke E and Pande, Vijay S
Journal of the American Chemical Society, ISSN 0002-7863, 02/2018, Volume 140, Issue 7, pp. 2386 - 2396
Markov state models (MSMs) are a powerful framework for analyzing dynamical systems, such as molecular dynamics (MD) simulations, that have gained widespread... 
MONOMOLECULAR REACTION SYSTEMS | VARIATIONAL APPROACH | PROTEIN-FOLDING KINETICS | HISTOGRAM ANALYSIS | MASTER EQUATION APPROACH | CONFORMATIONAL DYNAMICS | FREE-ENERGIES | MOLECULAR-DYNAMICS SIMULATIONS | CHEMISTRY, MULTIDISCIPLINARY | BIOMOLECULAR DYNAMICS | ALANINE DIPEPTIDE | Markov Chains | Protein Binding | Ligands | Proteins - chemistry | Drug Discovery | Molecular Dynamics Simulation | Protein Folding | Molecular simulation | Markov processes | Usage | Drug discovery | Research
Journal Article
Details down arrow
Digital rights down arrow
loading Loading Rights
3. Full Text Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9
by Schwantes, Christian R and Pande, Vijay S
Journal of Chemical Theory and Computation, ISSN 1549-9618, 04/2013, Volume 9, Issue 4, pp. 2000 - 2009
Markov State Models (MSMs) provide an automated framework to investigate the dynamical properties of high-dimensional molecular simulations. These models can... 
ENSEMBLE | PATHWAYS | PROTEIN | FREE-ENERGY LANDSCAPES | KINETICS | MUTATION | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | CHEMISTRY, PHYSICAL | MOLECULAR-DYNAMICS SIMULATIONS
Journal Article
Details down arrow
Digital rights down arrow
loading Loading Rights
4. Full Text Atomistic Folding Simulations of the Five-Helix Bundle Protein λ6−85
by Bowman, Gregory R and Voelz, Vincent A and Pande, Vijay S
Journal of the American Chemical Society, ISSN 0002-7863, 02/2011, Volume 133, Issue 4, pp. 664 - 667
Protein folding is a classic grand challenge that is relevant to numerous human diseases, such as protein misfolding diseases like Alzheimer’s disease. Solving... 
Journal Article
Details down arrow
Digital rights down arrow
loading Loading Rights
5. Understanding protein folding using markov state models
by Pande, Vijay S
Advances in Experimental Medicine and Biology, ISSN 0065-2598, 2014, Volume 797, pp. 101 - 106
Models, Molecular | Markov Chains | Proteins - chemistry | Protein Folding
Journal Article
Details down arrow
6. Simulated Dynamics of Glycans on Ligand-Binding Domain of NMDA Receptors Reveals Strong Dynamic Coupling between Glycans and Protein Core
by Anton V Sinitskiy and Vijay S Pande
Journal of Chemical Theory and Computation, ISSN 1549-9618, 11/2017, Volume 13, Issue 11, p. 5496
N-Methyl-d-aspartate (NMDA) receptors, key neuronal receptors playing the central role in learning and memory, are heavily glycosylated in vivo. Astonishingly... 
Proteins | Binding | Coupling (molecular) | Receptors | Computer simulation | Molecular dynamics | Ligands | Glycoproteins | Glycan | Molecular chains
Journal Article
Details down arrow
7. Full Text OpenMM: A Hardware-Independent Framework for Molecular Simulations
by Eastman, Peter and Pande, Vijay
Computing in Science & Engineering, ISSN 1521-9615, 07/2010, Volume 12, Issue 4, pp. 34 - 39
The wide diversity of computer architectures today requires a new approach to software development. OpenMM is an abstraction layer for molecular mechanics... 
