Class information for:
Level 1: MARKOV STATE MODEL//ENHANCED SAMPLING//TRANSITION PATH SAMPLING

Basic class information
Class id #P Avg. number of
references		 Database coverage
of references
6749 1448 44.8 80%


Bar chart of Publication_year

Last years might be incomplete

Hierarchy of classes
The table includes all classes above and classes immediately below the current class.


Cluster id Level Cluster label #P
0 4 BIOCHEMISTRY & MOLECULAR BIOLOGY//CELL BIOLOGY//ONCOLOGY 4064930
219 3       PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS//PROTEIN FOLDING//PROTEIN STRUCTURE PREDICTION 50409
260 2             PROTEIN FOLDING//JOURNAL OF CHEMICAL THEORY AND COMPUTATION//JOURNAL OF COMPUTATIONAL CHEMISTRY 19582
6749 1                   MARKOV STATE MODEL//ENHANCED SAMPLING//TRANSITION PATH SAMPLING 1448

Terms with highest relevance score


rank Term termType Chi square Shr. of publ. in
class containing
term		 Class's shr. of
term's tot. occurrences		 #P with
term in
class
1 MARKOV STATE MODEL authKW 285998 2% 59% 23
2 ENHANCED SAMPLING authKW 209159 2% 40% 25
3 TRANSITION PATH SAMPLING authKW 158945 1% 54% 14
4 JOURNAL OF CHEMICAL THEORY AND COMPUTATION journal 147237 12% 4% 179
5 IST SCI COMPUTAZ address 118066 1% 40% 14
6 MILESTONING authKW 87858 0% 83% 5
7 ACTION DERIVED MOLECULAR DYNAMICS authKW 84345 0% 100% 4
8 HYPER MOLECULAR DYNAMICS authKW 84345 0% 100% 4
9 METADYNAMICS authKW 75337 1% 19% 19
10 ACCELERATED MOLECULAR DYNAMICS authKW 72883 1% 31% 11

Web of Science journal categories


Rank Term Chi square Shr. of publ. in
class containing
term		 Class's shr. of
term's tot. occurrences		 #P with
term in
class
1 Physics, Atomic, Molecular & Chemical 22006 48% 0% 701
2 Chemistry, Physical 11910 59% 0% 860
3 Physics, Mathematical 941 8% 0% 112
4 Mathematical & Computational Biology 275 3% 0% 41
5 Computer Science, Interdisciplinary Applications 246 4% 0% 60
6 Biophysics 136 5% 0% 67
7 Physics, Multidisciplinary 112 6% 0% 84
8 Chemistry, Multidisciplinary 107 9% 0% 126
9 Physics, Fluids & Plasmas 104 3% 0% 38
10 Mathematics, Interdisciplinary Applications 43 2% 0% 25

Address terms


Rank Term Chi square Shr. of publ. in
class containing
term		 Class's shr. of
term's tot. occurrences		 #P with
term in
class
1 IST SCI COMPUTAZ 118066 1% 40% 14
2 COMPUTAT BIOPHYS GRIB IMIM 68874 0% 47% 7
3 MATH COMP SCI BIOINFORMAT 65891 0% 63% 5
4 SIMBIOS NIH BIOMED COMPUTAT 58569 0% 56% 5
5 SCI COMPUTAZ 56227 0% 67% 4
6 MICMAC PROJECT TEAM 42165 0% 33% 6
7 SYST BIOL HUMAN HLTH 42153 1% 17% 12
8 THEORET COMPUTAT BIOPHYS GRP 28868 1% 14% 10
9 MATHEON 28110 0% 33% 4
10 BIOMOL PHYS MODELING GRP 25449 1% 15% 8