Graphics | Power engineering computing | Multicore processing | Computational modeling | Computer architecture | Predictive models | Hardware | high performance computing | Programming profession | Radio access networks | simulations | DYNAMICS | COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS | GRAPHICS PROCESSING UNITS | Platforms | Mathematical models | Computer simulation | Software development | Computer programs | Abstraction Layer | Molecular Simulation | Graphics Processing Unit
Journal Article
Details down arrow
Digital rights down arrow
loading Loading Rights
8. Full Text Variational cross-validation of slow dynamical modes in molecular kinetics
by McGibbon, Robert T and Pande, Vijay S
Journal of Chemical Physics, ISSN 0021-9606, 03/2015, Volume 142, Issue 12, p. 124105
Markov state models are a widely used method for approximating the eigenspectrum of the molecular dynamics propagator, yielding insight into the long-timescale... 
POLARIZABLE FORCE-FIELD | APPROXIMATION | HIDDEN COMPLEXITY | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | CHEMISTRY, PHYSICAL | SYSTEMS | OPTIMIZATION | CONFORMATIONAL DYNAMICS | COMPONENT ANALYSIS | SIMULATIONS | MARKOV STATE MODELS | EXCITED-STATES | Markov Chains | Algorithms | Computer Simulation | Models, Molecular | Alanine - chemistry | Kinetics | Cluster Analysis | Peptides - pharmacology | Proteins | Operators (mathematics) | Eigenvalues | Molecular dynamics | Markov chains | ARTICLES
Journal Article
Details down arrow
Digital rights down arrow
loading Loading Rights
9. tICA-Metadynamics: Accelerating Metadynamics by Using Kinetically Selected Collective Variables
by Mohammad M Sultan and Vijay S Pande
Journal of Chemical Theory and Computation, ISSN 1549-9618, 06/2017, Volume 13, Issue 6, p. 2440
Metadynamics is a powerful enhanced molecular dynamics sampling method that accelerates simulations by adding history-dependent multidimensional Gaussians... 
Computer simulation | Independent component analysis | Molecular dynamics | Markov chains | Sampling | Molecular chains
Journal Article
Details down arrow
10. Full Text Everything you wanted to know about Markov State Models but were afraid to ask
by Pande, Vijay S and Beauchamp, Kyle and Bowman, Gregory R
Methods, ISSN 1046-2023, 09/2010, Volume 52, Issue 1, pp. 99 - 105
Simulating protein folding has been a challenging problem for decades due to the long timescales involved (compared with what is possible to simulate) and the... 
Molecular dynamics | Markov State Models | Computer simulation | Protein folding | Distributed computing | MECHANISM | GENERALIZED-ENSEMBLE ALGORITHMS | PROTEIN-FOLDING KINETICS | HAIRPIN | BIOCHEMISTRY & MOLECULAR BIOLOGY | BIOCHEMICAL RESEARCH METHODS | MOLECULAR-DYNAMICS TRAJECTORIES | MONTE-CARLO | SIMULATIONS | Markov Chains | Computer Simulation | Protein Folding | Models | Computer-generated environments | Analysis
Journal Article
Details down arrow
Digital rights down arrow
loading Loading Rights
11. Full Text Activation pathway of Src kinase reveals intermediate states as targets for drug design
by Shukla, Diwakar and Meng, Yilin and Roux, Benoît and Pande, Vijay S
Nature Communications, ISSN 2041-1723, 03/2014, Volume 5, Issue 1, p. 3397
Unregulated activation of Src kinases leads to aberrant signalling, uncontrolled growth and differentiation of cancerous cells. Reaching a complete mechanistic... 
ACTIVE CONFORMATION | MOLECULAR-DYNAMICS | CONFORMATIONAL-CHANGES | STRING METHOD | CRYSTAL-STRUCTURE | MULTIDISCIPLINARY SCIENCES | ABL KINASE | ATOMISTIC SIMULATIONS | HIV-1 PROTEASE | PROTEIN-KINASES | C-SRC | Thermodynamics | Humans | Allosteric Site | Computational Biology | Drug Design | src-Family Kinases - metabolism | src-Family Kinases - chemistry | Molecular Dynamics Simulation
Journal Article
Details down arrow
Digital rights down arrow
loading Loading Rights
12. Full Text Exploring the Helix-Coil Transition via All-Atom Equilibrium Ensemble Simulations
by Sorin, Eric J and Pande, Vijay S
Biophysical Journal, ISSN 0006-3495, 2005, Volume 88, Issue 4, pp. 2472 - 2493
The ensemble folding of two 21-residue -helical peptides has been studied using all-atom simulations under several variants of the AMBER potential in explicit... 
ISOLATED-PAIR HYPOTHESIS | FOLDING SIMULATIONS | ALPHA-HELIX | CIRCULAR-DICHROISM | BIOPHYSICS | RICH PEPTIDES | MECHANICS FORCE-FIELDS | SECONDARY STRUCTURE | MOLECULAR-DYNAMICS SIMULATIONS | POLYPROLINE II HELIX | ALANINE-BASED PEPTIDE | Markov Chains | Temperature | Peptides - chemistry | Protein Structure, Secondary | Molecular Conformation | Models, Molecular | Hot Temperature | Models, Statistical | Protein Folding | Thermodynamics | Algorithms | Time Factors | Computer Simulation | Polymers - chemistry | Software | Kinetics | Biophysics - methods | Diffusion | Cluster Analysis | Analysis | Peptides | Atoms & subatomic particles | Protein folding | Biophysical Theory and Modeling
Journal Article
Details down arrow
Digital rights down arrow
loading Loading Rights
13. Full Text Erratum: Corrigendum: Conformational heterogeneity of the calmodulin binding interface
by Shukla, Diwakar and Peck, Ariana and Pande, Vijay S
Nature Communications, ISSN 2041-1723, 11/2016, Volume 7, Issue 1
Journal Article
Details down arrow
Digital rights down arrow
loading Loading Rights
14. Full Text To milliseconds and beyond: challenges in the simulation of protein folding
by Lane, Thomas J and Shukla, Diwakar and Beauchamp, Kyle A and Pande, Vijay S
Current Opinion in Structural Biology, ISSN 0959-440X, 02/2013, Volume 23, Issue 1, pp. 58 - 65
► Millisecond simulations. ► Hardware and software advances. ► Simulation to understanding. Quantitatively accurate all-atom molecular dynamics (MD)... 
PATHWAYS | SPEED LIMIT | MODELS | EXPLICIT-SOLVENT | KINETICS | BIOCHEMISTRY & MOLECULAR BIOLOGY | TRP-CAGE | BIOMOLECULAR SIMULATION | MOLECULAR-DYNAMICS SIMULATIONS | FORCE-FIELDS | EFFICIENT | CELL BIOLOGY | Kinetics | Proteins - chemistry | Molecular Dynamics Simulation | Protein Folding
Journal Article
Details down arrow
Digital rights down arrow
loading Loading Rights
15. Full Text Effects of Familial Mutations on the Monomer Structure of Aβ42
by Lin, Yu-Shan and Pande, Vijay S
Biophysical Journal, ISSN 0006-3495, 12/2012, Volume 103, Issue 12, pp. L47 - L49
Amyloid beta (A ) peptide plays an important role in Alzheimer’s disease. A number of mutations in the A sequence lead to familial Alzheimer’s disease,... 
Biophysical Letter
Journal Article
Details down arrow
Digital rights down arrow
loading Loading Rights
16. Full Text Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements
by Beauchamp, Kyle A and Lin, Yu-Shan and Das, Rhiju and Pande, Vijay S
Journal of Chemical Theory and Computation, ISSN 1549-9618, 04/2012, Volume 8, Issue 4, pp. 1409 - 1414
Recent hardware and software advances have enabled simulation studies of protein systems on biophysically relevant time scales, often revealing the need for... 