Journals


Rank Term Chi square Shr. of publ. in
class containing
term		 Class's shr. of
term's tot. occurrences		 #P with
term in
class
1 JOURNAL OF CHEMICAL THEORY AND COMPUTATION 147237 12% 4% 179
2 JOURNAL OF CHEMICAL PHYSICS 34201 26% 0% 373
3 JOURNAL OF PHYSICAL CHEMISTRY B 8338 9% 0% 124
4 MULTISCALE MODELING & SIMULATION 5969 1% 2% 15
5 JOURNAL OF COMPUTATIONAL CHEMISTRY 4167 2% 1% 35
6 REVIEWS IN COMPUTATIONAL CHEMISTRY 2705 0% 4% 3
7 MOLECULAR SIMULATION 2290 1% 1% 17
8 WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2026 0% 2% 5
9 CURRENT OPINION IN STRUCTURAL BIOLOGY 1543 1% 1% 13
10 EUROPEAN PHYSICAL JOURNAL-SPECIAL TOPICS 1379 1% 1% 13

Author Key Words


Rank Term Chi square Shr. of publ. in
class containing
term		 Class's shr. of
term's tot. occurrences		 #P with
term in
class		 LCSH search Wikipedia search
1 MARKOV STATE MODEL 285998 2% 59% 23 Search MARKOV+STATE+MODEL Search MARKOV+STATE+MODEL
2 ENHANCED SAMPLING 209159 2% 40% 25 Search ENHANCED+SAMPLING Search ENHANCED+SAMPLING
3 TRANSITION PATH SAMPLING 158945 1% 54% 14 Search TRANSITION+PATH+SAMPLING Search TRANSITION+PATH+SAMPLING
4 MILESTONING 87858 0% 83% 5 Search MILESTONING Search MILESTONING
5 ACTION DERIVED MOLECULAR DYNAMICS 84345 0% 100% 4 Search ACTION+DERIVED+MOLECULAR+DYNAMICS Search ACTION+DERIVED+MOLECULAR+DYNAMICS
6 HYPER MOLECULAR DYNAMICS 84345 0% 100% 4 Search HYPER+MOLECULAR+DYNAMICS Search HYPER+MOLECULAR+DYNAMICS
7 METADYNAMICS 75337 1% 19% 19 Search METADYNAMICS Search METADYNAMICS
8 ACCELERATED MOLECULAR DYNAMICS 72883 1% 31% 11 Search ACCELERATED+MOLECULAR+DYNAMICS Search ACCELERATED+MOLECULAR+DYNAMICS
9 TEMPERATURE ACCELERATED DYNAMICS 69004 0% 55% 6 Search TEMPERATURE+ACCELERATED+DYNAMICS Search TEMPERATURE+ACCELERATED+DYNAMICS
10 COMMITTOR 67474 0% 80% 4 Search COMMITTOR Search COMMITTOR

Core articles
The table includes core articles in the class. The following variables is taken into account for the relevance score of an article in a cluster c:
(1) Number of references referring to publications in the class.
(2) Share of total number of active references referring to publications in the class.
(3) Age of the article. New articles get higher score than old articles.
(4) Citation rate, normalized to year.


Rank Reference # ref. in
cl.		 Shr. of ref. in
cl.		 Citations
1 SCHERER, MK , TRENDELKAMP-SCHROER, B , PAUL, F , PEREZ-HERNANDEZ, G , HOFFMANN, M , PLATTNER, N , WEHMEYER, C , PRINZ, JH , NOE, F , (2015) PYEMMA 2: A SOFTWARE PACKAGE FOR ESTIMATION, VALIDATION, AND ANALYSIS OF MARKOV MODELS.JOURNAL OF CHEMICAL THEORY AND COMPUTATION. VOL. 11. ISSUE 11. P. 5525 -5542 91 82% 20
2 VALSSON, O , TIWARY, P , PARRINELLO, M , (2016) ENHANCING IMPORTANT FLUCTUATIONS: RARE EVENTS AND METADYNAMICS FROM A CONCEPTUAL VIEWPOINT.ANNUAL REVIEW OF PHYSICAL CHEMISTRY, VOL 67. VOL. 67. ISSUE . P. 159 -184 86 65% 8
3 CHODERA, JD , NOE, F , (2014) MARKOV STATE MODELS OF BIOMOLECULAR CONFORMATIONAL DYNAMICS.CURRENT OPINION IN STRUCTURAL BIOLOGY. VOL. 25. ISSUE . P. 135 -144 51 75% 81
4 DELLAGO, C , BOLHUIS, PG , (2009) TRANSITION PATH SAMPLING AND OTHER ADVANCED SIMULATION TECHNIQUES FOR RARE EVENTS.ADVANCED COMPUTER SIMULATION APPROACHES FOR SOFT MATTER SCIENCES III. VOL. 221. ISSUE . P. 167 -233 114 51% 61
5 ELBER, R , (2016) PERSPECTIVE: COMPUTER SIMULATIONS OF LONG TIME DYNAMICS.JOURNAL OF CHEMICAL PHYSICS. VOL. 144. ISSUE 6. P. - 64 68% 2
6 NUSKE, F , KELLER, BG , PEREZ-HERNANDEZ, G , MEY, ASJS , NOE, F , (2014) VARIATIONAL APPROACH TO MOLECULAR KINETICS.JOURNAL OF CHEMICAL THEORY AND COMPUTATION. VOL. 10. ISSUE 4. P. 1739 -1752 49 83% 22
7 BOLHUIS, PG , DELLAGO, C , (2015) PRACTICAL AND CONCEPTUAL PATH SAMPLING ISSUES.EUROPEAN PHYSICAL JOURNAL-SPECIAL TOPICS. VOL. 224. ISSUE 12. P. 2409 -2427 46 88% 8
8 BANUSHKINA, PV , KRIVOV, SV , (2016) OPTIMAL REACTION COORDINATES.WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE. VOL. 6. ISSUE 6. P. 748 -763 55 75% 1
9 PETERS, B , (2016) REACTION COORDINATES AND MECHANISTIC HYPOTHESIS TESTS.ANNUAL REVIEW OF PHYSICAL CHEMISTRY, VOL 67. VOL. 67. ISSUE . P. 669 -690 57 68% 2
10 BONINSEGNA, L , GOBBO, G , NOE, F , CLEMENTI, C , (2015) INVESTIGATING MOLECULAR KINETICS BY VARIATIONALLY OPTIMIZED DIFFUSION MAPS.JOURNAL OF CHEMICAL THEORY AND COMPUTATION. VOL. 11. ISSUE 12. P. 5947 -5960 50 86% 2

Classes with closest relation at Level 1


Rank Class id link
1 8058 GENERALIZED ENSEMBLE ALGORITHM//REPLICA EXCHANGE METHOD//MULTICANONICAL MOLECULAR DYNAMICS
2 12575 VALLEY RIDGE INFLECTION POINT//GRADIENT EXTREMAL//NEWTON TRAJECTORY
3 13680 BETA HAIRPIN//TRP CAGE//SIDE CHAIN INTERACTIONS
4 5802 THERMODYNAMIC INTEGRATION//FREE ENERGY CALCULATIONS//FREE ENERGY PERTURBATION
5 22502 MULTIPLE TIME STEP//SHAKE//SYMPLECTIC INTEGRATION METHODS
6 4939 ELASTIC NETWORK MODEL//NORMAL MODE ANALYSIS//GAUSSIAN NETWORK MODEL
7 573 PROTEIN FOLDING//PHI VALUE//FOLDING RATE
8 2729 MEMPHYS BIOMEMBRANE PHYS//LIPID BILAYER//BIOPHYS STAT MECH GRP
9 10706 OPTOELECT MICROSYST ISOM//VANT HOFF PHYS OID CHEM//ADV MAT EDUC CHINA
10 25141 DIFFUSION MAPS//SIGNAL PROCESSING ON GRAPHS//GRAPH SIGNAL PROCESSING

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