WATER MODEL | MECHANICS | REPARAMETRIZATION | UBIQUITIN | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | DYNAMICS | ENERGETICS | CHEMISTRY, PHYSICAL | HELIX | SIMULATIONS | BACKBONE | PEPTIDE
Journal Article
Details down arrow
Digital rights down arrow
loading Loading Rights
17. Full Text Molecular Simulation of ab Initio Protein Folding for a Millisecond Folder NTL9(1−39)
by Voelz, Vincent A and Bowman, Gregory R and Beauchamp, Kyle and Pande, Vijay S
Journal of the American Chemical Society, ISSN 0002-7863, 02/2010, Volume 132, Issue 5, pp. 1526 - 1528
To date, the slowest-folding proteins folded ab initio by all-atom molecular dynamics simulations have had folding times in the range of nanoseconds to... 
TRANSITION | HETEROGENEITY | DYNAMICS | DESIGN | CHEMISTRY, MULTIDISCIPLINARY | KINETICS | Markov Chains | Arabidopsis - chemistry | Transcription Factors - chemistry | Time Factors | Protein Conformation | Molecular Dynamics Simulation | Protein Folding | Molecular dynamics | Usage | Solvation | Chemical reaction, Rate of | Protein folding | Analysis
Journal Article
Details down arrow
Digital rights down arrow
loading Loading Rights
18. Full Text Building Force Fields: An Automatic, Systematic, and Reproducible Approach
by Wang, Lee-Ping and Martinez, Todd J and Pande, Vijay S
The Journal of Physical Chemistry Letters, ISSN 1948-7185, 06/2014, Volume 5, Issue 11, pp. 1885 - 1891
The development of accurate molecular mechanics force fields is a significant challenge that must be addressed for the continued success of molecular... 
Molecular Structure, Quantum Chemistry, and General Theory | force field | water model | optimization | TIP4P | TIP3P | water | ForceBalance | MOLECULAR SIMULATION | MATERIALS SCIENCE, MULTIDISCIPLINARY | ALGORITHM | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | LIQUID WATER | CHEMISTRY, PHYSICAL | NANOSCIENCE & NANOTECHNOLOGY | BASIS-SETS | MODEL
Journal Article
Details down arrow
Digital rights down arrow
loading Loading Rights
19. Transferable Neural Networks for Enhanced Sampling of Protein Dynamics
by Mohammad M Sultan and Hannah K Wayment-Steele and Vijay S Pande
Journal of Chemical Theory and Computation, ISSN 1549-9618, 04/2018, Volume 14, Issue 4, p. 1887
Variational autoencoder frameworks have demonstrated success in reducing complex nonlinear dynamics in molecular simulation to a single nonlinear embedding. In... 
Proteins | Coders | Nonlinear dynamics | Alanine | Computer simulation | Neural networks | Independent component analysis | Linear transformations | Embedding | Sampling | Dynamical systems | Molecular chains
Journal Article
Details down arrow
20. Full Text Chemical Kinetics and Mechanisms of Complex Systems: A Perspective on Recent Theoretical Advances
by Klippenstein, Stephen J and Pande, Vijay S and Truhlar, Donald G
Journal of the American Chemical Society, ISSN 0002-7863, 01/2014, Volume 136, Issue 2, pp. 528 - 546
This Perspective presents a personal overview of the current status of the theory of chemical kinetics and mechanisms for complex processes. We attempt to... 
ANHARMONIC VIBRATIONAL PROPERTIES | STRAIGHT-LINE PATHS | PROTEIN-FOLDING KINETICS | POTENTIAL-ENERGY SURFACES | AB-INITIO | MASTER-EQUATION SIMULATION | PHENOMENOLOGICAL RATE COEFFICIENTS | DENSITY-FUNCTIONAL THEORY | MAIN-GROUP THERMOCHEMISTRY | CHEMISTRY, MULTIDISCIPLINARY | TRANSITION-STATE THEORY | Gases | Liquids | Chemical reaction, Rate of | Analysis | Research | Enzyme kinetics | Phase interfaces
Journal Article
Details down arrow
Digital rights down arrow
loading Loading Rights